Abstract: Provided herein are methods and systems for the detection of spores in a sample which comprise permeabilizing a protein-based spore coat with a protein degrading agent comprising a non-ionic detergent and in particular with a specific mixture of various protein degrading agents comprising a non-ionic detergent to allow contact of spore nucleic acids with fluorescent reagents suitable for detection.

Abstract: Methods are provided for selecting and treating patients with an anti-angiogenic agent and methods for reducing the risk of adverse events in patients from treatment with an anti-angiogenic agent, comprising the steps: obtaining a sample of tumor and normal tissues from a patient; determining the miRNA or protein expression in said samples; comparing the miRNA or protein expression in said tumor sample to the miRNA or protein expression in normal tissue; determining whether said tumor miRNA or protein expression is higher or lower than said normal miRNA or protein expression, wherein if said miRNA or protein expression indicates that the expression of at least one angiogenic gene is upregulated, the patient is scheduled for treatment with an anti-angiogenic agent. Preferably the anti-angiogenic agent is a VEGF-targeting agent or a tyrosine kinase inhibitor. In preferred embodiments, the VEGF-targeting agent is bevacizumab.

Abstract: The present invention relates to a diagnostic method for predicting the possible recurrence of tumours in cancer patients. The method comprises culturing blood cells from a patient suffering from cancer in the presence of a cytokine stimulating factor, where after the amount of induced cytokine thereby produced is determined giving an indication of the risk of recurrence of the cancer.

Abstract: A metal nanoantenna for use in a biosensing device is disclosed. The metal nanoantenna is arranged to exhibit at least two particle plasmon resonances or surface plasmon resonances (SPRs). The nanoantenna is for use in a sensor and allows detection at low concentration of biological components. In one aspect, the nanoantenna can have an asymmetric structural configuration and spectrally separated resonances. In one aspect, there is a location in its structure providing local electromagnetic field enhancement at all of the SPRs. The metal nanoantenna can be used for background free measuring of a quantity of a biological component.

Abstract: Methods for improving antibodies by a variety of DNA diversification and selection procedures are provided. Improvements include increases in affinity, alterations in specificity and effector function, as well as reduced antigenicity, e.g. humanization. Libraries of recombinant antibody sequences are provided, as are cells expressing members of such libraries. Novel phage display vectors are provided. Methods for the coevolution of an antibody and its cognate antigen are provided. Coevolution is used to evolve HIV envelope proteins with increased antigenicity and broadly neutralizing antibodies that interact therewith. Methods of improving antibodies for use in the detection of biological warfare agents are provided.

Abstract: Herein is described the use of a collection of 50 breast cancer cell lines to match responses to 77 conventional and experimental therapeutic agents with transcriptional, proteomic and genomic subtypes found in primary tumors. Almost all compounds produced strong differential responses across the cell lines produced responses that were associated with transcriptional and proteomic subtypes and produced responses that were associated with recurrent genome copy number abnormalities. These associations can now be incorporated into clinical trials that test subtype markers and clinical responses simultaneously.

Abstract: The present invention relates to methods of identifying IGF-IR modulators and hybrid-R modulators comprising contacting IGF-IR with a humanized anti-IGF-IR antibody and contacting hybrid-R with a humanized anti-hybrid-R antibody, respectively.

Abstract: A system for regulating a temperature of a measurement array is disclosed. The system includes a measurement array including a plurality of sensors, wherein the plurality of sensors are integrated onto an integrated circuit die. The system includes a thermal sensor integrated onto the integrated circuit die, wherein the thermal sensor senses a temperature associated with the plurality of sensors. The system further includes a heat pump coupled to the integrated circuit die, wherein the heat pump is controlled by a feedback control circuit including the thermal sensor.

Abstract: A method of inhibiting light-induced degradation of nucleic acids includes irradiating a portion of the nucleic acids in the presence of a detection solution comprising a polyphenolic compound. A method of detecting a nucleic acid having a fluorescent tag includes irradiating at least a portion of the nucleic acid with light of a suitable wavelength to induce a fluorescence emission and detecting the fluorescence emission. Optionally, the polyphenolic compound is gallic acid, a lower alkyl ester thereof, or mixtures thereof. A kit includes one or more nucleotides, an enzyme capable of catalyzing incorporation of the nucleotides into a nucleic acid strand and a polyphenolic compound suitable for preparing a detection solution.

Abstract: The present invention relates to means and methods for diagnosing or predicting endometriosis in a female subject. Particularly, the present invention relates to methods for determining the susceptibility to, predisposition for, presence of and/or risk of developing or suffering from endometriosis in a female subject. The present invention also relates to a kit useful for determining the risk of developing or suffering from endometriosis in a subject, a binding molecule specifically binding to the DBP GC*2 or DBP GC*1 allele product, and a binding molecule binding to the gene encoding the DBP GC*2 or GC*1 allele.

Abstract: The invention is related to a novel primate specific brain isoform of the potassium channel KCNH2 and genetic association with risk for schizophrenia and response to therapy.

Abstract: The invention provides a method of treating cancer in a subject comprising administering to said subject an miRNA that inhibits Six1. In some embodiments, the invention further provides for the administration of a second cancer therapy to the subject.

Abstract: The invention relates to methods for multiplex analysis of complex protein samples from plants using mass spectroscopy. In some embodiments, the disclosure concerns methods for maintaining a transgenic plant variety, for example by analyzing generations of a transgenic plant variety for presence and concentration of multiplexed transgenic proteins.

Abstract: The invention relates to assays for measuring the effect of a inactive test substance on a lipid bilayer, kits for measuring the effects of test substances on lipid bilayers and an apparatus for performing a high through-put assay that measures the effect of test substances on a lipid bilayer.

Abstract: In various embodiments, provided are methods for selecting and formulating compositions for treating and maintaining the quality of skin, wherein a composition is selected for use in a personal care product based on its demonstrated biological effect to improve skin quality as evidenced by one or more biomarker changes that correlate with improvement as evidenced by one or more objective measurements of skin health.

Abstract: Provided herein are fetal diagnostic methods, kits and computational products useful for non-invasively detecting genetic variations for which maternal nucleic acid sequences are utilized as a reference.

Abstract: Provided are methods for aiding in diagnosing autoimmune diseases in a mammal, comprising contacting a biological sample that is not a tear sample from the mammal with an antibody that specifically binds to a first polypeptide selected from the group Ctss, Ctsh, Ctsr, Ctsw, Ctsz, Ifng, IL-6ra, IL-10, IL-10ra, IL-15, Tnfa, Apo-F, or Lcn-2 or a second polypeptide selected from the group lactoperoxidase, lactoferrin or lysozyme under conditions favoring the formation of an antibody-polypeptide complex, and determining the amount of complex formed, wherein an increased formation of antibody-first-polypeptide complex or a decreased formation of antibody-second-polypeptide complex as compared to a suitable control, indicates a likely positive diagnosis of an autoimmune disease for the mammal, thereby aiding in the diagnosis. Methods of treating the autoimmune diseases are also provided.

Abstract: The present invention relates to modified and genomic sequences, to oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genomic DNA, as well as to a method for predicting the response of a subject with a cell proliferative disorder of the breast tissues, to endocrine treatment.

Abstract: A method of treating or preventing an immune disorder, such as graft versus host disease, in a subject. The method includes the administering a SHIP1 inhibitor, such as 3?-aminocholestane, to a subject in need of treatment. Thus, SHIP1 inhibitors taught herein represent a novel class of small molecules that have the potential to enhance allogeneic transplantation, boost innate immunity and improve the treatment of hematologic malignancies.

Abstract: Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.

Abstract: Disclosed is the identification, provision and use of a panel of biomarkers that predict sensitivity or resistance to EGFR inhibitors, and products and processes related thereto. In one embodiment, a method is described for selecting a cancer patient who is predicted to benefit from therapeutic administration of an EGFR inhibitor, an agonist thereof, or a drug having substantially similar biological activity as EGFR inhibitor. Also described is a method to identify molecules that interact with the EGFR pathway to allow or enhance responsiveness to EGFR inhibitors, as well as a plurality of polynucleotides or antibodies for detection of the expression of genes that are indicative of sensitivity or resistance to EGFR inhibitors, an agonist thereof, or a drug having substantially similar biological activity as EGFR inhibitors. A method to identify a compound with the potential to enhance the efficacy of EGFR inhibitors is also described.

Abstract: This invention provides polypeptides having lyase activity, polynucleotides encoding these polypeptides, and meth-°ds of making and using these polynucleotides and polypeptides. In one aspect, the invention is directed to polypeptides having ammonia lyase activity, e.g., phenylalanine ammonia lyase, tyrosine ammonia lyase and/or histidine ammonia lyase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural and industrial contexts. X?NO2, Cl, Br, NH2, OH, H, alkyl at one or several o, m, and p positions R?H or alkyl.

Abstract: The present invention provides compounds having a chelating moiety and an oligonucleotide sequence wherein the oligonucleotide includes one or more modified nucleobases, such as hydroxynucleobases. The disclosed compounds are suitable for antisense therapy. The chelating moiety can be complexed to an ion of a lanthanide metal. These compounds are efficient translation inhibitors of nucleic acids and have increased binding affinity for target nucleic acids. The invention also includes compositions and methods of using these compositions as antisense therapy.

Abstract: The present invention relates to methods and compositions that may be used to predict the risk of an individual, for example a smoker, for developing chronic obstructive pulmonary disease (“COPD”), emphysema or idiopathic pulmonary fibrosis (“IPF”).

Abstract: Mathematical models for the analysis of signal data generated by sequencing of a polynucleotide strand using a pH-based method of detecting nucleotide incorporation(s). In an embodiment, the measured output signal from the reaction confinement region of a reactor array is mathematically modeled. The output signal may be modeled as a linear combination of one or more signal components, including a background signal component. This model is solved to determine the nucleotide incorporation signal. In another embodiment, the incorporation signal from the reaction confinement region of a reactor array is mathematically modeled.

Abstract: A method and system for the identification and application of biological targets for peripheral treatment of diseases. Existing cellular mechanisms or pathways are exploited to identify novel genes or other molecule candidates that will be used to treat disease via a peripheral treatment system. Using the method, a novel Alzheimer's disease target is identified and used to treat an animal Alzheimer's disease model via peripheral expression of that target.

Abstract: Specialized microfluidic networks are utilized to deposit substances on sensor surfaces. In particular, a flow-based microfluidic printhead is used as an interface to deliver multiple analytes to a sensor for simultaneous analysis. Furthermore, internal referencing is incorporated into sensor regions for improved sensitivity.

Abstract: The present invention refers to human EGLN2 variants having at position 58 of the amino acid sequence a serine or a leucine and their use in the prevention or treatment of thromboembolic or coronary heart diseases, in particular stroke, prolonged reversible ischemic neurological deficit (PRIND), transitoric ischemic attack (TIA), myocardial infarction and/or early myocardial infarction.

Abstract: A method of determining the sequence of a target nucleic acid is provided. The method can include the steps of (a) performing a defined number of incremental extension cycles to produce a population of nucleic acid fragments having different portions of the target nucleic acid wherein the individual nucleic acid fragments in the population have a defined length that is correlated with the number of incremental extension cycles; (b) determining the sequence of the first end of individual nucleic acid fragments in the population, thereby providing first end sequences; (c) determining the sequence of the second end of individual nucleic acid fragments in the population, thereby providing second end sequences; and (d) determining the sequence of the target nucleic acid based on the first end sequences, the second end sequences and the defined length.

Abstract: The invention is in the field of nucleic acid amplification, hi particular, methods are described which utilise stem primers that improve the rapid and specific amplification of a test sample.

Abstract: The present invention is based, at least in part, on the development of a mating-based yeast two-hybrid screen that allows simultaneous screening for mutations that disrupt yeast two-hybrid interactions between a protein and multiple interacting partners. By coupling PCR mutagenesis and homologous recombination/gapped plasmid repair with a mating-based assay, the present invention allows screening for unique mutations that disrupt interaction with one partner, but not others. It also allows identification of specific mutations that may lie at protein-protein interfaces common to two or more partners, without employing multiple rounds of screening. In addition to screening against multiple interacting partners, the present invention removes the need for a two-step selection because truncations, frameshifts, or any mutations that affect folding are eliminated as disruptions that affect all protein partners.

Abstract: The present invention relates to methods and reagents for detecting analytes, e.g. nucleic acids. The new methods and reagents allow a simple and sensitive detection even in complex biological samples.

Abstract: Disclosed is a composition comprising a nucleic acid and a chemical compound, said composition forming a star structure defining 3 or more stems extending from a reaction center. The stems are formed by a nucleic acid duplex and the chemical compound has been formed in the reaction center as the reaction product of 3 or more chemical groups. The advantage of the composition is that a close proximity is provided between the chemical groups in the reaction center, thereby promoting a reaction. The invention also relates to a method for preparation of the composition. The advantage of the method is that it does not require the pre-synthesis of a large number of templates and that it is not dependent upon codon/anti-codon recognition for an encoded molecule to be formed.

Abstract: Disclosed herein are methods of predicting the risk of recurrence of cancer on the basis of the expression of microRNA of the miR-520 family.

Abstract: DNA methylations markers are associated with brain and behavioral mechanisms that underlie substance abuse disorders. These methylation markers present novel measures for predicting and/or identifying effective treatment options, risk of cancer development, risk of developing substance abuse disorders, and substance-abuse related behaviors such as binge drinking. These markers may further be useful in developing novel pharmaceuticals and treatment methodologies and provide mechanisms for following the course of an individual's treatment, risks, or behaviors over time.

Abstract: The invention provides methods to detect or quantify cells such as nucleated cells in a sample such as a physiological sample, which employ magnetic substrates and subjects the sample and the magnetic substrate to forms of energy so as to induce aggregate formation.

Abstract: Certain sequence variants have been found to be useful for correcting Prostate Specific Antigen levels in humans. The invention provides diagnostic applications based on such correction, including methods of diagnosis of prostate cancer.

Abstract: The present disclosure provides methods for determining phased nucleic acid sequence for a single chromosome of interest and/or a single chromosomal fragment of interest. The present disclosure also provides methods for determining phased nucleic acid sequence for a plurality of single chromosomes of interest and/or a plurality of single chromosomal fragments of interest. The plurality of single chromosomes of interest may be of one or more chromosome types. The present disclosure also provides a method for isolating a plurality of chromosomal fragments of a specified size range, where the chromosomal fragments are from one or more specified regions of the genome. The plurality of chromosomal fragments may be separated into single chromosomal fragments and sequenced to provide phased nucleic acid sequence for the single chromosomal fragments. Alternatively, the plurality of chromosomal fragments may be sequenced together to provide unphased nucleic acid sequence for the chromosomal fragments.

Abstract: The invention provides a method for making in vitro peptide expression libraries, and for the isolation of nucleotide sequences encoding peptides of interest, wherein the peptides or proteins are specifically associated with the DNA encoding them through non-covalent protein:DNA binding. The method describes ways of making the library itself, DNA molecules encoding the library and uses of the expression library.

Abstract: The invention relates to the treatment or prevention of an inflammatory skin disease, disorder or condition, by modulating a protein that is normally regulated by caspase-8 in the skin or by increasing caspase-8 activity or level in the skin. Another aspect of the invention relates to methods for diagnosing an inflammatory skin disease, disorder or condition or a predisposition to develop said disease disorder or condition in an individual. Further aspects of the invention relate to methods for identifying target proteins involved in the course or pathology of an inflammatory skin disease, disorder or condition and to methods of screening a candidate compound for treating said disease, disorder or condition. In particular, the invention relates to inflammatory skin diseases such as atopic dermatitis and psoriasis.

Abstract: Molecular signatures that function as very sensitive diagnostic biomarker for myocarditis, heart disease and disorders thereof, are identified.

Abstract: The present invention relates to methods to objectively assess treatment outcomes in Reward Deficiency Syndrome (RDS) behaviors by obtaining expression profiles (e.g., mRNA expression and/or protein expression profiles) for one or more genes at two or more different time points, for example, before and after treating a subject known to have or suspected of having an RDS affliction. Analysis, for example, of mRNA and/or protein expression levels and/or patterns can be conducted before admission to a treatment facility, followed by testing at one or more various designated times during and after a subject's treatment. Such methods may also be combined with other tests, and can be used in diagnosis and treatment of RDS and RDS behaviors, including drug and/or alcohol abuse and addiction, overeating, gambling, sexual addiction, etc.

Abstract: The invention provides methods and compositions for modulating the activity of XBP-I protein, or a protein in a signal transduction pathway involving XBP-I to modulate the TLR-mediated activation of cells of the innate immune system. Enhancing the TLR-mediated activation of cells of the innate immune system enhance inflammatory responses. The present invention also pertains to methods for identifying compounds that modulate Toll-like receptor-mediated signaling.

Abstract: The invention relates to a method for modifying one or more peptide ligands, comprising polypeptides covalently linked to a molecular scaffold at two or more amino acid residues, comprising the steps of providing one or more peptide ligands, wherein the polypeptide comprises two or more reactive groups which form a covalent linkage to the molecular scaffold, and at least one loop which comprises a sequence of two or more amino acids subtended between two of said reactive groups; exposing the peptide ligands to one or more proteases; and sorting the ligands according to the extent of proteolytic cleavage.

Abstract: Aspects of the subject invention are drawn to methods, compositions, systems and kits for the assessment of oxidative stress in an individual from a blood sample. In certain embodiments, the expression level of VNN1 in blood cells from a subject (or patient) is assessed and used to determine the subject's oxidative stress state, where an increased/high expression level of VNN1 indicates that the subject is in a state of oxidative stress. Expression of VNN1, and optionally other genes, may be done by assessing nucleic acid and/or protein levels in the blood cells obtained from the subject.

Abstract: Disclosed herein are methods of diagnosing and treating a malignant adrenocortical tumor, including adrenocortical carcinoma. In some examples, methods of diagnosing a malignant adrenocortical tumor include detecting expression of at least one microRNA (miR) gene product, such as miR-100, miR-125b, miR-195, miR-483-3p, miR-483-5p and IGF2 mRNA in a sample obtained from the subject with an adrenocortical tumor and comparing expression of at least one of these miR gene products and IGF2 mRNA in the sample obtained from the subject to a control. Altered expression of at least one of the miR gene products and IGF2 mRNA, such as a decrease in miR-100, miR-125b or miR-195 or an increase in miR-483-3p, miR-483-5p, and an increase in IGF2 mRNA, in the sample obtained from the subject compared to the control indicates a malignant adrenocortical tumor.

Abstract: Methods for the detection and screening of esophageal adenocarcinoma (EAC) patients and for the monitoring of EAC treatment using a panel or panels of small molecule metabolite biomarkers are disclosed. In other aspects, methods for detection and screening for the progression of high-risk conditions (BE and HOD) to EAC and to monitoring treatment using a panel or panels of small molecule metabolite biomarkers are disclosed. The biomarkers are sensitive and specific for the detection of EAC, and can also be used to classify Barrett's esophagus (BE) and high-grade dysplasia (HOD), which are widely regarded as precursors of EAC.

Abstract: A method and apparatus are provided for performing light-directed reactions in spatially addressable channels within a plurality of channels. One aspect of the invention employs photoactivatable reagents in solutions disposed into spatially addressable flow streams to control the parallel synthesis of molecules immobilized within the channels. The reagents may be photoactivated within a subset of channels at the site of immobilized substrate molecules or at a light-addressable site upstream from the substrate molecules. The method and apparatus of the invention find particularly utility in the synthesis of biopolymer arrays, e.g., oligonucleotides, peptides and carbohydrates, and in the combinatorial synthesis of small molecule arrays for drug discovery.

Abstract: The invention provides methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template.

Abstract: Methods and kits for selectively enriching non-random polynucleotide sequences are provided. Methods and kits for generating libraries of sequences are provided. Methods of using selectively enriched non-random polynucleotide sequences for detection of fetal aneuploidy are provided.