Abstract: Example embodiments relate to identity-by-descent (IBD) relatedness based on focal and reference segments. An example method includes determining, by a services platform based on personal information of a focal individual, a focal string. The method also includes retrieving, by the services platform from a reference database, a reference string of a reference individual. Additionally, the method includes computationally identifying, by the services platform, IBD segments between the focal string and the reference string. Further, the method includes determining, by the services platform and based on the merged set of IBD segments, a degree of relatedness between the focal individual and the reference individual. In addition, the method includes providing, by the services platform, access to the degree of relatedness via a user interface.

Abstract: The present invention discloses a set of novel epigenetic biomarkers for early prediction, treatment response, recurrence and prognosis monitoring of pancreatic cancer. Aberrant methylation of genes can be detected in tumor tissues and plasma samples from pancreatic cancer patients but not in normal healthy individual. The present disclosure also discloses primers and probes used herein.

Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.

Abstract: Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.

Abstract: The present invention features compositions and methods for amplifying a target oligonucleotide in a sample, including detection of the target oligonucleotide in real time.

Abstract: The present invention concerns therapeutics for autoimmune diseases and provides removal of inflammation-causing autoantibodies. In order to target the disease in the most efficient manner, a nanoconjugate complex is provided, comprising at least one specific antigen component recognized by autoantibodies related to the autoimmune disease, at least one helper moiety, and a nanoparticle carrier connecting the components. Each component of the therapeutic nanoconjugate complex has a specific function, yielding a nanoconjugate complex which facilitates specific binding, forming a stable antibody-therapeutic complex in the blood stream and rapid clearance of this complex to the liver.

Abstract: An automated nucleic acid extraction device includes a base body, a cassette, a driving unit, a moving frame and a syringe. The base body includes a sample accommodating area, a column accommodating area, a cassette accommodating area and a collection tube being arranged in a linear direction. The cassette is arranged in the cassette accommodating area and includes two parallel walls and at least four vertical walls. The parallel walls and the vertical walls jointly form a lysis buffer well, at least one wash buffer well and an elution buffer well. Each vertical wall includes a load-bearing abutment. The driving unit and the moving frame are arranged on the base body. The syringe is arranged on the moving frame and is driven by the driving unit to reciprocate along with the moving frame in the linear direction.

Abstract: A method of detecting the presence of a prostate cancer field defect in a human subject comprising the step of (a) obtaining genomic DNA from the human subject and (b) quantitating methylation in at least one target region selected from the group consisting of CAV1, EVX1, MCF2L, FGF1, NCR2 and WNT2 and EXT1 and SPAG4 target, wherein significant methylation changes indicate the presence of prostate cancer or a prostate cancer field defect, wherein the change is relative to tissue from a second human subject who does not have prostate cancer.

Abstract: Disclosed herein, inter alia, are methods and systems of image analysis useful for rapidly identifying and/or quantifying features.

Abstract: The present invention relates to methods of enriching target single-stranded nucleic acids in a mixed population of single-stranded nucleic acids. The method involves protecting the target single-stranded nucleic acids and using a 5? exonuclease to digest the non-target single-stranded nucleic acids. The invention also relates to methods of cloning target single-stranded nucleic acids into vectors, and to associated compositions and kits.

Abstract: The disclosed methods for preparing cytological samples may include placing a cytological sample in a concave filter in a filtration system, applying a negative pressure to an outer side of the concave filter with a vacuum device to withdraw a liquid from the cytological sample, applying a sectionable matrix material over the filtered cellular material within the concave filter, and removing an assembly including the filtered cellular material and the sectionable matrix material from the filtration system. Various other related methods, systems, and materials are also disclosed.

Abstract: Bacterial species and the associated microbiome persist in tumors and metastases. Antibiotic treatment selectively reduces microbiome-induced tumor growth and can advantageously be included in treatment regimens. Accordingly, the present disclosure relates to, for example, the diagnosing cancer in a subject and providing identifying an effective treatment regimen for the subject.

Abstract: A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to polymerase chain reaction (PCR) amplification, generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules assigned to the same location on the genome having a different tag, thereby obtaining genomic copy number information unaffected by amplification distortion.

Abstract: The present application provides certain advantageous ways of conducting multiplexed imaging.

Abstract: Electrode controlled hybridization is used to change local pH and selectively assemble oligonucleotide complexes on the surface of a microelectrode array. The oligonucleotide complexes have sticky ends that provide locations for subsequent oligonucleotide complexes to hybridize. The order in which specific oligonucleotide complexes are joined together encodes information. Controlled activation of individual electrodes in the microelectrode array creates negative voltages that reduces a buffer solution and raises the pH in proximity to the electrodes. At higher pH levels double-stranded oligonucleotides de-hybridize. Nicks between oligonucleotide complexes and oligonucleotides anchored to the microelectrode array are closed creating covalent attachments. De-hybridized single-stranded oligonucleotides are removed leaving only the oligonucleotides connected to microelectrode array.

Abstract: A matching support device which achieve matching between demand information and supply information, quickly and accurately reflecting changes in information. The matching support device acquires supply information and/or demand information, performs a matching between the demand information and the supply information, and transmits results of the matching to a supplier terminal and a consumer terminal. The matching support device, during a period specified from the supplier terminal and/or the consumer terminal, continues reception of the supply information and/or the demand information to reflect the changes in information and to continue matching. The matching support device may calculate, based on information of matchings, a schedule-to-result difference ratio of the supply plan information and/or the demand plan information.

Abstract: The subject invention provides a novel fluorescence-based, T5 exonuclease-amplified DNA cleavage assay for gyrase poisoning inhibitor discovery. According to the assay, multiple gyrase molecules can simultaneously bind to a plasmid DNA molecule to form multiple gyrase-DNA cleavage complexes on the same plasmid. These gyrase-DNA cleavage complexes, greatly stabilized by a gyrase poisoning inhibitor, and can be trapped by a detergent such as sarkosyl. Digestion of gyrase by proteinase K results in the production of small DNA fragments, which can be digested by T5 exonuclease. This fluorescence-based DNA cleavage HTS assay is also suitable for screening large compound libraries to identify inhibitors against DNA topoisomerases, including human DNA topoisomerase II?.

Abstract: Provided herein are compositions, systems, and methods for assessing and monitory disease stage and phases, predicting likelihood of disease progression, and predicting and monitoring responses to disease therapies (e.g., in HBV infection).

Abstract: A detection chip, a method of using a detection chip and a reaction system are provided. The detection chip includes a first substrate, a micro-chamber definition layer and a heating electrode. The micro-chamber definition layer is located on the first substrate and defines a plurality of micro-reaction chambers. The heating electrode is located on the first substrate and closer to the first substrate than the micro-chamber definition layer, and configured to release heat after being energized. The heating electrode includes a plurality of sub-electrodes, orthographic projections of the plurality of micro-reaction chambers on the first substrate overlap with orthographic projections of at least two of the plurality of sub-electrodes on the first substrate, and the at least two of the plurality of sub-electrodes have different heating values per unit time after being energized.

Abstract: There is described herein, a method of capturing cell-free methylated DNA from a sample having less than 100 mg of cell-free DNA, comprising the steps of: subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA; adding a first amount of filler DNA to the sample, wherein at least a portion of the filler DNA is methylated; denaturing the sample; and capturing cell-free methylated DNA using a binder selective for methylated polynucleotides.

Abstract: The present disclosure provides, in some aspects, nucleic acid-based molecular tools that enable the recording of molecular structure and soluble signals as well as the programmed assembly of molecular structures.

Abstract: The invention relates to a method, and a corresponding system, capable of checking whether genuine SERS or SERRS taggants having a unique characteristic surface enhancement scattering feature are present or not on a machine-readable marking applied on a value document by using a Raman spectrometer adapted to perform a Raman Spectroscopy analysis of the marking. The method according to the invention allows a reliable and fast detection of a presence of the SERS/SERRS taggants, and is particularly suitable for checking authenticity of value documents, e.g. such as banknotes, moving with respect to the Raman spectrometer with a given speed, and possibly with a high speed, or briefly exposed to the Raman spectrometer.

Abstract: The present invention is based, in part, on the identification of an IRE1?-XBP1-cMyc axis in NK cell immunity. The present invention provides compositions and methods for treating conditions that would benefit from modulating (e.g., upregulating or downregulating) an immune response using an agent that modulates the IRE1?-XBP1 pathway, or a composition comprising modified NK cells.

Abstract: The present disclosure provides a quantum-dot display substrate, a method for preparing the same, and a display device. The quantum dot display substrate includes a first electrode, a second electrode, and a quantum-dot-emitting layer located between the first electrode and the second electrode, and the quantum-dot-emitting layer includes: a DNA single-stranded structure of a specific pattern, with quantum dots attached to the DNA single-stranded structure.

Abstract: A virus lysis and nucleic acid preservation solution is disclosed, including the following components: isopropanol or ethyl alcohol, guanidinium chloride, tri (hydroxymethyl) aminomethane hydrochloride, and ethylenediaminetetraacetic acid. Furthermore, a kit including the virus lysis and nucleic acid preservation solution, a method for preserving viral nucleic acid, and a method for extracting a viral nucleic acid are also provided. The virus lysis and nucleic acid preservation solution of the present invention has the functions of lysing virus and preserving nucleic acid in the lysed virus samples, and it is compatible with lysis buffers, wash buffers, elution buffers, etc. in all kinds of viral nucleic acid extraction kit commonly available in the market.

Abstract: Provided are a microfluidic chip, and an apparatus and a method for detecting biomolecules by using the microfluidic chip. According to an example embodiment, the microfluidic chip includes: a first storage configured to accommodate a sample, the sample including target materials; a plurality of second storages connected to the first storage, the plurality of second storages including reactants for the target materials; and a plurality of well arrays connected to the plurality of second storages, respectively, and configured to accommodate a solution of the sample, in which the reactants for the target materials are dissolved.

Abstract: Described are methods for generating a reporter molecule in response to a target analyte in a cell-free system. A synthetic biological circuit is used to modify the level of the reporter molecule in response to the presence of the target analyte. The reporter molecule may be glucose or another molecule readily detected using a device such as glucose monitor or other portable sensor. Also provided are kits comprising a cell-free system with a synthetic biological circuit that generates or consumes a reporter molecule in response to a target analyte.

Abstract: Disclosed is an expression regulatory system for cell-specific transcription (expression) of a protein of interest, for example a cell cycle inducer that reactivates proliferation in adult or neonatal cardiomyocytes or insulin-producing beta cells. The expression regulatory system comprises a first nucleic acid that encodes a microRNA recognition element that specifically binds a target cell miR, and a translation suppressor protein; and a second nucleic acid that comprises a suppressor protein interaction motif that binds the translation suppressor protein, and a gene that encodes a protein of interest. When a cell of interest is co-transfected with the first and second nucleic acids of the system, the protein of interest expressed in a cell-specific fashion.

Abstract: A system for biology based anti-tamper and a method for detecting a tampering activity to an object using biological materials are provided. The system includes a biological medium that includes a biological member such as deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and/or live or hibernating organism. The biological medium is applied to a portion of an object that is required to monitor whether any tampering may have occurred. The biological member is engineered to change its state when exposed to a stimulus. Upon suspicion, the state of the biological member is examined to find if there is any change of state. The biological member is capable of being barcoded, which provides an extra security measure.

Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ?95% of them contain the identical mutation.

Abstract: The present invention relates to a method for generating primers and/or probes for use in analyzing a sample which may comprise a pathogen target sequence comprising providing a set of input genomic sequence to one or more target pathogens, generating a set of target sequences from the set of input genomic sequences, identifying one or more highly conserved target sequences, and generating one or more primers, one or more probes, or a primer pair and probe combination based on the one or more conserved target sequences.

Abstract: There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers.

Abstract: The present disclosure provides methods, device, and system for a hybridization assay to detect nucleic acid targets. The assay may use a probe array format with addressable microwells. Each microwell may retain a plurality of copies of one probe which may be complementary to a portion of a specific nucleic acid target. The plurality of copies of probes may be produced from a pooled library of probe sequences by amplification techniques, including, rolling circle amplification and emulsion-PCR. Detection of hybridization may rely on methods using ion-sensitive field effect transistor (ISFET) and optical detectors to detect signals indicating the presence of the nucleic acid targets.

Abstract: A method for multiplex analysis of amplification products using fluorescence-based multiple melting analysis is capable of analyzing multiple target nucleic acid sequences simultaneously in real time. A kit for performing the multiplex analysis contains target-specific primer/probe sets. The method and the kit allow a detection of multiple target nucleic acid sequences by a single polymerase chain reaction using a single fluorescence channel, thereby significantly reducing time and cost for multiplex nucleic acid detection. Therefore, the method and kit may be widely used in the companion diagnostic field in which multiple target nucleic acid genes need to be analyzed, the agricultural and livestock field in which multiple alleles need to be analyzed, and the clinical pathology field in which multiple infectious agents need to be analyzed simultaneously.

Abstract: The present teachings relate to methods, systems, and kits for the preparation, purification and/or analysis of a glycan or glycoconjugate, and specifically to a magnetic bead based sample preparation protocol. In some aspects, the sample preparation protocol can provide for glycoconjugate capture, glycan release, fluorescent derivatization, and glycan purification for subsequent capillary electrophoresis, liquid chromatography, or other glycoanalytical method using magnetic beads containing negatively charged carboxyl groups extending from the surface of the magnetic beads.

Abstract: Methods of preventing or treating autoimmune disease are disclosed. In some cases, subjects with having or at risk of developing autoimmune disease are identified as possessing one or more autoimmunity-susceptibility HLA alleles at one or more HLA loci. In many cases, the HLA loci are selected from Class I and Class II loci, for example Class I A, B, and C, and Class II DQ, DR, and DP. In many cases, subjects suffering from or at risk of developing an autoimmune disease may be administered a plurality engineered autologous HSCs modified to carry and express a variant susceptibility allele having at least one mutation in the antigen binding cleft that alters antigen binding and/or specificity of that variant HLA molecule. In many embodiments, the engineered HSCs are CD34+ immune cells that express one or more modified HLA proteins.

Abstract: The present application is directed to lettuce plants comprising a mutation in each of at least two different PPO genes, where said mutations reduce the activity of PPO protein compared to a wild type lettuce plant. The present application is also directed to methods for making such lettuce plants.

Abstract: The present disclosure provides methods and compositions for the multiplexed detection of multiple analytes from a sample. Analytes may be nucleic acid analytes. Detection of analytes may comprise contacting one or more sample subsets with hybridization probes, thereby generating one or more cumulative signal measurements capable of detecting the presence of absence of a plurality of analytes.

Abstract: Presented are methods, systems, and software products useful for determining the concentration of an analyte in a fluid specimen used to produce a dried sample, where the dried sample serves as a source of the analyte in a detection and quantification procedure. Particularly illustrated is the use of dried blood spots for quantifying a polynucleotide analyte.

Abstract: Methods for the rapid detection of the presence or absence of SARS-CoV-2, influenza A and influenza B in a biological or non-biological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers and probes targeting SARS-CoV-2, influenza A, and influenza B and kits are provided that are designed for the detection of SARS-CoV-2, influenza A and influenza B.

Abstract: Reversibly blocked nucleoside analogues and methods of using such nucleoside analogues for sequencing of nucleic acids are provided.

Abstract: Provided is a gene target region enrichment method and a kit. The method comprises (1) amplifying fragmented DNA comprising a target region by means of a specific probe so as to obtain a captured-extension product, wherein the specific probe comprises a sequence complementary to the target region of the fragmented DNA, and the 3? terminal nucleotide of the specific probe is modified to prevent a ligation reaction at the 3? terminal of the specific probe; and (2) linking the 3? terminal of the captured-extension product obtained in step (1) to linker DNA to obtain a ligation product.

Abstract: There is provided a method of detecting a microscopic body stored in a plurality of receptacles formed separately from each other. The method, which is provided as a technique for enclosing a to-be-detected substance such as nucleic acid, protein, virus, and cell by means of a simple operation in droplets of an extremely small volume and enabling highly sensitive detection, includes the steps of (1) introducing a solvent into a space between a lower layer part in which the receptacles are formed and an upper layer part facing a surface of the lower layer part in which surface the receptacles are formed, wherein the solvent contains the microscopic body; (2) introducing gas into the space to form a droplet of the solvent in the receptacles, wherein the droplet contains the microscopic body; and (3) detecting the microscopic body present in the droplet optically, electrically, and/or magnetically.

Abstract: A flu assay system including a sample module, a microfluidic nucleic acid amplification device, and an analyzer to facilitate fully automated nested recombinase polymerase amplification (RPA) on a sample delivered to the nucleic acid amplification device via the sample module. The assay includes providing a sample to a microfluidic device, and amplifying a target polynucleotide sequence in the sample. Amplifying the target polynucleotide sequence includes performing a first round of amplification on the sample to yield a first amplification product, and performing a second round of amplification on the first amplification product to yield a second amplification product. The second amplification product includes a smaller sequence completely contained within the first amplification product produced during the first round of amplification.

Abstract: The present invention provides an isolated peptide of SEQ ID NO: 1 needed for primase active as well as new replicative DNA polymerase enzymes, preferably that of SEQ ID NO: 2, comprising said peptide. Thus, these DNA polymerases are endowed with priming activity and do not require externally provided primers for initiating and performing DNA amplification. These polymerases are able to carry out a faithful and processive de novo DNA synthesis of DNA templates in the absence of pre-synthetized primers. Therefore, these enzymes of the invention act both as primases and DNA polymerases. Furthermore, they show translesion synthesis capacity, so that they may be useful not only for whole-genome amplification but also for the amplification of damaged DNAs. The invention further refers to methods for amplifying templates DNAs using these enzymes.

Abstract: The present disclosure provides, in part, modulators of prostate-specific G-protein receptor (OR51E2/PSGR) and methods of treating, preventing, and diagnosing prostate cancer using the same.

Abstract: The present invention relates in part to compositions and methods for treating a wound, or location of interest, in mammal by administering a decellularized extracellular matrix (ECM) lacking thrombospondin-2 (TSP-2-null ECM). In certain embodiments, the invention provides an acellular composition comprising a decellularized TSP-2-null ECM. In certain embodiments, the invention provides a tunable hydrogel comprising a decellularized TSP-2-null ECM. The invention also provides, in certain embodiments, methods for accelerating cellular migration, methods for enhancing cellular invasion, methods for enhancing vascular growth and maturation of a region to be treated, and/or methods for enhancing a wound repair in a mammal in need thereof.

Abstract: Disclosed herein are highly sensitive immunoassays that utilize a capture/release mechanism to reduce non-specific binding and achieve detection with attomolar-level sensitivity. Kits that can be used for carrying out these highly sensitive immunoassays are also disclosed herein.

Abstract: Disclosed herein, inter alia, are compositions and methods for efficient amplification and sequencing of nucleic acid templates.

Abstract: Inputs from sensors (e.g., image and environmental sensors) are used for real-time optimization of plant growth in indoor farms by adjusting the light provided to the plants and other environmental factors. The sensors use wireless connectivity to create an Internet of Things network. The optimization is determined using machine-learning analysis and image recognition of the plants being grown. Once a machine-learning model has been generated and/or trained in the cloud, the model is deployed to an edge device located at the indoor farm to overcome connectivity issues between the sensors and the cloud. Plants in an indoor farm are continuously monitored and the light energy intensity and spectral output are automatically adjusted to optimal levels at optimal times to create better crops. The methods and systems are self-regulating in that light controls the plant's growth, and the plant's growth in-turn controls the spectral output and intensity of the light.