Abstract: Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.

Abstract: A method for sequencing includes steps of (a) providing first and second nucleic acid templates, wherein the two templates have different sequences; (b) extending a first primer bound to the first template using a first polymerase species and a first set of nucleotide analogs; (c) extending a second primer bound to the second template using a second polymerase species and a second set of nucleotide analogs, wherein the first polymerase species is different from the second polymerase species and wherein the first set of nucleotide analog is different from the second set of nucleotide analog, (d) detecting the first and second primer extension products; and (e) repeating steps (b) through (d), thereby determining the different sequences of the first and second templates.

Abstract: Methods are provided for predicting the presence, subtype and stage of ovarian cancer, as well as for assessing the therapeutic efficacy of a cancer treatment and determining whether a subject potentially is developing cancer. Associated test kits, computer and analytical systems as well as software and diagnostic models are also provided.

Abstract: Biomarkers useful for identifying treatments for and monitoring treatment of patients with multiple sclerosis (MS) are provided, as well as methods for their identification, methods of diagnosing MS, relapse of MS patients and disease progression in MS patients.

Abstract: The disclosure provides methods for detecting the concurrent presence of at least two targets within a biological sample. The method includes contacting said biological sample with a first binding agent, said first binding agent operably linked to a first sortase molecule, wherein said first binding agent specifically binds to a first target; contacting said biological sample with a second binding agent, said second binding agent operably linked to a first sortase recognition sequence peptide, wherein said second binding agent specifically binds to a second target; adding a sortase substrate under conditions where a first sortase-mediated ligation of the sortase substrate to the first sortase recognition sequence will produce a ligation product, and detecting the ligation product, wherein detection of said ligation product indicates the concurrent presence of the first target and the second target in the biological sample. Also disclosed are kits comprising reagents for performing the methods as claimed.

Abstract: The present invention improves in vitro virus synthesis efficiency and stability of mRNA derived from screened cDNA in a cDNA display method to improve the efficiency and reliability of the production of a peptide by a molecular evolutionary engineering technique. Provided is a ligand which comprises three fingers formed from antiparallel ?-sheets and a loop region intercalated between the antiparallel ?-sheets, wherein at least a fingertip part formed by the loop region of each of the fingers is bound to the target molecule, and wherein the ligand comprises the amino acid sequence of SEQ ID NO: 1. In the amino acid sequence of SEQ ID NO: 1, X7 represents an arbitrary amino acid residue that constitutes the fingertip part of each of the fingers, each numeric character represents the number of amino acid residues, and X7 and X4 are not composed of the same amino acid residues as each other.

Abstract: A method of genotyping single nucleotide polymorphisms (“SNP”) and point mutations in nucleic acid based on chain extension by polymerase. This invention is based on the fact that the neighboring sequence immediately 3? adjacent to the site is known, and the nucleoside immediately 5? adjacent to any SNP/point mutation site is also known. An extension primer complementary to the sequence directly adjacent to the SNP on the 3? side of a target polynucleotide is used for chain extension. Up to four different polymerase reaction mixtures are provided in separate reaction containers, each containing one different potentially chain-extending Bridging Nucleotide. A Reporting Nucleotide having a base complementary to the nucleotide directly adjacent to the SNP on the 5? side of the target polynucleotide may also be added to each reaction container.

Abstract: The invention demonstrates an improved choice of biotinylation peptide to be used in a combination or fusion with an MHC molecule for immobilizing or multimerising such MHC molecules for a variety of purposes.

Abstract: Methods for diagnosing inflammatory bowel disease and ulcerative colitis using miRNA biomarkers for these diseases are provided. Differential expression of the miRNA biomarkers in blood fractions, e.g., platelets, of diseased individuals as compared to expression levels in normal individuals indicates the presence of IBD or ulcerative colitis. Also provided are microarrays for use in the diagnostic methods, wherein the features of the microarray consist essentially of nucleic acid sequences that hybridize to the miRNA biomarkers and normalization controls.

Abstract: Provided is a technique which can detect a physiologically active substance of biological origin or measure the concentration of the physiologically active substance of biological origin with higher accuracy or within a shorter period even when a sample that contains the physiologically active substance of biological origin at an extremely low concentration or a sample that contains a component capable of interfering with an AL is used. Microparticles capable of adsorbing a specific physiologically active substance, e.g., an endotoxin, is dispersed in a sample containing the specific physiologically active substance to cause the adsorption of the specific physiologically active substance onto the microparticles, thereby concentrating the specific physiologically active substance in the sample. Subsequently, the microparticles are separated and collected, then are reacted with an AL to cause an aggregation reaction, and the aggregation is detected by an optical means.

Abstract: The present invention relates to an in vitro method for diagnosing a complete congenital stationary night blindness (cCSNB) in a subject, which method comprises determining the presence of an alteration in the GPR179 gene in a biological sample of said subject. Screening methods and therapeutic applications are further described.

Abstract: A high throughput biological sample processing system includes a sample carrier with a plurality of wells that progresses through the high throughput biological sample processing system. The system further includes a sample dispensing module, a reagent dispensing module, an accumulation/incubation module, and a detection module. The detection module employs an optical measuring device to encapsulate a biological sample in one of the plurality of wells of the sample carrier and detect energy from the chemistry of the biological sample to determine the amount of an analyte in the biological sample.

Abstract: Gold nanoparticles having luminol covalently linked thereto and optionally functionalized with an oligonucleotide and bacterial or viral detection assays. In one aspect, the detection system for detecting an analyte in a sample comprises a light-shielding container having a fiberoptic cable for transmitting light generated within the light-shielding container to a photodetector; a plurality of functionalized nanoparticles deposited in solid form on or within a support, such that the support is located within the light-shielding container; wherein the functionalized nanoparticles comprise nanoparticles covalently attached to one or more chemiluminescent moieties; and a reagent system which causes the chemiluminescent moieties to produce light in the presence of the reagent system and the analyte in the sample.

Abstract: The present invention pertains to the field of diagnostics for neuronal toxicity and toxicological assessments for risk stratification of chemical compounds. Specifically, it relates to a method for diagnosing neuronal toxicity. It also relates to a method for determining whether a compound is capable of inducing such neuronal toxicity in a subject and to a method of identifying a drug for treating neuronal toxicity. Furthermore, the present invention relates to a device and a kit for diagnosing neuronal toxicity.

Abstract: The present invention provides a PCR-free, multiplexed ligation assay for miRNA expression analysis that produces highly quantitative, 10-100 plex miRNA profiling in a single reaction. The inventive methods use a 2-step ligation assay to generate an array of miRNA specific ligation products that can be decoded and quantified by a size discrimination method such as gel electrophoresis or single molecule separation. One embodiment is a low-cost assay that can be performed using standard tools available in nearly all molecular biology laboratories. This assay requires nothing more than a gel apparatus and reader for detection. Other embodiments include use of magnetic beads and other size exclusion apparatus which give increasingly higher sensitivity, lower sample consumption, and reduced processing steps.

Abstract: A method for classifying test body fluid samples into either of two groups selected from four groups consisting of chronic hepatitis C, chronic hepatitis B, non-alcoholic steatohepatitis (NASH) and normal liver, is provided. In one or plural embodiment(s), it relates to a method for classifying test body fluid samples into either of two groups selected from four groups consisting of chronic hepatitis C, chronic hepatitis B, non-alcoholic steatohepatitis (NASH) and normal liver. The method includes a measurement of an expression level of the one or plural non-coding RNA(s) in the test body fluid sample.

Abstract: The present invention relates to compositions comprising a porous nanostructure of a known characteristics and a fragment of nucleic acid having a known sequence. Methods of use of the compositions were also provided, for example in DNA amplification, detection, and DNA sequencing.

Abstract: The present invention relates to assays, diagnostic kits and methods for the real-time PCR detection of nucleic acids that are indicative of rifampicin and/or isoniazid susceptible and/or resistant Mycobacterium tuberculosis bacteria.

Abstract: Reagents, systems and methods for the detection of nucleic acids are described herein, including such methods which may be performed in a single reaction. Such reagents include a target specific indexing probe (TSIP) synthetic DNA structure comprising a detectable moiety and a quencher thereof, wherein in the presence of a target nucleic acid a portion (a tag) of the (TSIP) synthetic DNA structure comprising the detectable moiety is released, thereby increasing the signal emitted therefrom. The tag may in turn bind to a capture probe, facilitating signal detection.

Abstract: The invention relates to prognostic markers and prognostic signatures, and compositions and methods for determining the prognosis of cancer in a patient, particularly for melanoma. Specifically, the invention relates to the use of genetic and protein markers for the prediction of the risk of progression of a cancer, such as melanoma, based on markers and signatures of markers. In various aspects, the invention provides methods, compositions, kits, and devices based on prognostic cancer markers, specifically melanoma prognostic markers, to aid in the prognosis and treatment of cancer.

Abstract: Unsymmetrical cyanine dyes that incorporate an aza-benzazolium ring moiety are described, including cyanine dyes substituted by a cationic side chain, monomeric and dimeric cyanine dyes, chemically reactive cyanine dyes, and conjugates of cyanine dyes. The subject dyes are virtually non-fluorescent when diluted in aqueous solution, but exhibit bright fluorescence when associated with nucleic acid polymers such as DNA or RNA, or when associated with detergent-complexed proteins. A variety of applications are described for detection and quantitation of nucleic acids and detergent-complexed proteins in a variety of samples, including solutions, electrophoretic gels, cells, and microorganisms.

Abstract: A method for quantitative assessment of base excision repair (BER) and nucleotide excision repair (NER) DNA repair capacities of at least one cellular extract, which method entails: a) preparing a range of plasmids with at least one physical or chemical treatment or both and recovering a supercoiled fraction of each of said plasmids, b) characterizing the lesions present on each of the plasmids of the range of plasmids; c) depositing the plasmids of the range of plasmids, and at least one supercoiled control plasmid without lesions onto a single solid support, according to a pre-established configuration A, so as to form a functionalized support divided into different zones A1 to Ax, corresponding to an integer equal to the number of cellular extracts to be simultaneously tested, each zone containing supercoiled plasmids treated with at least one physical or chemical treatment that induces a lesion acted upon by BER mechanisms, and at least one other zone containing supercoiled plasmids treated with at least

Abstract: The invention relates to the field of diagnostic methods, in particular to detection of biological molecules using mass spectroscopy (MS). Provided is an automated high-throughput method for quantitating a low molecular weight protein-bound biomarker directly in an isolated biological sample, comprising the steps of: (a) automated prepurification of the sample using an effective amount of an acid protease under conditions that allow for digestion of one or more binding proteins; (b) applying said protease-digested sample onto an on-line SPE column to capture at least part of said biomarker, followed by sequential washing of the solid phase; (c) eluting a fraction comprising said biomarker directly onto a liquid chromatography (LC) column comprising an apolar stationary phase and subjecting it to LC-MS or LC-MS-MS measurements to determine the amount of at least one biomarker; and (d) quantitating the biomarker(s).

Abstract: A method comprising (a) obtaining one or more biological samples from a subject wherein the subject has undergone an organ transplant; (b) determining the amount and type of one or more volatile organic compounds in the biological sample; and (c) correlating the amount of volatile organic compounds to a degree of transplant rejection. A device comprising a plurality of sensors configured to detect a plurality of volatile organic compounds in a biological sample of a subject having undergone an organ transplant.

Abstract: A phage display system is provided comprising a mutant phage-infected host cell adapted to express a peptide of interest fused to a phage capsid protein, wherein the mutant phage includes a nonsense mutation which prevents expression of the capsid protein as a functional protein, and wherein expression of the peptide of interest is controlled by an inducible repressor and by a suppressor that suppresses the nonsense mutation.

Abstract: The present invention provides novel algorithms for designing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts. Such oligonucleotides are particularly useful as primers for reverse transcription. The invention also provides compositions containing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts.

Abstract: Described herein are compositions comprising a first aptamer, second aptamer and a target that are capable of forming a ternary complex, and wherein the first aptamer and the second aptamer comprise C-5 pyrimidine modification schemes that are different, and methods of making and using such compositions.

Abstract: There is provided an assay device comprising a lid and a base, said base comprising, a sample addition zone, a reaction zone and an absorbing zone, said components being in fluid connection and being part of a fluid passage leading from the sample addition zone to the absorbing zone, wherein: (a) a sample addition well is integrated in the lid, (b) the absorbing zone consists of an area on an non-porous substrate, having substantially perpendicular projections, said projections defining a volume, which together with the volume of the fluid passage defines the sample volume subjected to the assay, and (c) at least one filter is between the sample addition well and the sample addition zone. There is further provided methods for handling samples.

Abstract: A biochip used for quantitative analysis of a target DNA contained in a sample. The biochip includes a type I chamber that includes a primer designed to bind to the target DNA, an internal standard DNA of a first amount that has a sequence different from a sequence of the target DNA, and is amplifiable with the primer, and a fluorescent probe that is designed to bind to a part of a PCR product of the target DNA and to a part of a PCR product of the internal standard DNA. The fluorescent probe fluoresces differently for the PCR product of the target DNA and the PCR product of the internal standard DNA. The biochip also includes a type II chamber that includes the internal standard DNA of a second amount, the primer, and the fluorescent probe. The first and second amounts are different.

Abstract: Nanoemulsions, miniemulsions, microemulsion systems with excess oil or water or both (Winsor III) or single phase microemulsions (Winsor IV) may be formed in situ during hydrocarbon recovery operations after drilling with OBM or SBM using one or more fluid pills. The nanoemulsions, miniemulsions, microemulsion systems with excess oil or water or both or single phase microemulsions remove oil and solids from the well and wellbore surfaces. In one non-limiting embodiment, a single phase microemulsion (SPME) or other in situ-formed fluid may be created from a polar phase, a nonpolar phase, at least one viscosifier, and at least one surfactant.

Abstract: The present invention provides methods for protein engineering and serine protease variants produced there from. Specifically, the present invention provides serine protease variants having one or more substitutions as compared to a reference serine protease. In addition, the present invention provides compositions comprising these serine protease variants. In some embodiments, the present invention provides cleaning compositions comprising at least one of these serine protease variants.

Abstract: The present invention relates to compositions comprising granules of phthalocyanine compounds, to a process for the preparation thereof, and to the use thereof in washing agent and additive formulations. The composition comprises a) At least one water-soluble phthalocyanine compound; b) At least one cross-linked polyvinylpyrrolidone component; c) At least one hydrophilic binding agent; and, optionally, d) Further additives suitable for the preparation of solid agglomerates; and may be liquid, solid, paste-like or gel-like.

Abstract: This application relates to thiophene azo carboxylate dyes for use as hueing agents, laundry care compositions comprising such dyes that may serve as hueing agents, processes for making such dyes and laundry care compositions and methods of using the same. The aforementioned dyes contain a formally charged moiety and are generally comprised of at least two components: at least one chromophore component and at least one polymeric component. Suitable chromophore components generally fluoresce blue, red, violet, or purple color when exposed to ultraviolet light, or they may absorb light to reflect these same shades. Such dyes are advantageous in providing a hueing effect, for example, a whitening effect to fabrics, while not building up over time and causing undesirable blue discoloration to the treated fabrics. Such dyes are also generally stable to bleaching agents used in laundry care compositions.

Abstract: The cleaning performance of detergents and cleansers when washing textiles or cleaning hard surfaces was to be improved. This was successful substantially due to the use of microfibrillar cellulose.

Abstract: The invention relates to a liquid detergent or cleaning agent, comprising a) an anionic surfactant neutralized with an amine, b) an alkoxylated oxo alcohol having 7 or 8 alkoxy units, and c) up to 10 wt. %, relative to the entire detergent or cleaning agent, of water. The liquid detergent or cleaning agent has very good cleaning performance toward soiling containing fat and can be a component of water-soluble packagings.

Abstract: An aqueous cleaning solution for treating hydrocarbon-contaminated soil and for cleaning hydrocarbon-contaminated surfaces is provided. Suitably it is prepared by progressively diluting a concentrate comprising: i) 10-60% by volume of a first emulsifier; (ii) 10-60% by volume of a second emulsifier and (iii) 20-70% by volume of vegetable oil In a preferred embodiment the concentrate comprises a polyethylene glycol sorbitan trioleate, a polyoxyethylene sorbitan monopalmitate and corn oil with the two sorbitan molecules having different HLB-values.

Abstract: A cleaning composition comprises between about 10% to about 50% of at least one organic solvent comprising vegetable oil. The composition further comprises between about 2% to about 20% of at least one co-solvent. The composition further comprises at least one water-in-oil emulsifier and non-ionic surfactant. The composition also comprises at least one anionic surfactant and between about 20% to about 60% of water.

Abstract: The present invention relates to the field of perfumery. More particularly, it provides a perfuming composition capable of prolonging the release of a perfuming component into the surrounding environment when applied on a body surface such as skin or hair. The composition comprises Neopentyl Glycol Diethylhexanoate as a fragrance evaporation modulator in the presence of high amounts of ethanol. The invention also relates to consumer articles containing such compositions. It finally provides methods for the perfuming of a body surface and a method for increasing the long-lastingness of a perfuming component using these compositions.

Abstract: The present invention is directed to a process for the manufacture of methyl limonitrile comprising a mixture of 3,7-dimethyl-2,6-nonadiene nitrile, 3,7-dimethyl-3,6-nonadiene nitrile and 7-methyl-3-methylene-6-nonene nitrile comprising the following steps: a) reacting 6-methyl-5-octen-2-one with cyano acetic acid and removing carbon dioxide and water, wherein the reaction and the removal of carbon dioxide and water are performed in the presence of a base and a co-base in an organic solvent, wherein the base is pyridine, wherein the co-base is 1,4-diamino butane, and wherein the organic solvent is a solvent which forms a heteroazeotrop with water; b) removing the solvent and pyridine of the reaction mixture obtained after having performed step a) or step c) by distillation to obtain a reaction mixture; c) isomerizing the reaction mixture obtained after having performed step a) or step b) to obtain an isomerized reaction mixture; whereby step b) can be performed before or after step c).

Abstract: Novel fusion proteins compromising nuclear factor kB essential modulator-binding (NEMO) domain or a fragment thereof and MCoTI-I/II or a fragment thereof, and their use for the treatment of inflammatory diseases and other medical conditions.

Abstract: The invention provides compositions containing hemoglobin, particularly PEGylated hemoglobin. The PEGylated hemoglobin molecule is capable of transferring oxygen or carbon monoxide bound thereto to a tissue or red blood cells with which it is in proximity. Exemplary PEGylated hemoglobin formulations of the invention are virally inactivated. Various compositions of the invention include hemoglobin, which may be conjugated with one or more water-soluble polymer. PEGylated hemoglobin includes those species in which the iron atom of the hemoglobin molecule is not bound to oxygen or any other species, and hemoglobin molecules in which a species other than oxygen, e.g., carbon monoxide, is bound to the iron atom. The compositions of the invention are formulated as hypo-, iso- or hypertonic solutions of the PEGylated hemoglobin. The compositions are of use to treat and/or ameliorate disease, injury and insult by providing for the oxygenation of tissues and/organs.

Abstract: The present invention relates to designed polypeptide biosurfactants that may be prepared by recombinant technology in commercially useful amounts and purified by simple non-chromatographic methods. The designed polypeptide biosurfactants comprise at least one stimuli-responsive amino acid residue or at least one glutamine or asparagine residue and may be useful in modulating the stability of a foam, alone or in combination with an ?-helical peptide. The designed polypeptide biosurfactant may be useful in the formation and collapse of foams in foods, beverages, pharmaceuticals, personal care products, cosmetics, cleaning products, mineral recovery, bioremediation, oil recovery and laundry products. The designed biosurfactants may also be useful in recombinant production and purification of peptides, polypeptides and proteins.

Abstract: The present invention relates to variants of a parent antimicrobial peptide. The present invention also relates to polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the variants.

Abstract: Provided are compounds, the use of the said compounds in treatment, for example treatment of microbial infections, particularly by Gram negative bacteria. The compounds are polymyxin-based and are represented by the formula (I): and pharmaceutically acceptable salts thereof, where X is —NHC(O)—, —C(O)—, —OC(O)—, —CH2— or —SO2—; R5 represents C0-12 alkyl(C4-6 heterocyclyl), or C2-12 alkyl or C0-12 alkyl(C3-8 cycloalkyl). and the alkyl or cycloalkyl bears one, two or three hydroxyl groups, or a —NR6R7 group, or one —NR6R7 group and one or two hydroxyl groups; and R1 to R4 and R6 to R8 are as defined in the description.

Abstract: A compound as represented by Formula (I) is provided, wherein groups are defined in the description. The compound is used as HCV protease inhibitor for treating HCV infection.

Abstract: The invention provides a cyclic polypeptide of Formula I (SEQ ID NO: 1): X1-R-X3-X4-L-S-X7-X8-X9-X10-X11-X12-X13??I or an amide, an ester or a salt thereof, or a bioconjugate thereof, wherein X1, X3, X4, X7, X8, X9, X10, X11, X12 and X13 are defined herein. The polypeptides are agonist of the APJ receptor.

Abstract: The invention provides methods for treatment, prevention or management of obesity, obesity related disorders, diabetes mellitus, and metabolic syndrome in a subject by administering a ghrelin O-acyltransferase (GOAT) inhibitor and/or a ghrelin receptor antagonist to the subject. The invention also provides ghrelin receptor antagonists of formula (VII): A11-A12-A13-Gly-Ser-A14-Phe-Leu-A15-A16-A17-A18, wherein each of A11, A12, and A13 is independently absent, an amino acid, or an amino protecting group; each of A15, A16, A17, and A18 is independently absent or an amino acid; and A14 is a serine conjugated with a —C(O)C1-C20alky or a diaminopropionic acid conjugated with a —C(O)C1-C20alkyl group, provided that at least one of A11, A12, or A13 is present.

Abstract: The invention relates to granules and pharmaceutical compositions comprising a salt of N-(8-(2-hydroxybenzoyl)amino)caprylic acid and a lubricant obtained by mixing hereof for more than 5 minutes prior to granulation as well as processes for their preparation and use thereof in medicine.

Abstract: Compounds that exhibit aggregation induced emission (AIE), and more particularly to water-soluble conjugated polyene compounds that exhibit aggregation induced emission. The conjugated polyene compounds can be used as bioprobes for DNA detection, G-quadruplex identification, and potassium-ion sensing. The polyenes also can be utilized as an external fluorescent marker to study conformational structures, to monitor folding processes of label-free oligonucleotides with G-rich strand sequences, and to visualize DNA bands in PAGE assay. The polyenes have applications in high-throughput anticancer drug screening and are useful for the development of efficient anti-cancer drugs. Furthermore, the present subject matter can also be used to monitor fibrillation of amyloid proteins and to facilitate the storage and delivery thereof.

Abstract: The instant invention is drawn to a hepatocyte targeted composition comprising insulin associated with a lipid construct comprising an amphipathic lipid and an extended amphipathic lipid that targets the construct to a receptor displayed by an hepatocyte. The composition can comprise a mixture of free insulin and insulin associated with the complex. The composition can be modified to protect insulin and the complex from degradation. The invention also includes methods for the manufacture of the composition and loading insulin into the composition and recycling various components of the composition. Methods of treating individuals inflicted with diabetes.