Abstract: Microfluidic methods for barcoding nucleic acid target molecules to be analyzed, e.g., via nucleic acid sequencing techniques, are provided. Also provided are microfluidic, droplet-based methods of preparing nucleic acid barcodes for use in various barcoding applications. The methods described herein facilitate high-throughput sequencing of nucleic acid target molecules as well as single cell and single virus genomic, transcriptomic, and/or proteomic analysis/profiling. Systems and devices for practicing the subject methods are also provided.

Abstract: The present invention relates to a method for amplifying at least one target RNA in a fixed and, optionally, expanded biological sample. In an embodiment of the invention, the method comprises incubating the fixed biological sample with a pair of polynucleotides complementary to non-overlapping and proximal sequences of a target RNA, wherein the polynucleotide pair hybridizes to the target RNA; ligating the polynucleotide pair using a ligase; and amplifying the ligation product. The invention further provides methods for detecting and optionally quantifying and/or sequencing the amplification product. As the method comprises hybridizing polynucleotide pairs to a target RNA in a fixed biological sample, the target RNA can be hybridized in situ.

Abstract: Methods and systems are provided for sample preparation techniques and sequencing of macromolecular constituents of cells and other biological materials.

Abstract: Methods for controlling for non-systematic error in an amplification-based next generation sequencing (NGS) library preparation are described, which method includes using an internal amplification control (IAC) sharing identical priming sites to a native nucleic acid target template of interest in a NGS library preparation.

Abstract: Devices, containers, and methods are provided for performing biological analysis in a closed environment. Illustrative biological analyses include high density nucleic acid amplification and detection and immune-PCR.

Abstract: A method for preserving and processing cell-free nucleic acids located within a blood sample is disclosed, wherein a blood sample containing cell-free nucleic acids is treated to reduce both blood cell lysis and nuclease activity within the blood sample. The treatment of the sample aids in increasing the amount of cell-free nucleic acids that can be identified and tested while maintaining the structure and integrity of the nucleic acids.

Abstract: Methods for detecting nucleic acid sequences, where attenuator oligonucleotides are provided to reduce the number of detection products resulting from highly abundant sequences.

Abstract: The invention relates to a method of determining an infection of a patient with Stenotrophomonas species potentially resistant to antimicrobial drug treatment, a method of selecting a treatment of a patient suffering from an antibiotic resistant Stenotrophomonas infection, and a method of determining an antibiotic resistance profile for bacterial microorganisms of Stenotrophomonas species, as well as computer program products used in these methods. In an exemplary method, a sample 1, is used for molecular testing 2, and then a molecular fingerprint 3 is taken. The result is then compared to a reference library 4, and the result 5 is reported.

Abstract: The invention provides a diagnostic kit comprising means to determine the presence in a sample of preferred strains the nitrogen-fixing bacteria Gluconacetobacter diazotrophicus (Gd) which are based upon the finding that such strains comprises unique nucleic acid sequences and other features, that are detectable, even in the presence of plant genomic DNA. Methods for using the kits in agriculture are also described and claimed.

Abstract: Apparatus and methods to sequence DNA. A DNA sequencing device includes a passage, a first electrode, and a second electrode. The passage has a width and a length. The first and second electrodes are exposed within the passage and spaced apart from each other to form an electrode gap. The electrode gap is no greater than about 2 nm. The DNA sequencing device is operable to measure with the first and second electrodes a change in electronic signal in response to nucleotides of a DNA strand passing through the electrode gap.

Abstract: The present invention discloses a method of detecting the presence of mutated genes, mRNAs or microRNAs in a subject. The method comprises the following steps: (1) Provide a body fluid sample containing cells, circulating tumor cells (CTCs), and/or extracellular vesicles (EVs); and use an analyzer having overhang molecular beacons to measure fluorescence signals generated by interactions between the body fluid sample and the overhang molecular beacons, so as to detect the presence of the mutated genes, mRNAs or microRNA. Furthermore, a biochip comprising a gold coating substrate and tethered lipoplex nanoparticles encapsulating the overhang molecular beacons is also provided in the invention.

Abstract: Emulsion compositions are provided herein. Also provided herein are kits containing one or more emulsion compositions or components for making such emulsion compositions. Also provided herein are methods of using such emulsion compositions, such as for amplification of target nucleic acids in emulsion droplets.

Abstract: Disclosed are compositions and methods for making differentiable amplicon species at unequal ratios using a single amplification system in a single vessel. The number of differentiable amplicons and their ratios to one another are chosen to span the required linear dynamic range for the amplification reaction and to accommodate limitations of the measuring system used to determine the amount of amplicon generated. Unequal amounts of distinguishable amplicon species are generated by providing unequal amounts of one or more amplification reaction components (e.g., distinguishable amplification oligomers, natural and unnatural NTP in an NTP mix, or the like). The amount of target nucleic acid present in a test sample is determined using the linear detection range generated from detection of one or more amplicon species having an amount within the dynamic range of detection.

Abstract: Methods and compositions are disclosed for measuring low-abundance DNA variants from a complex mixture of DNA molecules. Embodiments of the methods allow for extremely sensitive detection and can distinguish true variants from sequencer misreads and PCR misincorporations.

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 invention relates to a new method of characterizing a target polynucleotide. The method uses a pore and a Hel308 helicase or amolecular motor which is capable of binding to the target polynucleotide at an internal nucleotide. The helicase or molecular motor controls the movement of the target polynucleotide through the pore.

Abstract: High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduce sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are methods and compositions for sequencing nucleic acids. Further provided are methods of identifying an error in a nucleic acid sequence.

Abstract: The invention pertains to construction of next-generation DNA sequencing (NGS) libraries for whole genome sequencing, targeted resequencing, sequencing-based screening assays, metagenomics, or any other application requiring sample preparation for NGS.

Abstract: A DNA sequencing device and related methods, wherein the device includes a substrate, a nanochannel formed in the substrate, a first electrode positioned on a first side of the nanochannel, and a second electrode. The second electrode is positioned on a second side of the nanochannel opposite the first electrode, and is spaced apart from the first electrode to form an electrode gap that is exposed in the nanochannel. At least a portion of first electrode is movable relative to the second electrode to decrease a size of the electrode gap.

Abstract: Apparatus and methods relating to DNA sequencing are provided. In one embodiment, a DNA sequencing device includes a nanochannel having a width that is approximately 0.3 nm to approximately 20 nm. A pair of electrodes having portions exposed to the nanochannel may form a tunneling current electrode (TCE) with an electrode gap of approximately 0.1 nm to approximately 2 nm, and more particularly about 0.3 nm to about 1 nm. In one embodiment, at least one of the pair of electrodes is formed as a suspended electrode. An actuator may be associated with the suspended electrode to displace it relative to the other electrode. In various embodiments, the nanochannel and/or the electrodes may be formed using thermal reflow processes to reduce the size of such features.

Abstract: A DNA sequencing device, and related methods, include a nanochannel sized to receive a DNA strand, a first electrode member exposed within the nanochannel, and a second electrode member exposed within the nanochannel and spaced apart from the first electrode to form an electrode gap. The second electrode member has a wedge shaped profile, and the first and second electrode members are operable to detect a change in electronic signal as the DNA strand passes through the electrode gap.

Abstract: The present invention relates to a microarray device for detecting a target molecule such as miRNA in a sample. The device comprises a carrier substrate such as glass, an anti-fouling polymer layer which is functionalised with N-Hydroxysuccinimide (NHS) or carboxyl-groups and a capture probe. In an embodiment, the capture probe is an oligonucleotide with a stem-loop structure. The invention further defines a method for fabricating the device, a kit for detecting the target nucleic acid molecule comprising the device and a detection probe.

Abstract: Disclosed is a method for identification and use of compounds which activate the expression or activity of uc.291 for improving skin barrier function, and/or for preventing and/or attenuating ageing, and/or for hydrating skin. The disclosed in vitro method for screening for candidate compounds for improving skin barrier function, and/or for preventing and/or attenuating ageing of the skin, and/or for hydrating the skin, includes: a. bringing at least one test compound in contact with a sample of keratinocytes; b. measuring the expression or the activity of uc.291 in the keratinocytes; and c. selecting the compounds for which an activation of at least 20%, preferably at least 30%, preferably at least 40% of the expression or an activation of at least 20%, preferably at least 30%, preferably at least 40% of the activity of uc.291 is measured in the keratinocytes treated in a. compared with the untreated keratinocytes.

Abstract: Disclosed are high concentration reagents for use in preparing DNA samples in low volume reactions. Such reagents include, for example, DNA end repair buffers for use in low volume DNA blunting and phosphorylating reactions, DNA adenylating buffers for use in a low volume DNA adenylating reaction, and DNA ligation buffers for use in low volume DNA adaptor ligation reactions with adaptors. Also disclosed are customized reagent plates and kits containing one or more of these low volume buffers for use in low volume DNA blunting, phosphorylating, adenylating, and ligation reactions. Methods of using the high concentration reagents (low volume buffers) and the customized reagent plates for preparing DNA sequencing libraries in low volume reactions are also disclosed.

Abstract: The present invention relates to a method, in particular an in vitro method, for identifying monocytes, comprising analyzing the methylation status of at least one CpG position in the mammalian gene region for parkin RBR E3 ubiquitin protein ligase (PARK2), wherein a de-methylation or lack of methylation of said gene region is indicative for a monocyte, when compared to a non-monocyte cell. The analyses according to the invention can identify monocytes on an epigenetic level and distinguish them from all other cells in complex samples, such as, for example, other blood or immune cells. The present invention furthermore provides an improved method for quantifying monocytes, in particular in complex samples. The method can be performed without a step of purifying and/or enriching cells, preferably in whole blood and/or non-trypsinized tissue. Also claimed are kits and specific oligonucleotides for use as primers or probes.

Abstract: The present invention relates to a method, in particular an in vitro method, for identifying B cells, comprising analyzing the methylation status of at least one CpG position in the mammalian gene region for Low density lipoprotein receptor-related protein 5 (LRP5), wherein a demethylation or lack of methylation of said gene region is indicative for a B cell, when compared to a non-B cell. The analyses according to the invention can identify B cells on an epi-genetic level and distinguish them from all other cells in complex samples, such as, for example, other blood or immune cells. The present invention furthermore provides an improved method for quantifying B cells, in particular in complex samples. The method can be performed without a step of purifying and/or enriching cells, preferably in whole blood and/or non-trypsinized tissue. Further claimed are kits and specific primers and probes for identifying methylation.

Abstract: A method for the detection of impaired responsiveness of CD4+ T-cells to regulatory T-cells (Treg), Treg resistance, by measuring the expression levels of peroxisome proliferator-activated receptor gamma coactivator 1-alpha, PPARGC1A (PGC-1?) in activated CD4+ T-cells, in particular in patients suffering from relapsing remitting multiple sclerosis. The invention relates to an in vitro screening method for the detection of an autoimmune disease or a condition, comprising the steps of generating a functional gene expression profile by measuring the expression levels of peroxisome proliferator-activated receptor gamma coactivator 1-alpha, PPARGC1A (PGC-1?) in Treg-resistant CD4+ T-cells from patients suffering of an autoimmune disease or condition, and comparing the obtained gene expression profile with the expression profile from Treg-sensitive CD4+ T-cells from healthy controls.

Abstract: The present invention relates to methods of diagnosing traumatic brain injury (TBI) in a subject. The present invention also relates to methods of monitoring the progression of the TBI in a subject.

Abstract: Provided herein, in some aspects, are methods of dosing opioid receptor agonists for treatment of opioid dependence and pain management.

Abstract: Provided are compositions and methods for use in polycystic ovary syndrome diagnosis (PCOS). The method involves a sample from a subject for a DENND1A Variant 2 mRNA or DENND1 A Variant 2 protein to make or aid in a diagnosis of PCOS. Also provided are methods for selecting an individual as a candidate for therapy for polycystic ovary syndrome by testing a biological sample from an individual for DENND1 A Variant 2 mRNA or DENND1 A Variant 2 protein and designating the individual as a candidate for the PCOS based on determining DENND1 A Variant 2 mRNA or DENND1 A Variant 2 protein in the sample. Also provided are products for use in aiding diagnosis of PCOS which contain reagents for detecting DENND1 A Variant 2 mRNA or DENND1 A Variant 2 protein, and packaging containing printed material describing use and indications for the product.

Abstract: Disclosed herein is a novel single nucleotide polymorphism (SNP) in HLA-B*15:02 that can be used as a biomarker for carbamazepine-induced severe adverse skin reactions in Asians. Also provided herein are methods and reagents for assessing the specific SNP, and applying the SNP in predicting an increased risk of carbamazepine-induced severe adverse skin reactions.

Abstract: Systems, methods, and apparatuses can determine and use methylation profiles of various tissues and samples. Examples are provided. A methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient. A methylation profile can be determined for fetal/tumor tissue using tissue-specific alleles to identify DNA from the fetus/tumor when the sample has a mixture of DNA. A methylation profile can be used to determine copy number variations in genome of a fetus/tumor. Methylation markers for a fetus have been identified via various techniques. The methylation profile can be determined by determining a size parameter of a size distribution of DNA fragments, where reference values for the size parameter can be used to determine methylation levels. Additionally, a methylation level can be used to determine a level of cancer.

Abstract: This invention relates, e.g., to a method for determining if a thyroid tumor in a subject is malignant, comprising determining in a sample from the subject the amount of TERT (telomerase reverse transcriptase) mRNA which lacks the ? sequence and the amount of TERT mRNA in the sample which comprises the ? sequence, wherein a preponderance (e.g., at least about 55%) of TERT mRNA in the sample which comprises the ? sequence indicates that the tumor is malignant, and wherein a preponderance of TERT mRNA which lacks the ? sequence indicates that the tumor is not malignant.

Abstract: The present invention relates to a method for predicting the survival time of a patient suffering from a solid cancer comprising i) determining in a tissue sample obtained from the patient the gene expression level of FcRn ii) comparing expression level determined at step i) with their predetermined reference value and iii) providing a good prognosis when expression level determined at step i) is higher than their predetermined reference value, or providing a bad prognosis when expression levels determined at step i) are lower than their predetermined reference values.

Abstract: Provided herein are methods of detecting pancreatic cancer in a subject, the method comprising measuring in a sample from the subject a level of CA19-9 polysaccharide relative to a reference, and a level of a polynucleotide or polypeptide of at least one marker selected from the group consisting of: OPN, MIA, CEACAM-1, MIC-1, SPON1, HSP27, POSTN, and LGALS3BP relative to a reference, wherein an increased level of the CA19-9 polysaccharide relative to a reference and an increased level of the polynucleotide or polypeptide relative to a reference indicates presence of pancreatic cancer in the subject.

Abstract: The present application provides methods for the detection and diagnosis of cancer. In one aspect, the application provides methods for detecting the presence of cancer in an individual by detecting the methylation state of a region in the promoter of the ZNF154 gene. Methods are provided for detection and diagnosis of cancer from circulating tumor DNA which are minimally invasive and have diagnostic utility across different types and sub-types of cancer. In a further aspect, bioinformatics methods are provided to analyze the methylation state of the ZNF154 promoter and relate the methylation state to the likelihood of cancer in the individual.

Abstract: This invention provides methods for the treatment of cancer in subjects having medium or low methylation level in the PD-L1 promoter region. Also provided are related kits and articles of manufacture.

Abstract: The present invention relates to methods, systems and kits for the diagnosis, prognosis, and treatment of bladder cancer in a subject. The invention also provides biomarkers that define subgroups of bladder cancer, clinically useful classifiers for distinguishing bladder cancer subtypes, bioinformatic methods for determining clinically useful classifiers, and methods of use of each of the foregoing. The methods, systems and kits can provide expression-based analysis of biomarkers for purposes of subtyping bladder cancer in a subject. Further disclosed herein, in certain instances, are probe sets for use in subtyping bladder cancer in a subject. Classifiers for subtyping a bladder cancer are provided. Methods of treating bladder cancer based on molecular subtyping are also provided.

Abstract: The present invention relates to a method of predicting the effectiveness of chemotherapy in a breast cancer patient, and more particularly, to a method for predicting the effectiveness of chemotherapy by measuring the expression levels of genes for predicting prognosis of breast cancer and a standard gene in a biological sample obtained from the breast cancer patient, and a method for predicting the difference between a patient group having a high effectiveness of chemotherapy and a patient group having a low effectiveness of chemotherapy. Therefore, the method of the present invention can accurately predict the effectiveness of chemotherapy for the breast cancer patient, and can be used for the purpose of presenting clues about the direction of breast cancer treatment in the future.

Abstract: The present invention relates to a method of predicting the effectiveness of chemotherapy in a breast cancer patient, and more particularly, to a method for predicting the effectiveness of chemotherapy by measuring the expression levels of genes for predicting prognosis of breast cancer and a standard gene in a biological sample obtained from the breast cancer patient, and a method for predicting the difference between a patient group having a high effectiveness of chemotherapy and a patient group having a low effectiveness of chemotherapy. Therefore, the method of the present invention can accurately predict the effectiveness of chemotherapy for the breast cancer patient and can be used for the purpose of presenting clues about the direction of breast cancer treatment in the future.

Abstract: Provided is an isolated mammalian negative strand RNA virus, metapneumovirus (MPV), within the sub-family Pneumoviridae, of the family Paramyxoviridae. Also provided are isolated mammalian negative strand RNA viruses identifiable as phylogenetically corresponding or relating to the genus Metapneumovirus and components thereof. In particular, provided is a mammalian MPV, subgroups and variants thereof. Also provided are genomic nucleotide sequences of different isolates of mammalian MPV, in particular, human MPV. Disclosed is the use of the sequence information of different isolates of mammalian MPV for diagnostic and therapeutic methods. Provided are nucleotide sequences encoding the genome of an MPV or a portion thereof, including both mammalian and avian MPV. Further described are chimeric or recombinant viruses encoded by the nucleotide sequences and chimeric and recombinant mammalian MPV that comprise one or more non-native or heterologous sequences.

Abstract: Disclosed are nucleic acid oligomers, including amplification oligomers, capture probes, and detection probes, for detection of a human papillomavirus (HPV) nucleic acid. Also disclosed are methods of specific nucleic acid amplification and detection using the disclosed oligomers, as well as corresponding reaction mixtures and kits.

Abstract: A cylindrical frame is fabricated to provide for a tray and heating system that facilitates the condensing of liquid through the process of evaporation. In exemplary embodiments, the barrel evaporator provides a suitable heating system to allow for evaporation at a rate at or above 4 gallons per hour on a tray that has approximately 600 square inches of surface area. In exemplary embodiments, the barrel evaporator has a removable tray that can be replaced by grill grates to allow for uses other than evaporating liquids.

Abstract: A delivery device for delivering filler material into a blast furnace, comprising: a housing provided with a transition channel for the filler material which defines a first axis X; a chute for the filler material arranged underneath said transition channel; first actuating means, defining a respective second axis A parallel to the first axis X, to actuate a tilt of the chute with respect to the first axis X; second actuating means, defining a respective third axis B parallel to the first axis X, to actuate a rotation of the chute about said first axis X; a first annular body inside said housing and coaxial to the first axis X, adapted to translate along the first axis X by means of said first actuating means; a second annular body inside said housing and coaxial to said first axis X, adapted to translate along the first axis X being coupled to the first annular body and/or adapted to rotate about the first axis X by means of said second actuating means; a mechanism coupled to the second annular body and t

Abstract: The present disclosure relates to a method for producing a press-quenched component from a hot-formable steel sheet blank, in which, in a first step, the blank is heated to a temperature of approximately 900° C. and, in a second step, the blank is arranged in a press mold and formed, wherein a drawing bead is created on the blank and the region of the press mold in which the drawing bead is arranged is heated prior to introduction of the blank into the press mold. The present disclosure also relates to a press mold for the above method.

Abstract: Methods for press hardening steel alloys comprised of medium-Mn are provided. The press-hardened steel alloy may have an ultimate tensile strength (UTS) of at least 1,700 MPa and a tensile elongation of at least 8%. The press-hardened steel alloy may be formed in two forming steps above the martensitic finish temperature. The press-hardened steel may have a microstructure comprising martensite at greater than or equal to about 80% to less than or equal to about 98% and retained austenite at less than or equal to about 20% to greater than or equal to about 2%.

Abstract: There is provided a steel sheet with strain induced transformation type composite structure having a predetermined chemical composition in which a microstructure at the ¼ thickness of the steel sheet includes, by area ratio, 50% to 85% of a polygonal ferrite, 3% to 10% of a residual austenite, 5% to 47% of bainite and 1% or less of a fresh martensite and a tempered martensite in total and satisfies the equation of 0.01<Ex.C/fsd?0.015, the microstructure includes 1×1016 pieces/cm3 or more of precipitates containing TiC, an average grain diameter of the residual austenite 1.0 ?m to 5.0 ?m at an equivalent circle diameter, an average of closest distances of the austenite is 3.0 ?m to 10.0 ?m, and an average diameter of the precipitates is 3 nm or less.

Abstract: The invention relates to a formable lightweight steel having improved mechanical properties and a high resistance to delayed hydrogen-induced cracking formation and hydrogen embrittlement comprising the following elements (in wt. %): C 0.02 to ?1.0; Mn 3 to 30; Si?4; P max. 0.1; S max. 0.1; N max. 0.03; Sb 0.003 to 0.8, particularly advantageously to 0.5, as well as at least one or more of the following carbide-forming elements in the specified proportions (in wt. %): Al?15; Cr>0.1 to 8; Mo 0.05 to 2; Ti 0.01 to 2; V 0.005 to 1; Nb 0.005 to 1; W 0.005 to 1; Zr 0.001 to 0.3; with the remainder consisting of iron including the usual steel-accompanying elements, with the optional addition of the following elements, in wt. %: max. 5 Ni, max. 10 Co, max. 0.005 Ca, max. 0.01 B and 0.05 to 2 Cu. The invention also relates to a method for producing the said lightweight steel.

Abstract: This invention provides a high-strength PC steel wire having a chemical composition containing, in mass %, C: 0.90 to 1.10%, Si: 0.80 to 1.50%, Mn: 0.30 to 0.70%, P: 0.030% or less, S: 0.030% or less, Al: 0.010 to 0.070%, N: 0.0010 to 0.010%, Cr: 0 to 0.50%, V: 0 to 0.10%, B: 0 to 0.005%, Ni: 0 to 1.0%, Cu: 0 to 0.50%, and the balance: Fe and impurities. A ratio between the Vickers hardness (HvS) at a location (surface layer) that is 0.1D [D: diameter of steel wire] from the surface of the steel wire and the Vickers hardness (HvI) of a region on the inner side relative to the surface layer satisfies the formula [1.10<HvS/HvI?1.15]. The steel micro-structure in the region from the surface of the steel wire to 0.01D (outermost layer region) consists of, in area %, a pearlite structure: less than 80%, and the balance: a ferrite structure and/or a bainitic structure.

Abstract: The above mentioned invention describes a process for producing uranium and/or at least one rare earth element selected from the group consisting of cerium, dysprosium, erbium, europium, gadolinium, holmium, lanthanum, lutetium, neodymium, praseodymium, promethium, samarium, scandium, terbium, thulium, ytterbium and yttrium out of an ore. The ore is mixed with sulphuric acid with an concentration of at least 95 wt.-% to a mixture, wherein the mixture is granulated to pellets. The pellets are fed into at least one fluidized bed fluidized by a fluidizing gas for a thermal treatment at temperatures between 200 and 1000° C. The at least one fluidized bed is developed such that it at least partly surrounds a gas supply tube for a gas or a gas mixture fed into the reactor and the gas or gas mixture is used as a heat transfer medium.