Abstract: A novel method that enables prostate cancer testing that is noninvasive and more accurate than conventional methods is disclosed. The present inventors intensively analyzed urine samples from prostate cancer patients, and non-cancer subjects, who are free of prostate cancer, and, as a result, newly discovered urinary peptides that can be used as indicators in prostate cancer testing. Use of these urinary peptides as indicators enables various prostate cancer-related tests including detection of prostate cancer, discrimination between prostate cancer and benign prostatic hyperplasia, monitoring of a therapeutic effect of prostate cancer therapy and monitoring of postoperative recurrence.

Abstract: Examples of integrated sensors are disclosed herein. An example of an integrated sensor includes a substrate and a sensing member formed on a surface of the substrate. The sensing member includes collapsible signal amplifying structures and an area surrounding the collapsible signal amplifying structures that enables self-positioning of droplets exposed thereto toward the collapsible signal amplifying structures.

Abstract: Method for diagnosis of heart failure, comprising the step of determining the presence or absence or amplitude of at least three polypeptide markers in a urine sample, the polypeptide markers being selected from the markers characterized in Table 1 by values for the molecular masses and the migration time.

Abstract: An apparatus is provided for sensing an analyte in a fluid.

Abstract: Methods for identifying and evaluating biochemical entities useful as biomarkers for bladder cancer, target identification/validation, and monitoring of drug efficacy are provided. Also provided are suites of small molecule entities as biomarkers for bladder cancer.

Abstract: Carbon monoxide (CO) is a member of the gasotransmitter family that includes NO and H2S and is implicated in a variety of pathological and physiological conditions. Whereas exogenous therapeutic additions of CO to tissues and whole animals have been well studied, the real-time spatial and temporal tracking of CO at the cellular level remains an open challenge. We now report a new type of turn-on fluorescent probe for selective CO detection by exploiting palladium-mediated carbonylation reactivity. The compounds of the invention are capable of detecting CO both in aqueous buffer and in live cells with high selectivity over a range of biologically relevant reactive small molecules, providing a potentially powerful approach for interrogating its chemistry in biological systems.

Abstract: A method is described for mass spectrometric analysis of a sample comprising phenolic OH, such as a steroid comprising a phenolic OH, using a quaternary amino oxy Cookson (QAOC) reagent. The QAOC reagent can improve ionization and fragmentation properties of phenolic OH samples, which can thereby improve quantitation and identification. The method can include derivatizing the phenolic OH sample with the QAOC reagent to create an adduct and analyzing the adduct using mass spectrometry. Derivatization of the sample can be a one-step reaction where the QAOC reagent comprises an aminooxy MS tag or can be a multi-step reaction, where the adduct is formed by the reaction of carbonyl substituted PTAD based reagent and the sample followed by combination with an aminooxy MS tag. The sample can also be enriched prior to reacting it with the reagent. The method can also allow for multiplexing.

Abstract: The application discloses new biomarkers or test panels useful in systemic inflammatory conditions such as sepsis; methods for the diagnosis, prediction, prognosis and/or monitoring systemic inflammatory conditions such as sepsis based on measuring said biomarkers or test panels; and related kits and devices.

Abstract: A method for screening a drug for cytochrome P450 (CYP) induction is provided and can include incubating the drug with a microsome-containing biological sample and then quantitating at least one cytochrome P450 isoform. The isoforms can be selected from 2B6, 3A4, 1A2, and 3A5 isoforms. In some embodiments, the method uses liquid chromatography tandem mass spectrometry (LC-MSMS). A quantitated value can be compared to a threshold value and the drug can be determined to exhibit an acceptable CYP induction potential when the quantitated value does not exceed the threshold value. Isolated peptides are also provided.

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 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: 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: The process for the diagnosis of a renal cell carcinoma comprises the step of determining the presence or absence or amplitude of at least three polypeptide markers in a urine sample, wherein said polypeptide markers are selected from the markers as characterized in Table 1 by molecular masses and migration times.

Abstract: The present invention relates to a biomarker set for diagnosing breast cancer comprising two or more protein markers of: apolipoprotein C1, apolipoprotein (a), neural cell adhesion molecule L1-like protein, carbonic anhydrase 1, and fibronectin; a method for detecting the biomarker set in a blood sample through a multiple reaction monitoring; a kit for diagnosing breast cancer comprising antibodies specific to each of the proteins of the biomarker set; and a method for detecting proteins of the marker set in a blood sample through an antigen-antibody binding reaction. The method for detecting the protein marker set in a blood sample by the MRM method or antigen-antibody binding reaction and the diagnostic kit can provide very high accuracy and sensitivity in comparison with the diagnosis method using a single marker and can very conveniently diagnose breast cancer using blood from patients, thereby being effectively used for early diagnosis of breast cancer.

Abstract: A method for determining prognosis, diagnosis and theronosis of a sepsis infection in a patient is disclosed. The method involves measuring the age, mean arterial pressure, hematocrit, patient temperature, and the concentration of one or more metabolites that are predictive of sepsis severity. The method can involve obtaining a blood sample from said patient and determining the concentration of the metabolite in the patient's blood; and then determining the severity of sepsis infection by analyzing the measured values in a weighted logistic regression equation.

Abstract: Apparatus, systems and methods for use in analyzing discrete reactions are provided. The analytical devices of the invention use an array of nanoscale regions (a chip) that has discrete patches of nanoscale regions. The chip mates with a collection device comprising an array of compact lens trains (CLTs) where each of the CLTs corresponds to a single patch of nanoscale regions. Each CLT collects the emitted light from a patch on the chip, collimates the light, performs color separation on the collimated emitted light, and focuses the separated light onto a portion of pixels on the detector below the CLT. Such systems are useful for monitoring many analytical reactions at one time including single molecule sequencing reactions.

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

Abstract: Systems and methods for arranging microdevices on an array substrate are described. Each microdevice contains a lipid bilayer region and a patterned magnetic material that has a predetermined preferential axis of magnetization. The microdevices are located at specific locations on the arraying substrates and a magnetic field is used to orient the microdevices to facilitate the study of lipids and lipid-associated moieties. The bilayer region can also contain a fluorescent reagent, which can be monitored during exposure to an excitation source. The fluorescent reagent can also be photobleached and monitored for fluorescence recovery.

Abstract: The invention relates to a method for diagnosing vascular diseases, comprising the step in which the presence, absence or amplitude of at least three polypeptide markers is determined in a urine sample, wherein the polypeptide markers are selected from the markers characterized in table 1 by values for the molecular masses and the migration time.

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

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

Abstract: A novel non-enzymatic assay for lipid modulating drugs is being described for biological samples. For the first time non-enzymatic mechanism of statin drugs in modulating lipid aggregates and forming lipid particles is being shown. A simple flow cytometer based testing for detection of lipid particles, the effect of lipid modulating drug such as statin in vitro and testing for efficacy of the drug for an individual, dosage adjustment and drug discovery mechanism is being described. The lipid modulating drugs either individually or in combination can be discovered, optimized or efficacy tested using this assay. A novel statin induced lipid particle formation described can be used for diagnosis, personalized medicine and biomarker identification as well.

Abstract: The present invention is based on the idea of determining certain molecular lipids from a subject's blood sample, for example from serum or plasma sample, and based on the amounts of the determined lipids determining the amount of liver fat and/or diagnosing NAFLD in the subject. More specifically the subjects with elevated liver fat amount and NAFLD are characterized by elevated triglycerides with low carbon number and double bond content in the blood sample. Lysophosphatidylcholines, ether phospholipids, sphingomyelins and PUFA-containing phospholipids are diminished in the blood samples of subjects with an elevated liver fat amount and NAFLD. The method of the present invention can be further used for monitoring the subject's response to the treatment of NAFLD or to the treatment of lowering of the liver fat amount in the subject.

Abstract: The present invention relates to methods and arrays for use in high resolution imaging of individual nucleic acid molecules and chromatin fragments, including native chromatin fragments. In one aspect, the present invention relates to a chromatin array that includes a transfer platform having a support and a transfer surface layered on the support. The chromatin array also includes a plurality of elongated individual native chromatin fragments coupled to the transfer surface in an orderly pattern suitable for high resolution imaging of the plurality of native chromatin fragments. The native chromatin fragments of the chromatin array include both DNA and histones.

Abstract: A method and apparatus for determining the presence or absence of microorganisms in a liquid sample. A vessel with an electrode disposed therein receives a volume of liquid to be tested. A second electrode is also provided, both electrodes in physical contact with the liquid sample. A time varying signal is applied to one electrode, and the other electrode is coupled to a phase sensitive signal detector. The phase sensitive signal detector determines a frequency at which an out of phase signal amplitude is zero. This zero-crossing frequency is used as a baseline, and changes in the zero-crossing frequency are an indication of microbial growth.

Abstract: Biomarkers relating to insulin resistance, pre-diabetes, type-2 diabetes, metabolic syndrome, atherosclerosis, and cardiomyopathy are provided, as well as methods for using such biomarkers as biomarkers for insulin resistance, pre-diabetes, type-2 diabetes, metabolic syndrome, atherosclerosis, and cardiomyopathy. In addition, methods for modulating the respective disorders or conditions of a subject are also provided. Also provided are suites of small molecule entities as biomarkers for insulin resistance, pre-diabetes, type-2 diabetes, metabolic syndrome, atherosclerosis, and cardiomyopathy.

Abstract: Processes and methods for creating a database of genomic samples from healthy human donors, methods that use the database to identify and correlate polymorphic genetic markers and other markers with diseases and conditions are provided.

Abstract: The invention relates to a method of diagnosing or monitoring schizophrenia or other psychotic disorder.

Abstract: Methods are provided that detect cognitive impairment including mild cognitive impairment and Alzheimer disease by using a protein or its partial peptide that differs in presence or absence. Novel biomarkers are also provided for cognitive impairment and non-psychiatric disease, as well as methods for detecting cognitive impairment using such biomarkers. Specifically, a biomarker for diagnosis is provided that comprises a protein fragment or peptide of not less than 5 amino acid residues arising from at least one protein or peptide selected from the group of proteins consisting of an amino acid sequence expressed by SEQ ID NO: 1, 3, 6, 8, 10, 13, 15, 18, or 20 and selected from the group of partial peptide in these proteins consisting of an amino acid sequence expressed by SEQ ID NO: 2, 4, 5, 7, 9, 11, 12, 14, 16, 17, 19, or 21.

Abstract: A method for absolute protein or peptide quantitation by mass spectroscopy. A sample containing a protein or peptide of interest is prepared for mass spectroscopy analysis. The sample is subjected to mass spectroscopy analysis at low resolution whereby a single additive mass spectroscopy peak is obtained, then is subjected to high resolution mass spectroscopy analysis whereby a plurality of mass spectroscopy peaks are obtained. The intensity of each of the plurality of mass spectroscopy peaks is quantitated either by comparison to an internal standard set, or by using a standard curve generated for each isotopologue set. Quantitation using a standard curve enhances quantitation across a dynamic range of analyte.

Abstract: An apparatus and method for counting nanoparticle probes is disclosed. In one embodiment, quantum dot-tagged proteins on optically transparent membranes or slides are counted. The transparent membranes or slides are loaded onto a stage (e.g., an X-Y stage or X-Y-Z stage), which can automatically reposition the transparent membrane or slides for image capture at varying locations. A microscope can be used for providing a light source to fluoresce the nanocrystals and for providing the magnification needed for image capture. Once one or more images are captured, the nanoparticles can be automatically counted using post-processing software that maintains a total count across multiple images, if desired.

Abstract: A method for analyzing the polypeptide content of animal tissue is described. The method includes the steps of (a) providing an animal tissue specimen; (b) depositing one or more portions of a hydrogel mixture including a protease on spatially discrete portions of the animal tissue specimen; (c) allowing sufficient time to pass for animal tissue under the hydrogel mixture to be form a digested mixture of animal tissue and hydrogel mixture; (d) removing the digested mixture from the animal tissue and extracting the polypeptides from the digested mixture to provide an extract; and (e) analyzing the polypeptide content of the extract by mass spectrometry.

Abstract: A system and method for isolating cells, comprising: a substrate having a broad surface; an array comprising a set of wells defined at the broad surface of the substrate, each well including: a base surface, an open surface directly opposing the base surface, defined at the broad surface of the substrate, and configured to receive one of a single cell and a single cluster of cells from a direction perpendicular to the broad surface of the substrate, and a set of channels that fluidly couple each well to at least one adjacent well; wherein the set of wells includes an interior subset and an exterior subset fluidly coupled to and surrounding the interior subset by way of the set of channels; and a fluid delivery module surrounding the array and fluidly coupled to each well in the set of wells.

Abstract: The disclosure provides for methods and apparatuses relating to technology for monitoring chemical and/or biological reactions. Some methods provided herein relate to utilization of NAPPA technology to create large protein arrays suitable for use in combination with various ISFET arrays to enable massive parallel assays of kinase activity and inhibition. Some devices provided herein relate to CMOS chips which utilize the NAPPA array technology to build protein inventories of interest upon an ISFET architecture. Further devices provided herein are capable, inter alia, of processing the arrays created by the combination of NAPPA technology and ISFET architecture.

Abstract: Disclosed herein are markers for diagnosing Alzheimer's Disease and/or mild cognitive impairment, for predicting risk of developing Alzheimer's Disease and/or mild cognitive impairment, and for monitoring the efficacy of treatment for Alzheimer's Disease and/or mild cognitive impairment. Also disclosed herein are methods of diagnosing Alzheimer's Disease and/or mild cognitive impairment in a subject in need thereof, for predicting risk of developing Alzheimer's Disease and/or mild cognitive impairment in a subject in need thereof, and for monitoring the efficacy of a treatment for Alzheimer's Disease and/or mild cognitive impairment in the subject.

Abstract: A peptide is cleaved at various bonding sites into oligopeptides or similar fragments by digestion using proteinase K (S3). The obtained fragments are separated according to their kinds by reversed-phase chromatography and fractionated (S4), and each fragment is subjected to mass spectrometry to determine its mass (S6). For each peptide fragment, an amino-acid composition is calculated from the measured mass, and amino-acid sequence candidates are deduced from that composition. The amino-acid sequence candidates of the other peptide fragments are searched for a fragment having an overlapping portion available for combining two peptide fragments to obtain amino-acid sequence candidates of the original peptide (S7). The masses of the amino-acid sequence candidates are compared with a measured mass derived from a result of mass spectrometry of the original peptide to select a correct sequence (S6 and S8).

Abstract: A method, a labeling reagent, sets of labeling reagents, and labeling techniques are provided for the relative quantitation, absolute quantitation, or both, of ketone or aldehyde compounds including, but not limited to, analytes comprising steroids or ketosteroids. The analytes can be medical or pharmaceutical compounds in biological matrices. Methods for labeling, analyzing, and quantifying ketone or aldehyde compounds are also disclosed as are methods that also use mass spectrometry.

Abstract: Disclosed herein are methods for large-scale, high-throughput identification of protein-protein interactions and the topologies thereof under physiologically relevant conditions. In one aspect, the disclosure provides methods for identifying one or a plurality of interacting peptides within a biological system comprising obtaining a population of proteins cross-linked with a cleavable protein interaction reporter (PIR) cross-linker, cleaving the PIR crosslinker to produce released peptides and cleaved reporter ions, and analyzing the population of released peptides to identify interacting peptides. Also disclosed are methods for identifying candidate drug compounds, as well as methods of data processing and visualization of protein-protein interactions.

Abstract: The present invention relates to a forensic method for identifying an organ penetrated by a corpus delicti.

Abstract: Provided in certain embodiments are new methods for forming azido modified nucleic acid conjugates of reporter molecules, carrier molecules or solid support. In other embodiments are provided methods for enzymatically labeling nucleic acids with an azide group.

Abstract: The present invention relates to a method of diagnosing an existing or developing acute pneumonia induced by a microorganism by detecting one or more volatile organic compound(s) in a subject's sample and the use of one or more volatile organic compound(s) for the detection of Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae or Haemophilus influenza and optionally opportunistic pathogen Candida albicans.

Abstract: A method for determining the sensitivity and/or resistance of a patient suffering from a cancer disease to Aurora kinase inhibitor therapy, which comprises determining in vitro in the cancer cells or body fluids taken from the patient the expression of at least one gene selected from a particular group and/or determining in vitro in the cancer cells or body fluids taken from the patient the level of at least one protein selected from a particular group.

Abstract: The present invention relates to the field of diagnostic methods. Specifically, the present invention contemplates a method for diagnosing pancreatic cancer in a subject, a method for identifying whether a subject is in need for a therapy of pancreatic cancer or a method for determining whether a pancreatic cancer therapy is successful. The invention also relates to tools for carrying out the aforementioned methods, such as diagnostic devices.

Abstract: A chemical sensor comprising: a hydrogel layer, comprising one or more molecular recognition agents and a 2DPC self-assembling array; and a mirror layer. A method for analyzing a sample or bodily fluid, comprising: obtaining a sample or bodily fluid; placing an amount of the sample or bodily fluid onto a chemical sensor, comprising: a hydrogel layer, comprising a molecular recognition agent and a 2DPC self-assembling array; a tethering hydrogel layer; a mirror layer; and a membrane filter layer, allowing the bodily fluid to interact with the hydrogel layer; and allowing ambient or artificial light to pass through the hydrogel layer onto the mirror layer and observing a change in diffraction versus a control.

Abstract: A composition including a triglyceride containing glycerol which is esterified with three fatty acids, wherein the three fatty acids include at least one fatty acid selected from caprylic acid, capric acid, ?-linolenic acid, linoleic acid, oleic acid, arachidonic acid, eicosapentaenoic acid, docosahexaenoic acid and docosapentaenoic acid. The total amount of caprylic acid, capric acid, a-linolenic acid, linoleic acid, oleic acid, arachidonic acid, eicosapentaenoic acid, docosahexaenoic acid and docosapentaenoic acid is greater than 60%, based on the total weight of the fatty acids in a base or starting emulsion. The various physical mixtures of triglycerides containing the primary therapeutic fatty acid can be blended to form pre-defined amounts for the treatment of various acute pathological conditions.

Abstract: A method of synthesizing a nucleic acid molecule, such as a gene, on a substrate or microchip is described. In particular, a method for synthesizing, amplifying, and assembling DNA oligonucleotides into a nucleic acid molecule or gene product, on a single substrate or microchip is described. Also described are a method of correcting a sequence error in a synthesized nucleic acid molecule, as well as a method for synthesizing and screening a library of codon variants to identify a nucleic acid molecule with an optimized level of protein expression.

Abstract: Improved compositions, methods, apparatus, and kits for high-throughput nucleic acid amplification, detection and sequencing are disclosed. A nucleic acid cluster having an identifiable center is produced by generating on a solid support an immobilized nucleic acid complement from a template, one of which comprises a detectable label; and amplifying the complement and the template to obtain a nucleic acid cluster on the support, the cluster having a substantially central location marked by the detectable label and a surrounding region comprising immobilized copies. Also disclosed are nucleotide sequence determination in nucleic acid clusters so produced, center position annotation in the clusters, assignment of sequence information to overlapping clusters, and related compositions and methods.

Abstract: This invention pertains to methods, mixtures, kits and compositions pertaining to analyte determination and/or quantification by mass spectrometry using compounds comprising a reporter moiety and a non-encoded detectable label. The compounds can be used in sets for the analysis of mixtures of labeled analytes.

Abstract: The disclosure provides biomarker panels, methods and kits for determining the probability for preeclampsia in a pregnant female. The present disclosure is based, in part, on the discovery that certain proteins and peptides in biological samples obtained from a pregnant female are differentially expressed in pregnant females that have an increased risk of developing in the future or presently suffering from preeclampsia relative to matched controls. The present disclosure is further based, in part, on the unexepected discovery that panels combining one or more of these proteins and peptides can be utilized in methods of determining the probability for preeclampsia in a pregnant female with relatively high sensitivity and specificity. These proteins and peptides disclosed herein serve as biomarkers for classifying test samples, predicting a probability of preeclampsia, monitoring of progress of preeclampsia in a pregnant female, either individually or in a panel of biomarkers.

Abstract: An entire complement or plurality of isotopically labeled amino acids are introduced into the diet of a test subject. Sufficient amounts of the isotopically labeled amino acids are provided to the subject in order to ensure that the subject incorporates a large percentage of isotopically labeled amino acids into newly synthesized proteins. Tissue samples are removed from the subject at different points in time and proteins are extracted and separated so that different proteins of different tissues can be individually analyzed and their amount and pattern of isotopic labeling can be determined. In a preferred embodiment, the methodology can be combined with proteolytic digestion to peptides and analysis by mass spectrometry in order to measure rates of protein turnover in vivo relating to thousands of different proteins.