Abstract: The present invention relates to agents and methods for screening, diagnosis and surveillance of cancer, in particular pancreatic cancer.

Abstract: The present disclosure provides compositions and methods for treating or reducing the risk of pancreatic cancer by administering compounds capable of inhibiting the expression or activity of RUNX3.

Abstract: A diagnostic method for predicting quantitatively whether a human tumor will be sensitive or resistant to treatment with an ERBB3 inhibitor, e.g, an anti-ERBB3 antibody, is disclosed. The method is based on measurement of NRG1 expression at the RNA level, or at the protein level, in a tissue sample from the tumor.

Abstract: Disclosed herein are diagnostic assays using surface enhanced Raman spectroscopy (SERS)-active particles, including liquid-based assays; magnetic capture assays; microparticle-nanoparticle satellite structures for signal amplification in an assay; composite SERS-active particles useful for enhanced detection of targets; and sample tubes and processes for using the same.

Abstract: Integrated circuit (100) comprising a semiconductor substrate (110); an insulating layer (120) over said substrate; an first transistor (140) on said insulating layer, said first transistor comprising an exposed channel region (146) in between a source region (142a, 142b) and a drain region (144); and a voltage waveform generator (150) conductively coupled to the semiconductor substrate for providing the first transistor with a bias voltage during a signal acquisition period, wherein the voltage waveform generator is arranged to generate an alternating bias voltage waveform (300) comprising a periodically increasing amplitude. A sensing apparatus including such an integrated circuit and a sensing method using such an integrated circuit are also disclosed.

Abstract: The present invention provides novel methods for diagnosing a state of health based on the determination of specific miRNAs that have altered expression levels in different conditions, e.g. disease states compared to healthy controls.

Abstract: Methods and systems are disclosed for extracting an image of a target fluorophore in a biological material, which involve inducing both autofluorescence of the biological material and fluorescence of the fluorophore, acquiring an image arising from both the autofluorescence of the biological material and the fluorophore, and an image arising only from the autofluorescence, subtracting the two images to produce an image representing only the fluorophore, wherein relative intensities of the excitation light used to induce the autofluorescence and the fluorescence are modulated prior to acquiring the images.

Abstract: Techniques and systems are disclosed for enabling a simulation environment for experimental design. The interactions of a configuration of molecules inside a biological structure or system, such as a cell (e.g., a neuron) or virtual test tube, are modeled using message-based techniques to communicate between molecules proximal to one another in a virtual 3-D geometric space. Some techniques and systems allow distributed processing of the individual molecular interactions across a plurality of work nodes. Some techniques and systems allow the storage of detailed information about the current state of the simulation of the biological model for each discrete time slice. This enables the ability for a 4-D playback/review of any particular spatial or temporal focus area of the simulation.

Abstract: The present disclosure provides methods that find use in determining a likelihood of adverse prostate cancer pathology in a subject. The methods generally involve detection of one or more diagnostic microRNAs (miRNAs), such as mir-19a, mir-19b, mir-519c-5p, and/or mir-345 in a biological sample from the subject, such as blood or blood product. The detection of one or more such diagnostic miRNAs can be used to determine a likelihood of adverse prostate cancer pathology in a subject. The methods of the present disclosure also find use in facilitating treatment decisions for a subject. Also provided are devices, systems, and kits that may be used in practicing methods of the present disclosure.

Abstract: The invention generally provides a sieve valve including: a substrate defining a channel; a flexible membrane adapted and configured for deployment at an intersection with the channel; and one or more protrusions extending into the channel from the substrate or the flexible membrane. The one or more protrusions define a plurality of recesses extending beyond the intersection between the channel and the flexible membrane; A microfluidic circuit including one or more sieve valves. In particular embodiments, the circuit comprises one or more input/output valves. The one or one or more input/output valves can include one or more input valves and one or more output valves. The microfluidic circuit can further include a mixing circuit. At least one of the sieve valves can be positioned between the one or more input/output valves and the mixing circuit. The invention further provides methods of using the device for the analysis of samples comprising cells.

Abstract: The application describes a method of screening for breast cancer by testing fro the amount of HAGE (Helicase antigen) in a sample of breast tissue. Methods of prognosis of samples of breast cancer tumours are also provided. HAGE+ ER? (estrogen receptor-) cancers are indicated as being amenable to chemotherapy. Methods of treating breast cancers with HAGE-specific CTA antigen or HAGE-specific antibodies are also provided.

Abstract: Identification of urokinase-type plasminogen, matrix metalloproteinase 9, and ?-2-microglobulin as novel biomarkers associated with liver fibrosis and uses thereof in diagnosing liver fibrosis.

Abstract: Compositions and methods for diagnosing an increased risk of NPSLE are provided.

Abstract: Methods and systems disclosed herein relate generally to processing data requests from external assessment systems. More specifically, an interface is availed to external assessment systems that accepts an identification of one or more genes. Upon receiving a request identifying one or more genes, a type of access authorized for the requesting external assessment system is assessed. When it is determined that the type of data access indicates that the external assessment system is authorized to access data for the one or more genes, a data repository is queried to identify client data that corresponds to the one or more genes and that indicates or can be used to detect a presence of client-associated variants. A response data set that includes at least some of the client data is transmitted to the external assessment system.

Abstract: The present methods are exemplified by a process in which maternal blood containing fetal DNA is diluted to a nominal value of approximately 0.5 genome equivalent of DNA per reaction sample. Digital PCR is then be used to detect aneuploidy, such as the trisomy that causes Down Syndrome. Since aneuploidies do not present a mutational change in sequence, and are merely a change in the number of chromosomes, it has not been possible to detect them in a fetus without resorting to invasive techniques such as amniocentesis or chorionic villi sampling. Digital amplification allows the detection of aneuploidy using massively parallel amplification and detection methods, examining, e.g., 10,000 genome equivalents.

Abstract: This invention provides methods for characterizing the amounts of nucleic acids, including plus/minus determinations, the use of different constructs, the use of a library and a reference library. Expression may also be compared in two or more samples using the methods of this invention. Also provided are heterophasic arrays comprising labeled positive copies of nucleic acids hybridized to the array and labeled negative copies of nucleic acids hybridized to the array, in which the labeled positive copies are separately quantifiable from the labeled negative copies.

Abstract: Compositions and methods for diagnosing an increased risk for the development of aggressive, invasive breast cancer are provided.

Abstract: The present disclosure describes environmentally responsive polypeptides capable of displaying stimuli-triggered conformational changes in a reversible or irreversible manner that may be accompanied by aggregation. Polypeptides include a number of repeated motifs and may be elastomeric or non-elastomeric. The polypeptides may be used to deliver therapeutics to a biological site and to develop bioactive polypeptides that are environmentally responsive.

Abstract: The present disclosure provides methods for detecting and identifying plant events that contain donor sequences inserted precisely into targeted genomic loci, and plants and plant cells comprising such targeted genomic loci. The method comprises the steps of amplifying a genomic DNA with a first round of PCR to produce a first amplicon from donor sequences inserted in the reverse orientation, amplifying the first amplicon with a second round of PCR and detecting the presence of the second amplicon, wherein the production of the first and second amplicon indicates the presence of the site specific integration event.

Abstract: The present invention relates to a novel method for detecting instantaneously a biomarker immobilized to a solid surface and related uses. The method comprises exposing the biomarker to a probe having a magnetic label in a solution; applying a magnetic field to the solution, whereby a complex of the biomarker and the probe is formed on the solid surface; withdrawing the magnetic field; removing the solution from the solid surface; and detecting the complex instantaneously, wherein the presence of the complex on the solid surface indicates the presence of the biomarker.

Abstract: An isolated plant-functional microRNA or an extract containing said plant-functional microRNA, a preparation method therefor, and an application thereof are provided. The plant-functional microRNA originates from the endogenous microRNA of a plant, is present in a water-soluble and/or fat-soluble extract of said plant, and is capable of regulating non-plant target-genes.

Abstract: Provided are compositions and methods of use thereof that modulate C/EBP homologous stress-related protein (Chop) activity in Myeloid-derived Suppressor Cells (MDSCs). Chop is a key point in the response of MDSCs to tumor-generated stress factors. In turn, the MDSCs release cytokines and other factors that function as immune suppressors, thereby allowing the tumors to thrive and expand. By inhibiting the level of Chop activity, the immunosuppressive function of MDSCs is disrupted. It has also been unexpectedly found that there is a concomitant increase in the ability of MDSCs to act as antigen-presenting and cytokine producing cells so as to act in increasing the efficacy of anti-tumor immune-based therapies.

Abstract: The present invention describes methods of treating cancer, cancer metastasis, and drug resistant cancers using miRNA inhibitors; for example, inhibitors of miR-409-5p, miR-409-3p, miR-154*. Also described are methods of using the miRNA as biomarkers; for example, to predict responsiveness to a cancer drug, to detect a disease state of cancer.

Abstract: MicroRNAs (miRNA) are a recently discovered class of small non-coding RNAs (17-14 nucleotides). Due to their function as regulators of gene expression they play a critical role both in physiological and in pathological processes, such as cancer. The present invention provides novel methods for diagnosing prostate cancer based on the determination of specific miRNAs that have altered expression levels in different conditions, e.g. disease states compared to healthy controls.

Abstract: Ordered (e.g., self-assembled) structures, arranged from peptide nucleic acids and/or analogs thereof, are disclosed. The peptide nucleic acids forming the ordered structures comprise from 1 to 10 PNA backbone units, at least one comprising a guanine nucleobase or an analog thereof. Processes of generating the ordered structures, uses thereof and articles-of manufacturing, devices and systems containing same are also disclosed.

Abstract: Methods for Identifying protein modulators of eukaryotic cells by expressing a combinatorial library of potential agonists inside a eukaryotic cell and then directly selecting for an agonist of a target molecule. Some methods involve co-culturing a cell expressing a combinatorial library of potential agonists and a second cell, and then selecting agents that modulate a phenotype of or a desired cellular response in the second cell. Preferably, the agonists are antibodies introduced into and expressed in the starting cells, such as agonist anti-EpoR, anti-TpoR, or G-CSFR antibodies. Also disclosed are methods for selecting from combinatorial antibody libraries bispecific antibodies that can regulate cell phenotypes.

Abstract: The present invention provides agents with tumor-inhibiting activity, and which are selective for cells expressing or abnormally expressing a tumor-associated antigen. Said tumor-associated antigen has a nucleotide sequence selected from the group consisting of: (a) a nucleotide sequence selected from the specific sequences set forth herein, or a 6-50 contiguous nucleotide residue portion thereof; (b) a nucleotide sequence of a nucleic acid which hybridizes with a nucleic acid having the nucleotide sequence of (a) under stringent conditions; (c) a nucleotide sequence which is degenerate with respect to the nucleotide sequence of (a) or (b); and (d) a nucleotide sequence which is complementary to the nucleotide sequence of (a), (b) or (c). Pharmaceutical compositions and kits comprising the agents are also provided, as well as methods treating, diagnosing or monitoring a disease characterized by expression or abnormal expression of the tumor-associated antigen.

Abstract: Provided herein are signal activatable molecular constructs for delivery of molecules and related components, compositions, methods, and systems, having a 17 to 30 bp targeting domain duplex RNA, at least one protection strand having a protection segment and linker segment and a sensor strand having a displacement segment and a toehold segment, in which in an inactive conformation the protection segment and the displacement segment form a sensor domain duplex polynucleotide covalently attached to the targeting domain and presenting the toehold segment for binding to a signal molecule. In an active conformation the sensor strand is bound to the signal molecule and is detached from the at least one protection strand and from the targeting domain; and the targeting domain attaches the at least one protection strand in a configuration allowing processing by Dicer and/or an Argonaute enzyme.

Abstract: An Accelerated Progression Relapse Test (APRT) and method is provided for use in the prognosis of a patient having an ER+ breast cancer. The APRT provides a determination of when a patient in a particular diseased state is likely to benefit from further disease treatment, or does not have a high probability of benefit with additional treatment. Four genetic probes are disclosed that target the MKI67, CDC6 and SPAG5 gene and gene products. The ER+ breast cancer patient population is stratified into two groups, with the low gene expression group identifying the patient/patient group that is less likely to benefit from additional treatment measures, and a high gene expression group identifying the patient group that is more likely to benefit from additional treatment measures.

Abstract: The invention pertains to a novel cell line, an HIV tat-rev dependent GFP-Gaussia luciferase Reporter cell line, known henceforth as the GGR cell line, that detects pseudotype and replication competent HIV (cloned or uncloned isolates, in cell media or human serum) rapidly and with high sensitivity. This GGR cell line provides an improved method of characterizing the entry phenotype of HIV envelope genes, and detecting and examining primary HIV samples in the context of laboratory research, clinical trial monitoring, and medical diagnostics. Examples include, but are not limited to, determining the functional HIV viral load, responsiveness to treatment, characterization of viral co-receptor usage (testing for viral co-receptor usage, i.e., CCR5 vs CXCR4, as required prior to prescribing FDA-approved CCR5 inhibitors), and characterization of other viral or drug resistance phenotypic properties to guide treatment.

Abstract: In order to address annotation bias in batch annotations, obtained via crowdsourcing, on a set of comments on user posts in a social network, a system determines an annotation probability distribution based on a factor-graph model of the batch annotations. In particular, during operation the system computes the factor-graph model that represents relationships between feature vectors that represent the comments and the annotations for the comments. Note that, for a given batch of k comments, the factor-graph model may include a statistically dependent combination of statistically independent models of the interrelationships between the feature vectors and the annotations for the k comments. Then, the system calculates the annotation probability distribution based on model parameters associated with the factor-graph model, a mapping function that maps from the feature vectors to the annotations, and an indicator function that represents the annotations for the comments in the batches.

Abstract: The present invention provides a method for classification of thyroid tumors through the analysis of the expression patterns of specific microRNAs in fine needle aspiration samples. Thyroid tumor classification according to a microRNA expression signature allows optimization of diagnosis and treatment, as well as determination of signature-specific therapy.

Abstract: Subject matter of the present invention is a method for predicting the risk of getting cancer in a female subject that does not suffer from cancer or alternatively diagnosing cancer in a female subject comprising: determining the level of Pro-Enkephalin or fragments thereof including Leu-Enkephalin and Met-Enkephalin of at least 5 amino acids in a bodily fluid obtained from said female subject; and correlating said level of Pro-Enkephalin or fragments thereof with a risk for getting cancer, wherein a reduced level is predictive for an enhanced risk of getting cancer or alternatively diagnosing cancer wherein an reduced level is correlated with the diagnosis of cancer.

Abstract: Disclosed are methods in which glucose metabolism is correlated to oncogenesis through certain specific pathways; inhibition of certain enzymes is shown to interfere with oncogenic signaling, and measurement of certain enzyme levels is correlated with patient survival. The present methods comprise measuring level of expression of at least one of the enzymes involved in glucose uptake or metabolism, wherein increased expression of the at least one of the enzymes relative to expression in a normal cell correlates with poor prognosis of disease in a patient. Preferably the genes whose expression level is measured include GLUT3, PFKP, GAPDH, ALDOC, LDHA and GFPT2. Also disclosed are embodiments directed towards downregulating the expression of some genes in glucose uptake and metabolism.

Abstract: The disclosure provides methods for the use of gene expression measurements to classify or identify among 54 cancer types in samples obtained from a subject in a clinical setting, such as in cases of formalin fixed, paraffin embedded (FFPE) samples.

Abstract: Compositions comprising SEQ ID NO: 1 and methods of treating a MUC16-expressing tumor cell are described.

Abstract: A method is provided for detecting one or more analytes in a sample. The method relies, in part, on the ability of functionalized particles added to the sample to partially or completely inhibit the transmission of electromagnetic radiation into and out of the sample through a detection surface in a reaction vessel containing the sample. In a microarray format, the invention can be used to screen millions, billions or more biological elements, such as an organism, cell, protein, nucleic acid, lipid, saccharide, metabolite, or small molecules. Methods, apparatuses and kits are described.

Abstract: The invention relates to therapeutic compounds which are inhibitors of serine proteases, to pharmaceutical compositions thereof and to their use in the treatment of the human or animal body. More specifically, the present invention relates to a method for the treatment of neutropenia comprising the administration to a subject in need thereof of a therapeutically effective amount of a serine protease inhibitor. The invention also comprises prevention of apoptosis of myeloid cells (1) during and after transfection of bone marrow cells performed for gene therapy, (2) during blood stem cell mobilization performed for reconstitution of hematopoiesis and (3) during infusion of cells of the myeloid lineage for reconstitution of hematopoiesis for gene therapy or for treatment of neutropenia by infusion of neutrophils.

Abstract: Thin parylene C membranes having smooth front sides and ultrathin regions (e.g., 0.01 ?m to 5 ?m thick) interspersed with thicker regions are disclosed. The back sides of the membranes can be rough compared with the smooth front sides. The membranes can be used in vitro to grow monolayers of cells in a laboratory or in vivo as surgically implantable growth layers, such as to replace the Bruch's membrane in the eye. The application further provides an implantable cage-like apparatus for culturing cells comprising the parylene membrane.

Abstract: Nucleic acids and proteins having a mutant C-RAF sequence, and methods of identifying patients having cancer who are likely to benefit from a combination therapy and methods of treatment are provided.

Abstract: Provided herein is technology relating to isolating nucleic acids. In particular, the technology relates to methods and kits for extracting nucleic acids from problematic samples such as stool.

Abstract: Described are bladder cancer specific biomarkers and lung cancer specific biomarkers comprising the nucleic acid sequence of the Engrailed-2 (EN2) gene or the amino acid sequence of the encoded EN2 protein. Also described are uses of the biomarkers in the treatment, diagnosis, monitoring and imaging of bladder cancer and lung cancer.

Abstract: The present invention provides a method for treating a human subject afflicted with multiple sclerosis or a single clinical attack consistent with multiple sclerosis with a pharmaceutical composition comprising glatiramer acetate and a pharmaceutically acceptable carrier, comprising the steps of: a) determining whether the human subject is a glatiramer acetate responder by evaluating expression of a biomarker selected from the group consisting of ERAP2, SIGLEC1, AAK1, KIAA1671, PLEKHA2, LOC730974, IFIT3, RWDD3, MYO6 SCARA3 and IFI44L, or a combination thereof, in human subject; and b) administering the pharmaceutical composition comprising glatiramer acetate and a pharmaceutically acceptable carrier to the human subject only if the human subject is identified as a glatiramer acetate responder.

Abstract: The present invention includes a method and system for enhancing the signal-to-noise ratio in emission detection comprising: selecting a probe capable of at least one of fluorescence, phosphorescence, or delayed fluorescence in or about a sample that comprises interfering background signal; and exposing the probe to one or more controllable bursts, each burst comprising two or more pulses, wherein the one or more controllable bursts of high repetition energy pulses enhance the signal from the probe above that of the background signal.

Abstract: The present invention provides sets of genes the expression of which is important in the prognosis of cancer. In particular, the invention provides gene expression information useful for predicting whether cancer patients are likely to have a beneficial treatment response to chemotherapy FHIT; MTA1; ErbB4; FUS; BBC3; IGF1R; CD9; TP53BP1; MUC1; IGFBP5; rhoC; RALBP1; STAT3; ERK1; SGCB; DHPS; MGMT; CRIP2; ErbB3; RAP1GDS1; CCND1; PRKCD; Hepsin; AK055699; ZNF38; SEMA3F; COL1A1; BAG1; AKT1; COL1A2; Wnt.5a; PTPD1; RAB6C; GSTM1, BCL2, ESR1; or the corresponding expression product, is determined, said report includes a prediction that said subject has a decreased likelihood of response to chemotherapy.

Abstract: The present invention provides nanoparticles and compositions comprising such nanoparticles, as well as methods for intracellular delivery of peptides, and methods of producing nanoparticles and related products. The nanoparticles comprise a core comprising a metal and/or a semiconductor atom; and a corona comprising a plurality of ligands covalently linked to the core, wherein at least a first ligand of said plurality comprises a carbohydrate moiety that is covalently linked to the core via a first linker, and wherein at least a second ligand of said plurality comprises a peptide of choice that is covalently linked to the core via a second linker. The second linker comprises a peptide portion and a non-peptide portion, wherein said peptide portion of said second linker comprises the sequence X1X2Z1, wherein: X1 is an amino acid selected from A and G; X2 is an amino acid selected from A and G; and Z1 is an amino acid selected from Y and F.

Abstract: The disclosure provides for methods, compositions, and kits for multiplex nucleic acid analysis of single cells. The methods, compositions and systems may be used for massively parallel single cell sequencing. The methods, compositions and systems may be used to analyze thousands of cells concurrently. The thousands of cells may comprise a mixed population of cells (e.g., cells of different types or subtypes, different sizes).

Abstract: The present invention provides methods of detecting cancer using biomarkers.

Abstract: Described herein are methods of triplex-induced apoptosis, in which multiple triplexes are formed in cells in which gene amplification has occurred (cells comprising/characterized by at least one amplified gene), referred to as target cells, and apoptosis is induced in the target cells.

Abstract: A method comprising: synthesizing a set of overlapping oligonucleotides that comprises probe sequences that hybridize to unique sequences in a chromosome, assembling the overlapping oligonucleotides in a way that produces one or more double stranded polynucleotides that each comprises multiple probe sequences, labeling the one or more double stranded polynucleotides to produce one or more labeled probes, and hybridizing the labeled probes to an intact chromosome, in situ, is provided.