Abstract: The present invention features methods, devices, and kits for detecting a level of one or more biomarkers in a patient with cancer or determining the responsiveness of a patient with cancer to a treatment, such as treatment with an anthracycline. The invention further includes methods of treating a patient with cancer by administering, e.g., the anthracycline.

Abstract: The present invention relates to a method for treating ocular inflammatory diseases in a subject in need of such treatment, which comprises administering a pharmaceutical composition comprising a therapeutically effective amount of at least one agonist of Formyl peptide receptor 2.

Abstract: The present disclosure provides various linker units and molecular constructs, each of which has a targeting element and an effector element linked therewith. Methods for treating various diseases using such linker units and molecular constructs are also disclosed.

Abstract: We found mutations of the R132 residue of isocitrate dehydrogenase 1 (IDH1) in the majority of grade II and III astrocytomas and oligodendrogliomas as well as in glioblastomas that develop from these lower grade lesions. Those tumors without mutations in IDH1 often had mutations at the analogous R172 residue of the closely related IDH2 gene. These findings have important implications for the pathogenesis and diagnosis of malignant gliomas.

Abstract: Systems and methods are provided for correlating functional magnetic resonance imaging (fMRI) with gene expression. Brains of first and second sets of patients are imaged at first and second times to provide first and second sets of fMRI images. Blood is drawn from each of the first and second sets of patients at the first and second times to provide first and second sets of gene expression transcripts. A therapeutic is administered to the first set of patients between the first and second times. A change in the connectivity of the brain for each patient is determined from the first and second sets of fMRI images. A set of changes in the peripheral lymphocyte gene expression that are correlated with changes in the connectivity of the brain are determined from the change in the connectivity of the brain for each patient and the collected imaging and gene expression data.

Abstract: The present invention refers to a fluorescent fusion polypeptide capable of changing its localization within the cell from the cell cytoplasmic membrane to the retention vesicles, upon an increase in the concentration of second messengers within the cell cytoplasm, comprising a membrane localization peptide, a second messenger transduction protein binding peptide, a reticulum retention signal and a fluorescent peptide wherein: a. the membrane localization peptide is located at the N-terminus of the fluorescent fusion polypeptide and is physically bound, optionally through a linker, to the fluorescent peptide, which in turn is physically bound, optionally through a linker, to the second messenger transduction protein binding peptide; and b. the second messenger transduction protein binding peptide is physically bound, optionally through a linker, to the reticulum retention signal, which in turn is located at the C-terminus of the fluorescent fusion polypeptide.

Abstract: In order to interpret an arbitrary sequence region in many genes in many cells, it is necessary to degrade a nucleic acid into fragments and introduce a sequence that is different from one cell to another into each of the fragments. However, in the conventional configuration for analyzing many cells, there has been a problem that mixing of the degraded fragments among areas occurs before a tag sequence unique for each of the areas is introduced. The present invention provides a system for capturing a nucleic acid extracted from a cell in each of plural areas on a substrate and synthesizing a complementary DNA (cDNA) of the nucleic acid for each of the areas, wherein the system also includes a means for immediately introducing a tag sequence unique for each of the areas to the reaction product.

Abstract: The present invention refers to a fluorescent fusion polypeptide capable of changing its localization within the cell from the cell cytoplasmic membrane to the retention vesicles, upon an increase in the concentration of second messengers within the cell cytoplasm, comprising a membrane localization peptide, a second messenger transduction protein binding peptide, a reticulum retention signal and a fluorescent peptide wherein: a. the membrane localization peptide is located at the N-terminus of the fluorescent fusion polypeptide and is physically bound, optionally through a linker, to the fluorescent peptide, which in turn is physically bound, optionally through a linker, to the second messenger transduction protein binding peptide; and b. the second messenger transduction protein binding peptide is physically bound, optionally through a linker, to the reticulum retention signal, which in turn is located at the C-terminus of the fluorescent fusion polypeptide.

Abstract: The invention includes a mutant Taq polymerase, which can significantly extend and amplify a target sequence where the extension conditions are time limited to as little as one second. The mutant Taq polymerase, or a biologically active fragment thereof, has one or more substitutions differing from the wild type as shown in Table I.

Abstract: This invention discloses applications of desogestrel in the preparation of anti-colon cancer/breast cancer ER-negative Ah receptor-positive products. This invention provides applications for desogestrel in the preparation of products to treat colon cancer and/or breast cancer. From carrying out cancer drug repositioning for the FDA- and CFDA-approved drug desogestrel, experiments for this invention show, based on screening of non-anti-cancer drugs for various cancer cell lines (tissue types) and mutation sites, that desogestrel has a new use as an anti-colon cancer medication, thus achieving a new purpose for an old drug.

Abstract: The present invention is in the technical field of breast cancer management, and more particularly relates to the diagnosis and/or prognosing of triple-negative breast cancer (TNBC). The invention is more particularly based on the finding that specific biomarkers are abberantly expressed in patients suffering from a triple-negative breast cancer recurrence, and are highly related to the aggressiveness of this disease, and thus to survival of said patient.

Abstract: Disclosed is a method for calculating a Polymerase Preference Index (PPI) for potential primers for DNA sequencing and/or amplification, and thereby increasing the efficiency of DNA sequencing and/or amplification performed using primers selected according to their PPI number.

Abstract: Provided herein is technology relating to genetic determinants of disease and particularly, but not exclusively, to methods, compositions, and systems for identifying single nucleotide polymorphisms that are functionally associated with a disease.

Abstract: Sepsis remains a leading cause of morbidity and mortality in neonates worldwide. There is also clinically a low threshold for suspicion of infection in neonates, in particular as presentation varies greatly from very subtle to catastrophic collapse. The lack of reliably sensitive tests and the potential life-threatening consequences of delayed treatment of infection results in the widespread use of empirical antibiotics exposing many infants without infection to broad-spectrum antibiotics. The present invention provides a series of patient-invariant biomarkers for screening neonates and other subjects for infection that predicts bacterial infection with high accuracy; and is further shown to have predictive value in identifying infection in suspected cases with blood-culture negative tests.

Abstract: Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.

Abstract: Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.

Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the unique molecular index sequences include variable-length nonrandom sequences. In some implementations, the unique molecular index sequences are associated with the individual polynucleotide fragments based on alignment scores indicating similarity between the unique molecular index sequences and subsequences of sequence reads obtained from the individual polynucleotide fragments. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

Abstract: Improvements on the basic method used for BEAMing increase sensitivity and increase the signal-to-noise ratio. The improvements have permitted the determination of intrinsic error rates of various DNA polymerases and have permitted the detection of rare and subtle mutations in DNA isolated from plasma of cancer patients.

Abstract: In one aspect the present invention is directed to mutant NGAL proteins that have the ability to bind to siderophores, such as enterochelin, and to chelate and transport iron, and that are excreted in the urine. Such NGAL mutants, and complexes thereof with siderophores, can be used to clear excess iron from the body, for example in the treatment of iron overload. The NGAL mutants of the invention also have antibacterial activity and can be used in the treatment of bacterial infections, such as those of the urinary tract.

Abstract: The present invention relates to methods for monitoring, diagnosis, prognosis, and determination of treatment regimens in subjects suffering from or suspected of having a renal injury. In particular, the invention relates to using assays that detect one or more markers selected from the group consisting of Insulin-like growth factor-binding protein 7 and Metalloproteinase inhibitor 2 as diagnostic and prognostic biomarkers in renal injuries.

Abstract: Disclosed herein are methods for molecularly characterizing cervical cell samples as being negative for intraepithelial lesion or malignancy (NILM), low-grade squamous intraepithelial lesion (LSIL), or high-grade squamous intraepithelial lesion (HSIL).

Abstract: The present invention relates to a method for discrimination of p16.sup.INK4a overexpressing metaplasias from neoplastic or preneoplastic p16.sup.INK4a overexpressing lesions by determination of the level of high risk HPV encoded gene-products such as e.g. HPV E2 and/or HPV E7 molecules in biological samples in the course of cytological testing procedures. The method thus enables for reduction of false positive results in the p16.sup.INK4a based detection of anogenital lesions in cytological testing procedures.

Abstract: The invention relates to improved alkaline phosphatases, pharmaceutical compositions comprising improved alkaline phosphatases and the use of improved alkaline phosphatases for preventing, treating or curing diseases.

Abstract: The invention relates to a method of identifying stereodefined phosphorothioate oligonucleotide variants with reduced toxicity by creating and screening libraries of stereodefined chiral phosphorothioate variants for compounds with reduced toxicity, either in vitro or in vivo.

Abstract: This disclosure is in the field of molecular diagnostics and relates to a method for classifying samples obtained from patients diagnosed with multiple myeloma into three newly defined clusters. The disclosure also relates to a method for determining the prognosis of an individual diagnosed with multiple myeloma as well as a method for the prediction of the response to treatment of an individual diagnosed with multiple myeloma. More in particular, the disclosure provides a method for determining the disease outcome or the prognosis of a patient diagnosed with multiple myeloma by classifying said patient into a high risk or a low risk category, based on a 92-gene classifier.

Abstract: The present invention relates to compositions which may comprise a non-naturally occurring or engineered artificial transcription factor, wherein the transcription factor may comprise a sequence specific DNA binding domain, a sliding domain, and one or more linkers, wherein the DNA binding domain and the sliding domain are operably connected by the one or more linkers, and uses thereof. Methods involving the use of a non-naturally occurring or engineered artificial transcription factors and pharmaceutical compositions, methods for treating cancer, a degenerative disease, a genetic disease or an infectious disease as well as diagnostic methods are also contemplated by the present invention.

Abstract: The present disclosure provides systems and methods for sorting a cell. The system may comprise a flow channel configured to transport a cell through the channel. The system may comprise an imaging device configured to capture an image of the cell from a plurality of different angles as the cell is transported through the flow channel. The system may comprise a processor configured to analyze the image using a deep learning algorithm to enable sorting of the cell.

Abstract: The present invention relates to the field of cancer therapy. Specifically, provided are methods of treating cancer in a subject having clinical signs of bone marrow homing of myeloid cells, including neutropenia, isolated neutropenia, a low percentage of peripheral blood blasts with or without a high percentage of bone marrow blasts, and/or a low ratio of peripheral blood blasts to bone marrow blasts, with a farnesyltransferase inhibitor (FTI) that include determining whether the subject is likely to be responsive to the FTI treatment based on hematological characteristics indicating bone marrow homing of myeloid cells.

Abstract: The present invention provides methods for diagnosis and prognosis of lung cancer using expression analysis of one or more groups of genes, and a combination of expression analysis with bronchoscopy. The methods of the invention provide far superior detection accuracy for lung cancer when compared to any other currently available method for lung cancer diagnostic or prognosis. The invention also provides methods of diagnosis and prognosis of other lung diseases, particularly in individuals who are exposed to air pollutants, such as cigarette or cigar smoke, smog, asbestos and the like air contaminants or pollutants.

Abstract: The present invention pertains to the field of cancer prediction. Specifically, it relates to a method for predicting the risk of recurrence of bladder cancer in a subject after treatment of bladder cancer comprising the steps of determining the amount of at least one biomarker selected from the biomarkers shown in Table, and comparing the amount of said at least one biomarker with a reference amount for said at least one biomarker, whereby the risk of recurrence of bladder cancer is to be predicted. The present invention also contemplates a method for identifying a subject being in need of a further bladder cancer therapy. Encompassed are, furthermore, diagnostic devices and kits for carrying out said methods.

Abstract: The present invention relates to methods of determining a cancer treatment prognosis for a subject in need thereof by evaluating epigenetic and genetic changes within a tumor sample from the subject. The present invention further provides methods of treating cancer in a subject by evaluating epigenetic and genetic changes within a tumor sample from the subject. In addition, the present invention provides methods of screening test agents to identify agents that decrease tumor cell plasticity.

Abstract: Methods are provided for identifying biomarker proteins that exhibit differential expression in subjects with a first lung condition versus healthy subjects or subjects with a second lung condition. Also provided are compositions comprising these biomarker proteins and methods of using these biomarker proteins or panels thereof to diagnose, classify, and monitor various lung conditions. The methods and compositions provided herein may be used to diagnose or classify a subject as having lung cancer or a non-cancerous condition, and to distinguish between different types of cancer (e.g., malignant versus benign, SCLC versus NSCLC).

Abstract: Analysis of 13,023 genes in 11 breast and 11 colorectal cancers revealed that individual tumors accumulate an average of ˜90 mutant genes but that only a subset of these contribute to the neoplastic process. Using stringent criteria to delineate this subset, we identified 189 genes (average of 11 per tumor) that were mutated at significant frequency. The vast majority of these genes were not known to be genetically altered in tumors and are predicted to affect a wide range of cellular functions, including transcription, adhesion, and invasion. These data define the genetic landscape of two human cancer types, provide new targets for diagnostic and therapeutic intervention and monitoring.

Abstract: Observation of random, non-repetitive phenomena is of critical importance in astronomy, spectroscopy, biology and remote sensing. Heralded by weak signals, hidden in noise, they pose basic detection challenges. In contrast to repetitive waveforms, a single-instance signal cannot be separated from noise by averaging. The present invention demonstrates that a fast, randomly occurring event can be detected and extracted from a noisy background without conventional averaging. An isolated 80-ps pulse was received with confidence level exceeding 99%, even when accompanied by noise. The detector employed in the present invention relies on instantaneous spectral cloning and a single-step, coherent field processor. The ability to extract fast, sub-noise events is expected to increase detection sensitivity in multiple disciplines. Additionally, the new spectral-cloning receiver can potentially intercept communication signals that are presently considered secure.

Abstract: The present invention relates to a method for the treatment or prophylaxis of a PCV2 infection or for reduction of clinical symptoms caused by or associated with a PCV2 infection in animals a) having anti-PCV2 antibodies and/or b) being young piglets of 1 to 22 days of age, comprising the step of administering an effective amount of a PCV2 antigen to that animal in need of such treatment. Preferably, those animals are pigs or young piglets.

Abstract: An isolated oligonucleotide comprising ribonucleotides is disclosed. The oligonucleotide comprises a nucleic acid sequence which encodes at least one copy of a splicing-factor binding site. The oligonucleotide is no more than 150 bases and may be devoid of a sequence that allows hybridization thereof to cellular RNA under physiological conditions. The oligonucleotide inhibits overall cellular splicing activity of a specific splicing factor. Pharmaceutical compositions comprising the oligonucleotide and uses thereof are further disclosed.

Abstract: Embodiments predict biochemical recurrence (BCR) or metastasis by accessing a set of images of a region of tissue demonstrating cancerous pathology, including a tumor region and a tumor adjacent benign (TAB) region, the set of images including a first stain type image, and a second stain type image; segmenting cellular nuclei represented in the first and second image; generating a combined feature set by extracting at least one feature from each of a tumor region and TAB region represented in the first image, and a tumor region and TAB region represented in the second image, providing the combined feature set to a machine learning classifier; receiving, from the classifier, a probability that the region of tissue will experience BCR or metastasis; and generating a classification of the region of tissue as likely to experience BCR or metastasis, or unlikely to experience BCR or metastasis.

Abstract: The invention provides an assay useful in predicting risk of 5-fluorouracil (FU) toxicity in a subject. The subject may be screened for the presence of at least one TYMS polymorphism and/or at least one DPYD polymorphism. Suitable TYMS and DPYD polymorphisms are provided. The presence of one or more of the polymorphisms indicates an increased risk of developing FU toxicity; a negative result may indicate a decreased risk of developing FU toxicity.

Abstract: A method and apparatus for determining the progressive potential of a disease is disclosed. The forward to backward propagating second harmonic generation signal derived from a second harmonic generation instrument is used to assess the collagen microstructure of imaged body tissue by way of numerical values that are in turn used to determine the progressive or metastatic potential of the disease. The disease may, for example, be a cancer such as breast cancer, lung fibrosis, colorectal adenocarcinoma, or the like. The apparatus may include in vivo instruments or laboratory diagnostic instruments with methods disclosed herein.

Abstract: The disclosure concerns a method for cancer treatment by in vivo priming and activation of natural killer cells for achieving tumor cell lysis. The method includes introducing into a patient a priming tumor cell preparation (PTCP) derived from a first tumor cell line, which is irradiated to inactivate the first tumor cells or a membrane preparation thereof, the first tumor cells having known priming ligands on the membrane surface thereof. The patient's rest NK cells are contacted by the PTCP in vivo, resulting in primed NK cells, which are characterized by upregulation of CD69, shedding of CD16, or a combination of CD69+ and CD16?. These primed NK cells then contact second tumor cells, the cancer, and are configured to lyse and kill the second tumor cells.

Abstract: The invention provides cellular assays for detecting the activity of one or more kinase from multiple conditions simultaneously, by encoding biochemically identical substrates with isotope labels that enable them to be distinguished in pooled samples by mass spectrometry.

Abstract: The invention provides, inter alia, methods of prognosing a subject with, or suspected of having, multiple myeloma. In certain embodiments, the methods entail testing the gene expression levels of enolase 1 (ENO1), fatty acid binding protein 5 (FABP5), thyroid hormone receptor interactor 13 (TRIP13), transgelin 2 (TAGLN2), and replication factor C (activator 1) 4 (RFC4) in a biological sample isolated from the subject. The invention also provides methods of treatment for multiple myeloma, as well as kits, oligonucleotides, and systems for performing the methods provided by the invention.

Abstract: The present invention provides methods and kits for preparing a collection of degraded DNA fragments isolated from a biofluid sample of an individual. The prepared collection of nucleic acid sequences can be used in a diagnostic method such as for example detection and/or prognosis of cancer.

Abstract: The present invention is directed to methods of prognosing relapsed leukemia in a subject. These methods are based on the detection of one or more relapse-specific gene mutations in a patient sample. The present invention further relates to methods of preventing and treating relapse leukemia in a subject based on the determined prognosis of the subject.

Abstract: The invention provides, inter alia, methods for uniquely labeling populations of agents of interest using random combinations of oligonucleotides. The oligonucleotides may comprise a unique nucleotide sequence and/or one or more non-nucleic acid detectable moieties.

Abstract: The present invention, SMASH (Short Multiply Aggregated Sequence Homologies), is a technique designed to pack multiple independent mappings into every read. Specifically, the invention relates to a composition comprising a first mixture of different chimeric genomic nucleic acid fragments, wherein each different fragment in the mixture comprises randomly ligated DNA segments, wherein each DNA segment in the fragment is a nucleic acid molecule at least 27 base pairs in length resulting from random fragmentation of a single genome. The invention also relates to methods for generating said composition and use of said composition to obtain genomic information, for example, copy number variation.

Abstract: The present invention relates to the field of medicine and biology. It concerns a new test for screening and therapeutic follow-up in oncology. More particularly, it relates to diagnostic and/or therapeutic tests in oncology and on neurodegenerative diseases. Molecular targeting by peptide vectors and antibodies or by small interfering RNAs (siRNAs) opens a new concept of interdependence for diagnostic and therapeutic tools.

Abstract: In some aspects, the disclosure relates to the reactivation of inactive X chromosomes (Xi). In some embodiments, the disclosure provides compositions and methods for the reactivation of inactive X chromosomes. In some embodiments, the compositions and methods described by the disclosure may be useful for the treatment of dominant X-linked diseases.

Abstract: The invention relates to a method for the detection of oligonucleotides using anion exchange high performance liquid chromatography. Fluorescently labelled peptide nucleic acid oligomers, complementary to the oligonucleotide are hybridized to the oligonucleotides. Anion exchange high performance liquid chromatography is then performed and the hybridized moieties detected and quantitated. The invention also relates to a method for the simultaneous detection of both strands of an oligonucleotide in parallel from one sample, and a kit for use in qualitative and quantitative detection of one or two strands of an oligonucleotide.

Abstract: The present invention provides kits and primers for colony multiplex PCR for the detection of class A, B, C, and D ?-lactamase genes. The rapid detection of bla genes by using the kits and primers according to the present invention allows appropriate prescribing of antibiotics, which can reduce patient mortality and minimize antibiotic resistance. The present invention provides kits and primers for a rapid and accurate molecular method to overcome (a) to detect all clinically-important bla genes and (b) to explain phenotypic tests' results well by using 54 primer pairs, which are designed through novel and elaborate optimization processes. With perfect specificity and sensitivity in 172 control strains and 403 clinical strains, the present invention provides prompt and clinical application to the identification of all bla genes in bacterial pathogens.