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.

Abstract: The present application provides methods for detecting a target nucleic acid molecule in a sample comprising contacting said sample with a ligatable probe comprising one or more parts and allowing said probe to hybridise to the target nucleic acid molecule, ligating any probe which has hybridised to the target nucleic acid molecule, amplifying the ligated probe, and detecting the amplification product, thereby to detect the target nucleic acid molecule, wherein said probes comprise at least one ribonucleotide at or near to a ligation site and/or wherein the probe or a probe part comprises an additional sequence 5? to a target-specific binding site which is not hybridised to the target nucleic acid molecule upon hybridisation of the probe to the target nucleic acid molecule and forms a 5? flap containing one or more nucleotides at its 3? end that is cleaved prior to ligation, and methods of synthesising a DNA molecule with Phi29 DNA polymerase using a template nucleic acid molecule comprising at least one ribo

Abstract: The present disclosure relates to an in vivo fluorescent or radioactive probe represented by a compound of formula I which is capable of longitudinal imaging of inducible nitric oxide synthase (iNOS) expression in living cells and living animals on a real time basis. The probe of the present disclosure can exhibit specific and high affinity binding to the iNOS enzyme with reduced enzyme inhibitory property and also enables longitudinal monitoring of iNOS expression along with its activity or NO production in a same experimental subject throughout the progression of a physiological or disease process without employing separate subjects as controls and experimental. The present disclosure further provides a rapid and inexpensive real time method for visualizing iNOS expression and its activity in living cells and living animals precisely, conveniently and reversibly along with simultaneous in vivo imaging of its catalytic product, nitric oxide (NO) in live physiological settings.

Abstract: This disclosure provides methods and compositions for sample processing, particularly for sequencing applications. Included within this disclosure are bead compositions, such as diverse libraries of beads attached to large numbers of oligonucleotides containing barcodes. Often, the beads provides herein are degradable. For example, they may contain disulfide bonds that are susceptible to reducing agents. The methods provided herein include methods of making libraries of barcoded beads as well as methods of combining the beads with a sample, such as by using a microfluidic device.

Abstract: Disclosed is a method of performing a non-isothermal nucleic acid amplification reaction, wherein the temperature at which the method is performed is non-isothermal and subject to a reduction of at least 2° C. during amplification process steps. The present invention provides an improved nucleic acid amplification technique having one or more advantages over existing techniques including, for example, decreased reaction time, increased yield, and decreased non-specific amplification products.

Abstract: This invention relates to a novel approach for the identification and stratification of subtypes of cancer, particularly subtypes of cancer characterized by an increased expression of BCAT1, particularly Acute Myeloid Leukemia (AML). The invention furthermore relates to a novel approach with respect to the treatment of cancer, particularly subtypes of cancer characterized by an increased expression of BCAT1, particularly Acute Myeloid Leukemia (AML).

Abstract: The present invention relates to the use of a control marker for implementing analysis methods on spots, in particular in the context of multiplex analyses. The present invention thus relates to solid supports containing said control marker, their preparation method and their use in analysis methods. The present invention makes it possible to verify the presence, location and/or integrity of the spots at the end of the analysis method, and thus to secure the obtained results while guaranteeing that the yielded result indeed results from a present, intact and localized spot.

Abstract: Fluidic systems and reagent carriers suitable for storing reagents in a desirable manner are generally provided. In some embodiments, a reagent carrier stores a liquid film comprising a solid reagent and/or stores different reagents in different locations. In some embodiments, a fluidic system comprises a reagent carrier constrained such that it comprises an elongated axis positioned within 30° of a vertical axis of the fluidic reservoir.

Abstract: The present invention provides a use of a Cas protein, and a method and a kit for detecting target nucleic acid molecules. The method for detecting target nucleic acid molecules comprises adding a guide RNA, a Cas12a, and a nucleic acid probe into a reaction system containing target nucleic acid molecules to be detected, and detecting it after the reaction is completed.

Abstract: A bio-information detection substrate and a gene chip are provided. The substrate includes a first main surface, the first main surface includes a test region and a dummy region located around the test region, at least one accommodation region is disposed on the first main surface, and the accommodation region is located in the dummy region.

Abstract: Provided are compounds, methods, and pharmaceutical compositions for reducing the amount or activity of ATXN3 mRNA in a cell or animal, and in certain instances reducing the amount of Ataxin-3 protein in a cell or animal. Such compounds, methods, and pharmaceutical compositions are useful to prevent or ameliorate at least one symptom or hallmark of a neurodegenerative disease. Such symptoms and hallmarks include ataxia, neuropathy, and aggregate formation. Such neurodegenerative diseases include SCA3.

Abstract: DNA is sequenced by (a) independently sequencing first and second strands of a dsDNA to obtain corresponding first and second sequences; and (b) combining the first and second sequences to generate a consensus sequence of the dsDNA. By independently sequencing first and second strands the error probability of the consensus sequence approximates a multiplication of those of the first and second sequences.

Abstract: A system and associated method measures anomalous diffusion of biomolecules in cell membranes of intact cells and includes a laser that illuminates a cell membrane within an intact cell to express fluorescently tagged biomolecules. The laser photobleaches a region of interest and illuminates the region of interest over time. A detector detects the fluorescence recovery over time within the region of interest to yield fluorescence recovery after photobleaching (FRAP) data. A controller computes the mean square displacement (MSD) of diffusing biomolecules and a time-dependent diffusion coefficient D(t) from a plurality of time points of the FRAP data and determines the anomalous diffusion in the cell membrane.

Abstract: The present invention relates to a method for preparing a DNA oligomer into which a single nucleotide is incorporated using a terminal deoxynucleotidyl transferase. According to the present invention, by using a base hydrolysis reaction or a ribose-borate complex formation method, single incorporation of normal and modified nucleotides in a TdT enzyme-based DNA oligomer modification method can be facilitated. In addition, the method simultaneously provides the usability of TdT and the quantitativeness of modification group incorporation, thereby being effectively usable in the development of a quantitative detection technique or in a crosslinking reaction, both of which require quantitativeness and, according to the present invention, a DNA oligomer, into which a single nucleotide which is a product of a TdT reaction is incorporated, has an exposed a 3? hydroxyl terminus, which is an enzyme recognition site, such that an additional enzymatic technique such as primer extension or ligation can be introduced.

Abstract: A disposable cartridge for mitigating cross-contamination of fluid sample reagents. The disposable cartridge includes a cartridge body defining a syringe barrel having an barrel port operative to inject and withdraw assay fluids in response to the displacement of a syringe plunger. Furthermore, the disposable cartridge includes a rotor defining a plurality of assay chambers in fluid communication with the barrel port through one of a plurality of rotor ports disposed about the periphery of the rotor. Finally, the disposable cartridge includes a flow control system between the barrel and rotor ports which prevents cross-contamination of fluid sample reagents from one assay chamber to another assay chamber.

Abstract: A device for luminescent imaging includes an array of imaging pixels, a photonic structure over the array of imaging pixels, and an array of features over the photonic structure. A first feature of the array of features is over a first pixel of the array of imaging pixels, and a second feature of the array of features is over the first pixel and spatially displaced from the first feature. A first luminophore is within or over the first feature, and a second luminophore is within or over the second feature. The device includes a radiation source to generate first photons having a first characteristic at a first time, and generate second photons having a second characteristic at a second time. The first pixel selectively receives luminescence emitted by the first and second luminophores responsive to the first photons at the first time and second photons at the second time, respectively.

Abstract: In some aspects, the present disclosure provides methods for enriching amplicons, or amplification products, comprising a concatemer of at least two or more copies of a target polynucleotide. In some embodiments, a method comprises sequencing the amplicons comprising at least two or more copies of a target polynucleotide. In some embodiments, the target polynucleotides comprise sequences resulting from chromosome rearrangement, including but not limited to point mutations, single nucleotide polymorphisms, insertions, deletions, and translocations including fusion genes. In some aspects, the present disclosure provides compositions and reaction mixtures useful in the described methods.

Abstract: A laboratory system for analyzing biological samples is presented. The laboratory system comprises a plurality of laboratory instruments configured to receive and identify biological samples and to query a laboratory control unit for a processing order indicative of processing steps to be carried out on the biological sample. The laboratory control unit is configured to validate sequence of queries from the plurality of laboratory instruments against a valid query sequence pattern.

Abstract: Novel methods of generating a localized population of immobilized clonal amplicons on a support are provided.

Abstract: Provided is an information processing apparatus (100) including: an image acquiring unit (112) that acquires captured image information of a sample (20) dyed with a fluorescent dye reagent (10), an information acquiring unit (111) that acquires information related to the fluorescent dye reagent (10), a correcting unit (131) that corrects the luminance of the captured image information using a fluorescence fading coefficient that represents the rapidness at which the fluorescence intensity of the fluorescent dye reagent (10) drops, the fluorescence fading coefficient being included in the fluorescent dye reagent (10), and a calculating unit (132) that calculates information corresponding to fluorescent molecules in the captured image information, using the corrected luminance.

Abstract: In some aspects, fusosome compositions and methods are described herein that comprise membrane enclosed preparations, comprising a fusogen. In some embodiments, the fusosome can the target cell, thereby delivering complex biologic agents to the target cell cytoplasm.

Abstract: The present invention relates to antigen-binding compounds that inhibit the enzymatic activity of soluble human CD39. The invention also relates to cells producing such compounds; methods of making such compounds, and antibodies, fragments, variants, and derivatives thereof; pharmaceutical compositions comprising the same; methods of using the compounds to diagnose, treat or prevent diseases, e.g., cancer.

Abstract: A detection apparatus having a read head including a plurality of microfluorometers positioned to simultaneously acquire a plurality of the wide-field images in a common plane; and (b) a translation stage configured to move the read head along a substrate that is in the common plane. The substrate can be a flow cell that is included in a cartridge, the cartridge also including a housing for (i) a sample reservoir; (ii) a fluidic line between the sample reservoir and the flow cell; (iii) several reagent reservoirs in fluid communication with the flow cell, (iv) at least one valve configured to mediate fluid communication between the reservoirs and the flow cell; and (v) at least one pressure source configured to move liquids from the reservoirs to the flow cell. The detection apparatus and cartridge can be used together or independent of each other.

Abstract: The invention is directed to modified oligonucleotide compositions and methods for selectively reducing unwanted nucleic acid contaminants and enriching for desired nucleic acid targets from complex genomic nucleic acid mixtures for sequencing applications. The modified oligonucleotide compositions include one or more modified groups that increase the Tm of the resultant oligonucleotide composition.

Abstract: This disclosure relates to methods and systems for processing of sequencing data streams. The system receives sequences from a sequencer and stores them as data records on a database. The sequences are associated with a counter indicative of a number of times the associated sequence has been sequenced. The system progressively receives a further sequence as streaming data from the sequence. While receiving the further sequence, the system matches the streaming data against the stored sequences to determine a matching score. Upon the matching score exceeding a matching threshold for one of the multiple sequences in the database, the system selects the one of the sequences in the database based on the matching score and stores the further sequence on non-volatile memory where the counter value associated with the selected sequence is below a saturation threshold. The system also terminates the receiving where the counter value is above the saturation threshold.

Abstract: Systems and methods for assaying a test entity for a property, without measuring the property, are provided. Exemplary test entities include proteins, protein mixtures, and protein fragments. Measurements of first features in a respective subset of an N-dimensional space and of second features in a respective subset of an M-dimensional space, is obtained as training data for each reference in a plurality of reference entities. One or more of the second features is a metric for the target property. A subset of first features, or combinations thereof, is identified using feature selection. A model is trained on the subset of first features using the training data. Measurement values for the subset of first features for the test entity are applied to thereby obtaining a model value that is compared to model values obtained using measured values of the subset of first features from reference entities exhibiting the property.

Abstract: Described herein are methods of preparing dual-indexed nucleic acid libraries for methylation profiling using bisulfite conversion sequencing. In various embodiments, the methods use a two-step indexing process to tag bisulfite-treated DNA with unique molecular identifiers (UMIs).

Abstract: The present disclosure is directed, among other things, to automated systems and methods for analyzing, storing, and/or retrieving information associated with biological objects having irregular shapes. In some embodiments, the systems and methods partition an input image into a plurality of sub-regions based on localized colors, textures, and/or intensities in the input image, wherein each sub-region represents biologically meaningful data.

Abstract: The present disclosure relates to the pharmaceutical use of antagonists (e.g., an antibody or antigen-binding portion thereof) that specifically bind to FAM19A5 to promote a blood vessel normalization and treat a disease (e.g., cancer) in a subject in need thereof, e.g., by promoting a blood vessel normalization.

Abstract: A method for searching data includes storing a probe data and a target data expressed in a first orthogonal domain. The target data includes potential probe match data each characterized by the length of the target data. The probe data representation and the target data are transformed into an orthogonal domain. In the orthogonal domain, the target data is encoded with modulation functions to produce a plurality of encoded target data, each of the modulation functions having a position index corresponding to one of the potential probe match data. The plurality of encoded target data is interfered with the probe data in the orthogonal domain and an inverse transform result is obtained. If the inverse transform result exceeds a threshold, information is output indicating a match between the probe data and a corresponding one of the potential probe match data.

Abstract: The present invention has an object to provide a simpler and quicker method for diagnosing tinea, method for detecting a Trichophyton, or method for detecting the Trichophyton gene. Use of at least four kinds of specific primers each designed based on a DNA sequence of the Trichophyton gene makes it possible to simply and quickly detect the Trichophyton gene.

Abstract: Systems and methods to automatically de novo assemble a set of unordered read sequences into one or more, larger nucleotide sequences are presented. The method involves first creating two identical sets of the reads, dividing each read in both sets into smaller sorted mer sequences and then comparing the mers for each read in set 1 to the mers from each read in set 2 to exhaustively identify overlapping segments. Overlap information is used to construct a modified assembly string graph, traversal of which produces a sorted string graph layout file consisting of all the reads ordered left to right including their approximate starting offset position. The sorted string graph layout file is then processed by a novel multiple sequence alignment system that uses mer matches between all the overlapping reads at a given position to place matching individual bases from each read into columns from which an overall consensus sequence is determined.

Abstract: Kits and methods for detecting pathogens without the need for laboratory equipment are disclosed. The kits and methods described herein allow for near-room temperature amplification of pathogen polynucleotides in a biological sample in a one-compartment reaction vessel. The kits and methods may be used to detect any target nucleic acid, such as DNA or RNA from a bacterial, fungal, or viral pathogen.

Abstract: A method for characterizing the interaction between a protein and a small molecule by detecting a change in fluorescence emitted by a fluorescent dye and a nucleic acid structure which can be used in said method.

Abstract: Disclosed is a method for evaluating in vivo protein nutrition based on an LC-MS-MS technique, including the following steps: (1) collecting contents from different intestinal segments, and extracting and isolating protein ingredients; (2) determining the concentration of proteins; (3) treating before carrying out mass spectrometry: including digestion and desalting of a whole protein solution; (4) LC-MS-MS analysis; (5) database searching; and (6) data processing. Proteomic technology is used to identify proteins in the contents of different intestinal segments and digestive products thereof, and the source of the proteins in the contents of different intestinal segments and the contents thereof can be determined therefrom.

Abstract: Systems and methods are provided for microbial identification using cleavable tags. Control information is sent to a mass spectrometer to fragment one or more nucleic acid primers labeled with a first tag and monitor for an intensity of the first tag in a mass spectrometry (MS) method. An ion source provides a beam of ions from a polymerase chain reaction amplified sample that includes one or more nucleic acid primers labeled with the first tag. The first tag binds to one or more nucleic acid primers of a known microbe and is cleaved from the nucleic acid primers during the MS method. The mass spectrometer receives the beam of ions and is adapted to perform the MS method on the beam of ions. If the intensity of the first tag received from the mass spectrometer exceeds a threshold value, the known microbe is identified in the sample.

Abstract: The present invention discloses a gene sequencing data compression preprocessing, compression and decompression method, a system, and a computer-readable medium. The preprocessing method implementation steps include: obtaining reference genome data; obtaining a mapping relationship between a short string K-mer and a prediction character c to obtain a prediction data model P1 containing any short string K-mer in the positive strand and negative strand of a reference genome and the prediction character c in a corresponding adjacent bit. The compression and decompression methods relate to performing compression/decompression on the basis of the prediction data model P1. The system is a computer system including a program for executing the previous method. The computer-readable medium includes a computer program for executing the previous method.

Abstract: Provided herein are functionalized nanoparticle compositions and methods of using the same. The functionalized nanoparticles provided include a nuclease cleavage site and are, inter alia, useful for the formation of nanoparticle aggregates and detection of nuclease activity through nanoparticle aggregate formation.

Abstract: A reaction processor is provided with a reaction processing vessel in which a channel is formed, a liquid feeding system, a temperature control system for providing a high temperature region and a low temperature region to the channel, and a fluorescence detector for detecting the sample passing through a fluorescence detection region of the channel, and a CPU for controlling the liquid feeding system based on a signal that is detected. A target stop position X[L]0(n+1) of the sample in the low temperature region in an (n+1)th cycle is corrected from a target stop position X[L]0(n) of the sample in the low temperature region in the nth cycle based on the result of stopping control on the sample in the nth cycle.

Abstract: A test container includes a container main body including a first-accommodation-portion, a second-accommodation-portion, and a third-accommodation-portion each accommodating a liquid and internally provided, a first flow path connecting the first-accommodation-portion and the second-accommodation-portion to each other at respective upper end positions thereof and internally provided, and a second flow path connecting the second-accommodation-portion and the third-accommodation-portion to each other at respective upper end positions thereof and internally provided, in which at least a portion forming an upper wall surface of the second-accommodation-portion has flexibility to be deformable inwards of the second-accommodation-portion; and a liquid return prevention structure which prevents a backflow of the liquid to the first-accommodation-portion, when the liquid accommodated in the second-accommodation-portion is fed to the third-accommodation-portion via the second flow path due to deformation of the portio

Abstract: A method, software, database and system for attribute partner identification and social network based attribute analysis are presented in which attribute profiles associated with individuals can be compared and potential partners identified. Connections can be formed within social networks based on analysis of genetic and non-genetic data. Degrees of attribute separation (genetic and non-genetic) can be utilized to analyze relationships and to identify individuals who might benefit from being connected.

Abstract: The present invention generally relates to droplet libraries and to systems and methods for the formation of libraries of droplets. The present invention also relates to methods utilizing these droplet libraries in various biological, chemical, or diagnostic assays.

Abstract: Disclosed herein are compositions and methods for detecting RNA binding sites and RNA interacting partners involving the use of a modified capture oligonucleotide having a dual toehold design.

Abstract: The recently developed liquid-based Papanicolaou (Pap) smear allows not only cytologic evaluation but also collection of DNA for detection of HPV, the causative agent of cervical cancer. We tested these samples to detect somatic mutations present in rare tumor cells that might accumulate in the cervix once shed from endometrial and ovarian cancers. A panel of commonly mutated genes in endometrial and ovarian cancers was assembled and used to identify mutations in all 46 endometrial or cervical cancer tissue samples. We were able also able to identify the same mutations in the DNA from liquid Pap smears in 100% of endometrial cancers (24 of 24) and in 41% of ovarian cancers (9 of 22). We developed a sequence-based method to query mutations in 12 genes in a single liquid Pap smear without prior knowledge of the tumor's genotype.