Abstract: There is provided a method of identifying risk of cancer in a human subject, the method comprising: determining in a biological sample of the subject, whether a copy number amplification of at least one continuous genomic region specific to human chromosome 1q21 is present, wherein the presence of a copy number amplification of the region specific to human chromosome 1q21 represents an elevated risk of cancer in the subject and the at least one continuous genomic region is selected from the group consisting of: a human TUFT 1 gene or a gene from the human S100 family. It is also provided a method of treating cancer in a subject determined to have a copy number amplification of a region specific to human chromosome 1q21, the method comprising administering a therapeutic agent capable of suppressing IRAK1, IRAK4 or a S100 family member, such as Pacritinib. There are also provided a method of treating cancer, related polynucleotides, kits, therapeutic agents and use of the therapeutic agents.

Abstract: The invention provides compositions and methods related to selective inhibition of PPO11 and use for improving shelf life of a plant or parts thereof. In accordance with the invention, for example, compositions for topical application to a plant or part thereof, are provided that can reduce browning of the plant or part thereof to extend shelf life.

Abstract: The present disclosure provides resonator networks adapted to a variety of applications. The networks include fluorophores, quantum dots, dyes, plasmonic nanorods, or other optical resonators maintained in position relative to each other by a backbone (e.g., a backbone composed of DNA). The networks may exhibit optical absorption and re-emission according to specified temporal decay profiles, e.g., to provide temporally-multiplexed labels for imaging or flow cytometry. The networks can include resonators that exhibit a dark state, such that the behavior of the network can be modified by inducing the dark state in one or more resonators. Such networks could be configured as logic gates or other logical elements, e.g., to provide multiplexed detection of analytes by a single network, to permit the temporal decay profile of the network to be adjusted (e.g., to use the networks as a controllable random number generator), or to provide other benefits.

Abstract: An example system includes a primary channel having a first end and a second end, at least two reagent reservoirs coupled to the first end, and a controller. Each reservoir contains a reagent in a fluid solution and is associated with an integrated pump to drive a reagent droplet from the corresponding reagent reservoir into the primary channel towards the second end. The controller is coupled to the integrated pumps and operates according to a sequence to actuate the integrated pumps, the sequence being indicative of reagents in the reagent reservoirs. The actuation of the pumps is to drive the reagent droplets from the reagent reservoirs into the primary channel in accordance with the sequence. The example system also includes a shell material reservoir with a shell material and an associated shell material pump to drive the shell material into the primary channel to encapsulate the reagent droplets.

Abstract: The present invention relates to complexes of oligonucleotide-encoded libraries and methods of tagging and using such libraries. In particular, the oligonucleotides and methods can include complexes having at least one linkage for which a polymerase has reduced ability to read or translocate through.

Abstract: A wavelength converter material and a method of A method of preparing a wavelength converter material may include providing an optionally oxide coated phosphor material, mixing the optionally oxide coated phosphor material with an optionally oxide coated paramagnetic nanoparticle, coating the optionally oxide coated phosphor material and the optionally oxide coated paramagnetic nanoparticle with an oxide coating, thereby preparing a coated phosphor-nanoparticle particle, and separating the coated phosphor-nanoparticle particle, thereby preparing a wavelength converter material. The separating of the coated phosphor-nanoparticle particle may be manipulated by applying a magnetic field. Furthermore, a wavelength converter material, as well as a light emitting diode are described herein.

Abstract: An example method includes identifying training data indicating features of a sample population and clinical outcomes of the sample population. The clinical outcomes are associated with a heterogeneous condition. The method further includes generating decision trees in a Random Forest (RF) based on the training data, each one of the decision trees being configured to divide the sample population into multiple categories based on the features of the sample population. In response to generating the decision trees, a proximity matrix comprising multiple entries is generated using the RF. One of the entries indicates a proportion of the decision trees that categorize a first individual among the sample population and a second individual among the sample population into the same categories among the multiple categories. The method further includes identifying subgroups of the heterogeneous condition by detecting communities of the proximity matrix.

Abstract: Disclosed is an adaptor for sequencing DNAs at ultratrace levels and its uses. The adaptor contains, from 5?terminus to 3?terminus, a Tag sequence, PolyNs, a first stem sequencing, a first loop sequence, dUTP(s), a second loop sequence, and a second stem sequence, wherein the second stem sequence is complementary to the first stem sequence when read in opposite directions, and the 5?terminus of the adaptor is phosphorylated. The adaptor is designed to form a hairpin structure itself in use and then ligated to a DNA molecule of interest, so that adaptor-adaptor ligation can be effectively avoided, eliminating the inefficient adaptor-DNA ligation problem. Such an adaptor is especially suitable for library construction and sequencing of DNAs at ultratrace levels, laying a good basis for accurate sequencing of ctDNAs.

Abstract: Methods and biomarker panels for detecting and treating pancreatic disease, including pancreatic cancer, are provided in association with determining and inhibiting expression levels of certain GPCRs, including GPR68, in particular in pancreatic cancer associated fibroblasts.

Abstract: An object of the present invention is to provide a kit and a method which are capable of measuring a measurement target substance in a biological sample with high precision in a measurement range from a low concentration range to a high concentration range. According to the present invention, there is provided a kit for measuring a measurement target substance in a biological sample, including a labeled particle having a first binding substance capable of binding to a measurement target substance in a biological sample, and a substrate having a second binding substance capable of binding to any one of the measurement target substance or the first binding substance, in which the labeled particle is a luminescent labeled particle containing at least one kind of compound represented by Formula (1) and a particle. Each symbol in Formula (1) has the meaning described in the present specification.

Abstract: The present invention provides synthetic DNA strands that find use as controls or in nucleic acid testing methods. In particular, provided herein are synthetic DNA strands of known composition for use as control molecules in stool DNA testing, e.g., of mutations and/or methylation of DNA isolated from stool samples.

Abstract: Provided herein are compositions and methods for isolating cell-free nucleic acid, e.g., cell-free DNA, from a sample. In particular embodiments, provided herein are compositions and methods using anti-dsDNA antibodies for isolating cell-free DNA from a sample, and for providing a sample of isolated cell-free DNA, e.g., for a nucleic acid assay. In particular embodiments, the technology relates to providing cell-free DNA from a maternal sample that is enriched for fetal cell-free fetal DNA.

Abstract: Disclosed are compositions and methods for template-free nucleic acid synthesis.

Abstract: Provided herein are products and processes for detecting the presence or absence of multiple target nucleic acids. Certain methods include amplifying the target nucleic acids, or portion thereof; extending oligonucleotides that specifically hybridize to the amplicons, where the extended oligonucleotides include a capture agent; capturing the extended oligonucleotides to a solid phase via the capture agent; releasing the extended oligonucleotide by competition with a competitor; detecting the extended oligonucleotide, and thereby determining the presence or absence of each target nucleic acid by the presence or absence of the extended oligonucleotide.

Abstract: Methods, assays, compositions and kits for the ligation of short polynucleotides are presented herein. The short polynucleotides are optionally no more than 7 nucleotides in length, and can be as short as 3 or 4 nucleotides in length. The ligation is optionally performed by CV ligase.

Abstract: Compositions and methods for generating maize plants that exhibit resistance to northern leaf blight are provided herein. Isolated polynucleotides encoding a polypeptide that confers resistance to northern leaf blight, polynucleotide constructs comprising such, and maize plants comprising the polynucleotide constructs are provided. The methods include expressing an isolated polynucleotide in a maize cell via standard transformation methods and obtaining a maize plant from said maize cell.

Abstract: The disclosure provides various systems and methods for identifying individuals from one or more samples. In particular, improved systems and methods of analysis are provided for handling multiple contributors, as well as systems and methods that model not only individual error rates per locus but factor in amplification of errors induced through PCR cycles. In some embodiments, modeling of error rates can be applied in multi-contributor settings to more accurately establish real alleles from artifacts. Other aspects involve application of sequencing in error modeling. Further, methods are provided for determining the presence of common individual DNA profiles in one or more complex DNA mixtures and for deconvolution of multiple complex DNA mixtures into shared individual components.

Abstract: The present invention relates to methods of detecting novel mutations in a PKD1 and/or PKD2 gene that have been determined to be associated with autosomal dominant polycystic kidney disease (ADPKD) in order to detect or predict the occurrence of ADPKD in an individual.

Abstract: A method of performing a non-isothermal nucleic acid amplification reaction, the method comprising the steps of: (a) mixing a target sequence with one or more complementary single stranded primers in conditions which permit a hybridization event in which the primers hybridize to the target, which hybridization event, directly or indirectly, leads to the formation of a duplex structure comprising two nicking sites disposed at or near opposite ends of the duplex; and performing an amplification process by; (b) using a nicking enzyme to cause a nick at each of said nicking sites in the strands of the duplex; (c) using a polymerase to extend the nicked strands so as to form newly synthesized nucleic acid, which extension with the polymerase recreates nicking sites; (d) repeating steps (b) and (c) as desired so as to cause the production of multiple copies of the newly synthesized nucleic acid.

Abstract: Disclosed are compositions and methods for increasing virus production. In particular, disclosed herein are cell or cell line comprises reduced expression of one or more cellular genes selected from the group comprising COQ9, FGF2, NAT9, NDUFA9, NEU2, PLA2G1B, PYCR1, RAD51AP1, STRADA, SVOPL, and/or ZFYVE9 for use in increasing viral production.

Abstract: Sets of experimentally validated gene specific primer pairs are provided. Embodiments of the sets include 10 or more gene specific primer pairs of forward and reverse primers. The forward and reverse primers of each primer pair include gene specific primers that are experimentally validated as suitable for use in a multiplex amplification assay. In some instances, each of the forward and reverse primers includes an anchor domain that includes a universal primer binding site. The sets find use in a variety of different applications, including high-throughput sequencing applications.

Abstract: Determining relative relationships of people who share a common ancestor within at least a threshold number of generations includes: receiving recombinable deoxyribonucleic acid (DNA) sequence information of a first user and recombinable DNA sequence information of a plurality of users; processing, using one or more computer processors, the recombinable DNA sequence information of the plurality of users in parallel; determining, based at least in part on a result of processing the recombinable DNA information of the plurality of users in parallel, a predicted degree of relationship between the first user and a user among the plurality of users, the predicted degree of relative relationship corresponding to a number of generations within which the first user and the second user share a common ancestor.

Abstract: This disclosure provides improved cell lines for manufacture of protein-based pharmaceutical agents, considerably reducing the cost of commercial production. The cell lines are obtained by selecting cells from a mixed population for one or more characteristics that support protein production on a non-specific basis, such as the level of endoplasmic reticulum, Golgi apparatus, and/or other desired phenotypic features, compared with other cells in the starting mixture. Particularly effective producer cell lines can be obtained by preparing the cells for functional selection by making cell hybrids. A gene encoding a therapeutic protein of interest may be transfected into the cells before or after one or more cycles of fusion and selection. Depending on the protein product being expressed, cell lines may be obtained that produce eight grams or more of protein per liter of culture fluid.

Abstract: Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.

Abstract: Provided are a nucleic acid sequencing method and a nucleic acid sequencing kit. The kit comprises a nucleic acid probe, a ligase, dNTP having a blocking group attached to a 3? end, a polymerase, a reagent 1 for excising the blocking group attached to the 3? end of the dNTP, and a reagent 2 for excising the remaining nucleotides on the nucleic acid probe that are not bound to a to-be-tested base group.

Abstract: The invention provides methods of analyzing an individual's mtDNA by transforming available reference sequences into a directed graph that compactly represents all the information without duplication and comparing sequence reads from the mtDNA to the graph to identify the individual or describe their mtDNA. A directed graph can represent all of the genetic variation found among the mitochondrial genomes across all of a number of reference organisms while providing a single article to which sequence reads can be aligned or compared. Thus any sequence read or other sequence fragment can be compared, in a single operation, to the article that represents all of the reference mitochondrial sequences.

Abstract: The present invention relates to substituted benzene compounds. The present invention also relates to pharmaceutical compositions containing these compounds and methods of treating cancer by administering these compounds and pharmaceutical compositions to subjects in need thereof. The present invention also relates to the use of such compounds for research or other non-therapeutic purposes.

Abstract: The present invention relates to a method for detecting C. perfringens induced diseases in animals, the method comprising: a) collecting sample material of a specific animal or of a specific group of animals at consecutive points in time; b) determining the amount of a first marker and a second marker contained in the sample material; and c) determining the ratio of the first marker to the second marker contained in the sample material; wherein the first marker comprises a polynucleotide sequence being specific for the C. perfringens sub-species inducing the targeted disease; and the second marker comprises a polynucleotide being specific for the species C. perfringens; and wherein an increase in the ratio of the first marker to the second marker in the analyzed sample material over time is an indication of the targeted disease.

Abstract: Disclosed herein are methods for use in detection of single nucleotide variants (SNVs) or indels. The methods may comprise enriching cell-free DNA molecules for a panel of genomic regions and deep sequencing the enriched cfDNA to detect the SNVs or indels.

Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.

Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

Abstract: Methods, kits and systems are disclosed for analyzing one or more molecules in a sample. Analyzing the one or more molecules may comprise quantitation of the one or more molecules. Individual molecules may quantitated by PCR, arrays, beads, emulsions, droplets, or sequencing. Quantitation of individual molecules may further comprise stochastic labeling of the one or more molecules with a plurality of oligonucleotide tags to produce one or more stochastically labeled molecules. The methods may further comprise amplifying, sequencing, detecting, and/or quantifying the stochastically labeled molecules. The molecules may be DNA, RNA and/or proteins.

Abstract: The present disclosure provides a method for the treatment of a neuropathic pain including a central neuropathic pain or a peripheral neuropathic pain in a subject comprising the administration of antibodies that specifically bind to human FAM19A5 and compositions comprising such antibodies. The present disclosure also provides methods for treating a neuropathic pain including a symptom of neuropathic pain, and/or an underlining cause of a neuropathic pain, by administering an antibody that specifically binds to human FAM19A5. In a specific aspect, the method comprises administering antibodies specifically bind to human FAM19A5, e.g., binds to soluble human FAM19A5 with a KD of 10 nM or less, or binds to membrane bound human FAM19A5 with a KD of 10 nM or less, or both, as measured by a method known in the art, e.g., ELISA.

Abstract: Provided herein are methods for preparing and treating an analyte (e.g., a macromolecule or a plurality of macromolecules, peptides, polypeptides, and proteins) for analysis. In some embodiments, the analyte is prepared and treated in a method that includes the use of bait and capture nucleic acids, solid supports, and reaction mixtures including the bait and capture nucleic acids. In some embodiments, the analyte is coupled to a solid support. Also provided are kits containing components for performing the provided methods for preparing the analytes. In some embodiments, the methods are for preparing an analyte for sequencing. Provided herein are methods for preparing and treating an analyte (e.g., a macromolecule or a plurality of macromolecules, peptides, polypeptides, and proteins) for analysis. In some embodiments, the analyte is prepared and treated in a method that includes the use of bait and capture nucleic acids, solid supports, and reaction mixtures including the bait and capture nucleic acids.

Abstract: Devices and methods for measuring the quantity of multiple analytes in a sample can include a device designed such that each of the analyte sensing elements is configured to measure the quantity of a predetermined analyte and machine executable instructions configured to select the proper analyte sensing element corresponding to the analyte to be measured.

Abstract: This invention relates to methods and compositions for detecting the presence or absence of a Respiratory Syncytial Virus target nucleic acid in a biological sample using isothermal nucleic acid amplification.

Abstract: Methods and kits for diagnosing and/or treating a lower respiratory infection in a subject include obtaining a biological sample from the subject; detecting RNA expression levels of one or more biomarkers in the biological sample and comparing the expression levels of the one or more three biomarkers to at least one invariant control marker wherein an increase or decrease in the level of expression of the one or more biomarkers as compared to the at least one invariant control marker is indicative of a lower respiratory infection.

Abstract: Methods and kits for determining the efficiency of plasma separation from whole blood are provided, using real-time PCR amplification of two amplicons, namely, a short amplicon of e.g. 70-150 bps and a long amplicon of e.g. 350-600 bps. The separation efficiency is determined based on the difference in amplification patterns of the two amplicons.

Abstract: The present invention is directed to methods, compositions and systems for analyzing sequence information while retaining structural and molecular context of that sequence information.

Abstract: Dysregulated expression of microRNAs (miRNAs) has emerged as a hallmark feature in human cancers. Aspects of the disclosure relate to methods for selecting optimal therapy for a patient from several alternative treatment options. A major clinical challenge in cancer treatment is to identify the subset of patients who will benefit from a therapeutic regimen, both in metastatic and adjuvant settings. The number of anti-cancer drugs and multi-drug combinations has increased substantially in the past decade, however, treatments continue to be applied empirically using a trial-and-error approach. Here methods and compositions are provided to determine the optimal treatment option for cancer patients.

Abstract: A method for quenching a polymerisation process is described. The reaction of carbon dioxide with an epoxide in the presence of a bimetallic metal complex catalyst to produce a polymer comprises the quenching step of deactivation of the catalyst by contacting the catalyst with an acid effective to deactivate the catalyst. The deactivated catalyst may be removed from the polymer product by contacting the catalyst and polymer product with a solid phase and/or by precipitation; and the catalyst may also be optionally reactivated by contacting the deactivated catalyst with an anion. The acid may contain an anion effective to initiate the polymerisation process and effective to deactivate the catalyst and the molar ratio of acid to catalyst in the deactivation step may be less than or equal to 20:1 of the acid to catalyst mole ratio for the reaction.

Abstract: A farming machine is configured to identify and treat plants in a field. The farming machine includes one or more light sensors for measuring a characteristic of light. The one or more light sensors are coupled to the farming machine and are directed a substantially upwards orientation away from the plants. A control system adjusts settings of an image acquisition system based on a characteristic of light measured by the one or more light sensors. The image acquisition system captures an image of a plant using one or more image sensors coupled to the farming machine, the one or more image sensors directed in a substantially downwards orientation towards the plants. The control system identifies a plant in the image and actuates a treatment mechanism to treat the identified plant.

Abstract: The invention describes the method allowing for efficient predictive ranking of clinical efficiencies of the existing targeted medicinal products for individual patient with proliferative or oncology disease. The method makes it possible to use a wide range of experimental data received from the patients' pathological tissue samples and relevant control samples: information on gene mutations, transcription factor binding profile, protein (considering harmonization), mRNA (considering harmonization) and microRNA expression strength. The method also uses information on molecular targets of the medicinal products. This method can be automated to prevent potential errors associated with manual calculation and makes it possible to consider patient-specific changes in hundreds and thousands molecular pathways which include tens and hundreds of gene products. This method also considers the features and mode of action of various classes of target drugs.

Abstract: Provided herein are methods for the prevention and treatment of cardiovascular diseases and disorders in a subject diagnosed as having suffered a cerebrovascular injury by administering agents that contain or induce the expression of microRNA-126.

Abstract: NAzyme activity surface plasmon resonance sensors include a first DNA probe that is covalently connected to a sensing surface, and a second DNA probe that is covalently connected to a nanoparticle or a nanoparticle cluster. The first DNA probe and the second DNA probe are ligated together to provide a selected single strand DNA probe connected to the sensing surface and the nanoparticle. The single strand DNA probe includes a ligation zone within a selected NAzyme substrate. The sensor measures DNAzyme activity by NAzyme binding at the NAzyme substrate and cleavage at the ligation zone. Fiber optic surface plasmon resonance sensor tips are adapted to measure activity of a NAzyme when the NAzyme substrate is recognized by the selected NAzyme through hybridization and the metallic nanoparticle is released from the sensor by cleavage of the single strand DNA at the ligation zone by the selected NAzyme.

Abstract: Provided herein are methods, systems, and compositions for determining a base in a polynucleotide. In various aspects, the methods, systems, and compositions presented herein are useful for performing 4-base, 5-base, or 6-base sequencing of polynucleotide molecules, for example, from liquid biopsy samples or wherein the base is a low frequency mutation.

Abstract: Embodiments discussed herein facilitate building and/or employing a clinical-radiomics score for determining tumor prognoses based on a combination of a radiomics risk score generated by a machine learning model and clinico-pathological factors. One example embodiment can perform actions comprising: accessing a medical imaging scan of a tumor; segmenting a peri-tumoral region around the tumor; extracting one or more intra-tumoral radiomic features from the tumor and one or more peri-tumoral radiomic features from the peri-tumoral region; providing the one or more intra-tumoral radiomic features and the one or more peri-tumoral radiomic features to a trained machine learning model; receiving a radiomic risk score (RRS) associated with the tumor from the machine learning model; determining a clinical-radiomics score based on the RRS and one or more clinico-pathological factors; and generating a prognosis for the tumor based on the clinical-radiomics score.

Abstract: The present disclosure is directed to conjugates of a specific binding entity and an oligomer, i.e. [Specific Binding Entity]-[Oligomer]n, wherein n is an integer ranging from 1 to 12, and where the Oligomer includes, in some embodiments, a PNA sequence having at least one substituent at a gamma carbon position. In some embodiments, the substituent at the gamma carbon position, e.g. an amino acid, a peptide, a miniPEG, or a polymer, includes at least one reporter moiety.

Abstract: The present invention generally relates to a combination of molecular barcoding and emulsion-based microfluidics to isolate, lyse, barcode, and prepare nucleic acids from individual cells in a high-throughput manner.

Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described methods.