Abstract: One embodiment provides methods to identify known and unknown gene fusions by creating a cDNA circle and analyzing the circle cDNA by amplification or sequencing. The circle cDNA is created in two approaches: 1) reverse transcribe a target RNA to cDNA, ligate the 3?end of the cDNA to its 5?end to form a circle cDNA, or 2). ligate the 3?end of target RNA to its 5? end to form a circle RNA, reverse transcribe the RNA to a cDNA, and ligate the cDNA to form a circle cDNA. The circle cDNA is amplified using a primer designed from a known sequence of a wild type target gene by rolling circle amplification or PCR methods. The known or unknown fusion gene sequences in the circle cDNA are amplified and identified by sequencing analysis.

Abstract: A method of tracking proximity relationships is disclosed, comprising: (a) introducing a body into a solution of bio-molecule(s), said body comprising at least two capture probes, wherein each capture probe comprises a barcode and a capture domain, and at least one capture probe is a releasable capture probe, connected to the body via at least one cleavable linker; (b) allowing at least two capture probes to bind to their respective target bio-molecule(s) via their respective capture domains; and (c) releasing the at least one releasable capture probe from the body by cleaving its at least one cleavable linker.

Abstract: Provided herein are methods of detecting an analyte of interest to interrogate spatial gene expression in a sample using RNA-templated ligation.

Abstract: A system and method for automatically calculating an accurate recommended dosage for hormone replacement therapy and automating the life cycle of a patient's treatment over time. The system and method can automatically acquire relevant patient parameters and apply a consistent formulaic approach to help reduce incorrect dosage determinations. A pellet insertion size may be determined and documented based on a calculated dosage, and an insertion side and lot numbers may be tracked and managed. In addition, corresponding revenues may be tracked and profitability may be reported for hormone replacement therapy practices.

Abstract: A machine learning (ML) architecture may be trained to determine an estimated epigenetic status at a target DNA locus based at least in part on epigenetic data associated with one or more other DNA loci. The ML architecture may additionally or alternatively be used to detect a failed epigenetic assay and/or determine a likelihood that a subject has falsified information provided about the subject.

Abstract: Personalized treatment plan generation from an inference engine of a system. The system may receive or retrieve data from a plurality of sources and parse the data to generate individual data fields defining characteristics of a patient. The inference engine may process the contents of the individual data fields in relation to rule blocks suggesting certain treatment actions and combinations thereof in response to satisfied conditions. The inference engine may implement machine learning to refine rule blocks and improve functioning of the system to optimize healthcare.

Abstract: The present disclosure provides method and products for the selective enrichment of one population of DNA in a mixed sample comprising multiple populations of DNA. In some embodiments, the mixed sample comprises one or more populations of microbial DNA and the mammalian host DNA, particularly including pathogenic microbial DNA mixed with mammalian host DNA in a clinical sample from an infected individual.

Abstract: The invention provides methods and compositions for separately denaturing a probe and target in hybridization applications. The invention may, for example, eliminate the use of, or reduce the dependence on formamide in hybridization applications. Compositions for use in the invention include an aqueous composition comprising at least one polar aprotic solvent in an amount effective to denature double-stranded nucleotide sequences.

Abstract: Methods, primers, sets of primers, probes, compositions, and kits for detecting presence or absence of SARS-CoV-2 in a sample are provided.

Abstract: To reduce an arithmetic processing load or an influence of noise at the time of virtual curve calculation processing, provided is a data processing device for a chromatograph, which is configured to execute data processing based on plot data measured by using a chromatograph, the data processing device including a virtual curve calculation data generator configured to obtain a smaller number of pieces of virtual curve calculation data than a number of pieces of the measured plot data; and an arithmetic processor (163) functioning as a virtual curve calculator configured to obtain a virtual curve based on the virtual curve calculation data.

Abstract: Disclosed is a substance which down-regulates the activity of a MAST gene, or the activity of a transcription or translation product of a MAST gene, for use in the prevent and/or treatment of an inflammatory skin condition in a mammalian subject.

Abstract: Embodiments of a system and method for characterizing a panel of conditions associated with a set of taxa related to microorganisms can include a taxonomic database including reference microbiome features for the set of taxa associated with the panel of conditions; a handling operable to collect a container including biological material from a user, the handling system comprising a sequencer system operable to determine a microorganism sequence dataset; and a panel characterization system operable to: determine user microbiome features for the set of taxa for the user based on the microorganism sequence dataset, generate a comparison between the user microbiome features and the reference microbiome features, and determine a panel characterization for the panel of conditions for the user based on the comparison; and a treatment system operable to promote a therapy for a condition of the panel of conditions based on the panel characterization.

Abstract: The present invention provides systems, apparatuses, and methods to detect the presence of fetal cells when mixed with a population of maternal cells in a sample and to test fetal abnormalities, e.g. aneuploidy. The present invention involves labeling regions of genomic DNA in each cell in said mixed sample with different labels wherein each label is specific to each cell and quantifying the labeled regions of genomic DNA from each cell in the mixed sample. More particularly the invention involves quantifying labeled DNA polymorphisms from each cell in the mixed sample.

Abstract: Described herein are biological devices and methods for using the same to produce oxidized zinc. The biological devices include microbial cells transformed with a DNA construct containing genes for producing a zinc-related protein, an alkaline phosphatase, and an alcohol dehydrogenase. In some instances, the biological devices also include a gene for lipase. The oxidized zinc compositions produced herein have numerous applications.

Abstract: Methods and apparatuses for mechanically controlling microfluidic movement using a force applicator and an elastically deformable sheet are described herein. These apparatuses may include a mechanical microfluidics actuator devices and a cartridge. A microfluidic droplet may be moved or displaced within an air gap of the cartridge by applying a compressive force locally and selectively reduce the gap width of the air gap near the microfluidic droplet causing the microfluidic droplet to move toward the reduced gap. Compressive forces may also be used to divide, join, mix or perform other operations on the microfluidic droplets.

Abstract: A contaminant detection system includes a light source configured to emit excitation light on an object to be inspected; a detector configured to detect fluorescence emitted from a contaminant adhering to the object to be inspected; and a processor. The fluorescence is caused by emission of the excitation light from the light source onto the object to be inspected. The processor is configured to perform a determination of a location of the contaminant and a type of the contaminant, based on the fluorescence emitted from the contaminant; and output a result of the determination.

Abstract: Methods and compositions for detecting the presence of a pathogen are described. In particular, this document provides a method of detecting a pathogen-associated nucleic acid in a biological sample of a subject, where the method comprises using one or more unimolecular aptamer-based sensors comprising an aptamer-fluorophore complex and an amplification step to detect the pathogen-associated nucleic acid. Methods specific for detecting the presence of malaria and other mosquito-borne virus infections are also provided.

Abstract: Some embodiments of the methods and compositions provided herein relate to the selective cleavage of a target nucleic acid. Some such embodiments include the selective cleavage of a target nucleic acid that is associated with a DNA-binding protein or comprises a methylated CpG island, with a recombinant nuclease. In some embodiments, the DNA-binding protein comprises a chromatin protein. Some embodiments also include the enrichment of non-target nucleic acids in a sample by selective cleavage of target nucleic acids in the sample, and removal of the cleaved target nucleic acids from the sample.

Abstract: Provided herein are compositions and methods for the multiplexed profiling of RNA and DNA modifications across transcriptomes and genomes, respectively. The methods combine molecular recognition of non-canonical features (e.g., base modifications, backbone modifications, lesions, and/or structural elements) of a target nucleic acid with a step of writing the information from this recognition event into the neighboring genetic sequence of the target nucleic acid using a barcode. The resultant barcoded nucleic acids are then converted into sequencing libraries and read by DNA/RNA sequencing methods. This step reveals the sequence of the barcode, which is correlated with the non-canonical feature in the target nucleic acid(s). The high throughput profiling methods described herein allow for localization of one or more modifications in a target nucleic acid. The methods also allow for identification of the nature and location of several or all DNA/RNA modifications in parallel.

Abstract: Disclosed herein include systems, methods, compositions, and kits for sample analysis. Nucleic acid fragments comprising a capture sequence (or a complement thereof) can be generated from double-stranded genomic deoxyribonucleic acid (gDNA), barcoded to generate single-stranded DNA (ssDNA) fragments, and sequenced. Information relating to the gDNA (e.g., genome, chromatin accessibility, methylome) can be determined based on the sequences of the ssDNA fragments in the sequencing data obtained.

Abstract: The invention relates to a method for analyzing the diversity of the catalogue of T and/or B lymphocytes in an individual, based on the amplification, from a sample, of genomic DNA fragments by PCR multi-n-plexes, with n?2, carried out with a combination of at least 3 primers defining at least 2 primer couples, each of which includes a primer specifically hybridizing upstream and/or in a given V or D gene and a primer specifically hybridizing downstream and/or in a given J gene, in order to obtain the amplification of at least two fragments characteristic of two distinct V-J or D-J rearrangements from each primer couple. The invention also relates to the applications of this method, in particular in the treatment follow-up or in the diagnosis and/or prognosis of certain diseases.

Abstract: Provided herein are synthetic size standards that allow one to detect size bias in a sample that includes a plurality of polynucleotides. The size standards can provide an internal control to detect and correct for size bias in data obtained after manipulating and/or processing of sample polynucleotide. Also provided herein are methods for detecting size bias in a sample or in a sequencing run.

Abstract: A quantum flow cytometer for detecting an analyte with photon-number statistics includes: a flow cytometer that: receives a pump light in a first direction; receives an analyte flow comprising the analyte in a second direction; and produces scattered light from scattering the pump light by the analyte; a single photon detector in optical communication with the flow cytometer and that: receives, in a third direction, the scattered light from the flow cytometer; provides a correlative time-of-arrival waveform comprising photon-number statistics as an amplitude and an integrated area, the integrated area being proportional to a number of photons received by the single photon detector, wherein the first direction, the second direction, and the third direction are arranged at oblique angles.

Abstract: A polypeptide probe for detecting G-quadruplexes (G4s), includes: from two to four G4-binding domains, and one or more linkers disposed between every two G4-binding domains. Each G4-binding domain includes a specific motif including a sequence of amino acids PGHLKGREIGMWY (SEQ ID NO: 1).

Abstract: Biomarkers and methods for identifying circulating serum-based cfDNA sequences. The cfDNA sequences (PDcRAs) can be used to differentiate patient's suffering from Parkinson's disease (PD) from non-PD patients.

Abstract: Disclosed is a bioprocessing system comprising apparatus (200) including a centrifugal separation housing (210) having a temperature controllable compartment (215) for removably accepting a separation chamber (50), the apparatus further comprising at least one mixing station (250) for supporting one or more fluid storage vessels (10, 20, 30, 40), the station including a temperature controllable area (252) for increasing or decreasing the temperature of the contents of the or each supported vessel. The system further includes a disposable fluidic arrangement (100) including a centrifugal separation chamber (50) removably mountable within the compartment (215) and having one or more ports (52) allowing fluid ingress into, or egress out of the chamber, via the one or more ports in use, said ports being in fluid communication with one or more of said fluid storage vessels via fluid conduits (12, 22, 32, 42) and via one or more valve arrangement.

Abstract: The present disclosure provides a novel loop-de-loop method of detecting a target nucleic acid using a biosensor-labeled oligonucleotide. Further provided herein is a looped primer and a kit for use in the method.

Abstract: The present disclosure provides systems and methods that can provide portable, real-time accessible DNA memories. An example DNA-based data storage system includes a loading region configured to receive a plurality of DNA-based data storage elements in a suspension fluid and a plurality of microtubes disposed in a capture/release region. The microtubes are configured to capture and release the DNA-based data storage elements. The DNA-based data storage system also includes a linearization region configured to linearize the DNA-based data storage elements and a readout region with a readout device configured to provide information indicative of the respective DNA-based data storage elements.

Abstract: Disclosed herein is the use of CER-001, a negatively charged lipoprotein complex which comprises recombinant human apolipoprotein A-I (ApoA-I), sphingomyelin (SM), and 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1?-rac-glycerol) (Dipalmitoylphosphatidyl-glycerol; DPPG) for treating kidney diseases, and methods for treating a subject having kidney diseases with CER-001. For example, the kidney disease can be associated with a lecithin cholesterol acyl transferase (LCAT) deficiency.

Abstract: An improved decision support tool is provided for detecting and treating human patients at risk for having (or developing) venous thromboembolism VTE. The tool determines a quantitative probability of VTE by utilizing a smart sensor based on a particular machine-learning model for detecting specific biomarkers determined to be related to VTE. In particular, a quantitative probability of VTE may be determined via a model based on interrelationships between multiple components of the human body's complement cascade and their coupling to coagulation processes. In one aspect, a quasi-Dirichlet distribution “mixture” relationship between total hemolytic complement (CH50) activity and complement protein C3 levels is employed as part of a smart sensor and decision support tool to provide predictive, diagnostic, and prognostic applications and for guiding prevention and treatment of acute VTE. Where the smart sensor determines a risk for VTE, then the decision support tool may initiate an intervening action.

Abstract: The invention provides methods of digital amplification using primers of limited nucleotide composition. Limited nucleotide composition means that the primers are underrepresented in at least one nucleotide type. Such primers have much reduced capacity to prime from each other or to extend initiated by mispriming from other than at their intended primer binding sites in a target nucleic acid.

Abstract: Biomarkers and methods for identifying, verifying and confirming circulating serum-based microRNAs. The microRNAs (PrognomiRs) can be used to differentiate patient's suffering from rapid progressing Parkinson's disease (PD) from slow progressing PD patients.

Abstract: Non-human animal genomes, non-human animal cells, and non-human animals comprising a humanized coagulation factor XII (F12) locus and methods of making and using such non-human animal genomes, non-human animal cells, and non-human animals are provided. Non-human animal cells or non-human animals comprising a humanized F12 locus express a human coagulation factor XII protein or a chimeric coagulation factor XII protein, fragments of which are from human coagulation factor XII. Methods are provided for using such non-human animals comprising a humanized F12 locus to assess in vivo efficacy of human-coagulation-factor-XII-targeting reagents such as nuclease agents designed to target human F12. A short isoform of F12 that is produced locally in the brain, and methods of using the short isoform, are also provide.

Abstract: Methods for the rapid detection of the presence or absence of Hepatitis B Virus (HBV) 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, competitive blocking oligonucleotides, and probes targeting HBV (in particular HBV RNA, in particular, HBV RNA transcribed from cccDNA, such as pgRNA) and kits are provided that are designed for the detection of HBV (in particular HBV RNA, in particular, HBV RNA transcribed from cccDNA, such as pgRNA).

Abstract: Various examples are directed to kits, apparatuses, and methods for determining a presence of Burkholderia pseudomallei (BP) in a biological sample. An example method includes causing a physical interaction between a biological sample from a subject and a set of first agents by exposing the biological sample to the set of first agents, the set of first agents being specific to one or more of a set of BP biomarkers associated with one or more proteins released from BP or associated with other molecules released from BP. The method further includes determining a presence of BP in the biological sample based on detected binding between one or more of the set of first agents and the one or more of the set of BP biomarkers.

Abstract: A method for testing target nucleic acid includes the steps from (1) through (5) below: (1) mixing a specimen containing target nucleic acid with positive control nucleic acid to obtain a specimen mixture of the specimen and the positive control nucleic acid; (2) mixing the specimen mixture with a PCR buffer solution containing a surfactant to obtain a buffer solution mixture; (3) adding a portion of the buffer mixture to a solid composition for PCR control containing DNA polymerase, positive control nucleic acid, and PCR reaction control nucleic acid; (4) adding a portion of the buffer mixture to a solid composition for PCR reaction containing DNA polymerase and one or more kinds of PCR primer pair; and (5) detecting a PCR product generated as a result of the steps (3) and (4).

Abstract: Methods for measuring diffusion in a medium. One method includes dissolving a fluorescent sample in a medium, imaging the fluorescent sample with a patterned illumination Fluorescence Recovery After Photobleaching (FRAP) technique, and analyzing a set of microscope images of the photobleached dissolved fluorescent sample with the patterned illumination using a Fourier Transform (FT) FRAP technique.

Abstract: The present disclosure is directed to a method for purifying a sample containing nucleic acids to obtain isolated nucleic acids of a desired size range, either above a size cut-off, below a cut-off, or within a defined band of sizes, including: a) combining a nucleic acid-containing sample with a binding buffer to provide a binding mixture; b) contacting the binding mixture with a silica nanomembrane, wherein the silica nanomembrane adsorbs nucleic acids from the binding mixture within a desired size-range; and c) separating the bound nucleic acid from the remaining sample. Kits including a silica nanomembrane, a binding buffer and one or wash buffers are also provided herein.

Abstract: A method of data interpretation from a multiplex cancer assay is described. The aggregate normalized score from the assay is transformed to a quantitative risk score quantifying a human subject's increased risk for the presence of cancer as compared to the known prevalence of the cancer in the population before testing the subject.

Abstract: Microfluidic methods for barcoding nucleic acid target molecules to be analyzed, e.g., via nucleic acid sequencing techniques, are provided. Also provided are microfluidic, droplet-based methods of preparing nucleic acid barcodes for use in various barcoding applications. The methods described herein facilitate high-throughput sequencing of nucleic acid target molecules as well as single cell and single virus genomic, transcriptomic, and/or proteomic analysis/profiling. Systems and devices for practicing the subject methods are also provided.

Abstract: The invention provides components and methods for polymerase chain reaction assays. The assays minimize both handling of material and time spent running samples. For example, a single internal positive control (IPC) polynucleotide pair can provide a means to ensure proper nucleic acid purification for both RNA and DNA test targets. Additionally, standard cycling conditions for all diagnostic tests allow the user to run both RNA and DNA targets side-by-side.

Abstract: Methods and compositions are provided herein for preparing high-throughput cDNA sequencing libraries.

Abstract: The present disclosure provides methods, compositions, kits and systems for nucleic acid amplification. In some embodiments, nucleic acid amplification methods include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, nucleic acid amplification methods include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the nucleic acid amplification method employs an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel and/or in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.

Abstract: The present invention relates to microfluidic fluidic devices, methods and systems as microfluidic kidney on-chips, e.g. human Proximal Tubule-Kidney-Chip, Glomerulus (Kidney)-Chip, Collecting Duct (Kidney)-Chip. Devices, methods and systems are described for drug testing including drug transport and renal clearance. Further, such devices, methods and systems are used for determining drug-drug interactions and their effect upon renal transporter functions. Importantly, they may be used for pre-clinical and clinical drug development for treating kidney diseases and for personalized medicine.

Abstract: The present invention relates to an in vitro method for determine the prognosis of the survival time of a patient suffering from a cancer comprising the steps consisting of i) determining the expression level of the couple DNMT3A/ISGF3? in a sample from said patient, ii) comparing said expression level with a predetermined reference value and iii) providing a good prognosis when the expression level is lower than the predetermined reference value and a poor prognosis when the expression level is higher than the predetermined reference value. The invention also relates a compound which is a DNMT3A/ISGF3? antagonist or a compound which is a DNMT3A/ISGF3? gene expression inhibitor for use in the treatment and prevention of cancer.

Abstract: Methods, systems, and apparatus are provided for determining whether a nucleic acid sequence imbalance exists within a biological sample. One or more cutoff values for determining an imbalance of, for example, the ratio of the two sequences (or sets of sequences) are chosen. The cutoff value may be determined based at least in part on the percentage of fetal DNA in a sample, such as maternal plasma, containing a background of maternal nucleic acid sequences. The percentage of fetal DNA can be calculated from the same or different data used to determine the cutoff value, and can use a locus where the mother is homozygous and the fetus is heterozygous. The cutoff value may be determined using many different types of methods, such as sequential probability ratio testing (SPRT).

Abstract: The present disclosure is directed to one or more engineered peptide inhibitors against the lactate dehydrogenase A (LDHA) activity in cells. The disclosure also provides compositions, and kits including the one or more peptide inhibitors, and methods of using the one or more peptide inhibitors. The peptide inhibitors and compositions can be used for treatment of conditions in which there is abnormally high LDHA activity, such as cancer or metabolic diseases, infectious diseases, mendelian disorders, inflammatory diseases, neurodegenerative and neuropathological diseases, neuropsychological disorders, obesity and eating disorders, chronic diseases and genetic diseases.

Abstract: The invention relates to new methods of attaching one or more polynucleotide binding proteins to a target polynucleotide. The invention also related to new methods of characterising target polynucleotides.

Abstract: In certain embodiments, this application discloses methods for detecting lung cancer. The method includes characterization of cells extracted from human sputum, which is a valuable tissue surrogate and source of upper respiratory cells that become cancerous early in the process of lung cancer development. The method includes the staining of extracted cells with fluorescent reporters that produce a specific pattern in the nuclei of labeled cells, which can be made visible by light microscopy. The pattern is relevant to a type of epigenetic coding of DNA known as DNA methylation, which changes in specific cells of the lung during cancer development, in comparison to normal respiratory cells.

Abstract: The present invention relates to lipid comprising docosapentaenoic acid and/or docosahexaenoic acid wherein the docosapentaenoic acid and/or docosahexaenoic acid may be preferentially esterified at the sn-2 position of triacylglycerol, and processes for producing and using the lipid.