Abstract: The invention provides a method for identifying a modified cytosine residue, which may be 5-methylcytosine or 5-hydroxymethylcytosine, in a nucleotide sequence. The method comprises oxidising the modified cytosine residue through a non-enzymatic, one-electron process to form 5-formylcytosine. The presence of 5-formylcytosine can be established by labelling and identifying this residue. The invention also provides a method of modifying a polynucleotide containing a 5-methylcytosine and/or a 5-hydroxymethylcytosine residue, a method of oxidising 5-methylcytosine, 5-hydroxymethylcytosine, a 5-methylcytosine residue, or a 5-hydroxymethylcytosine residue, use of a non-enzymatic radical initiator to oxidise a 5-methylcytosine or 5-hydroxymethylcytosine residue, and a kit for use in the methods.

Abstract: Technology described herein includes a method that includes obtaining an image of a fluid of a microfluidic analysis system. The microfluidic analysis system includes or receives a container that contains the fluid for measurement of analyte or quality determination. A region of interest (ROI) is identified based on the image. The ROI is a set of pixel values for use in the measurement of the analyte or the quality determination of the fluid, fluidic path, or measuring system. Identifying the ROI includes: determining an alignment of the container of the fluid with the imaging device based on the image, and identifying the ROI based on information about the measurement of the fluid or based on information about non-analyte features of the fluid. An analysis of the image of the fluid is performed using the set of pixel values of the ROI.

Abstract: Technology described herein includes a method that includes obtaining an image of a fluid of a microfluidic analysis system. The microfluidic analysis system includes or receives a container that contains the fluid for measurement of analyte or quality determination. A region of interest (ROI) is identified based on the image. The ROI is a set of pixel values for use in the measurement of the analyte or the quality determination of the fluid, fluidic path, or measuring system. Identifying the ROI includes: determining an alignment of the container of the fluid with the imaging device based on the image, and identifying the ROI based on information about the measurement of the fluid or based on information about non-analyte features of the fluid. An analysis of the image of the fluid is performed using the set of pixel values of the ROI.

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: Technology described in this document can be embodied in a system for detecting analytes in a biochemical sample. The system includes a container configured to contain the biochemical sample. The system also includes a light source, an optical detector, a lens, and an optical aperture. The lens is disposed between the container and the optical detector, and the optical aperture is disposed between the lens and the optical detector. The system further includes a structure configured to house the container, the optical aperture, the lens, and the optical detector.

Abstract: The invention provides a method of identifying a modified cytosine residue in a polynucleotide. The method includes the steps of reducing and deaminating a 5-methylcytosine residue within the polynucleotide and sequencing the polynucleotide, such that the location of the modified cytosine residue can be identified. The invention also provides a method of identifying a 5-methylcytosine residue, a 5-carboxylcytosine residue or a nucleotide in a polynucleotide. The method involves treating the polynucleotide with a radical initiator. The presence of the 5-methylcytosine residue, 5-carboxylcytosine residue or nucleotide can be identified as a residue such as thymine detected by sequencing of the treated polynucleotide.

Abstract: The invention provides a method for labeling a nucleic acid comprising N6-methyl adenine. The method comprises forming an alpha-amino radical on the N6-methyl group of N6mAde, and capturing the alpha-amino radical with a radical acceptor comprising a nitrosopyridyl group. The presence of N6mAde in a nucleic acid may then be established by detection of the labeled nucleic acid, or the labeled nucleic acid may be extracted or further modified using the label. Also provided is a method for mapping the position of N6mAde within a target nucleic acid, and probe molecules and kits for use in the method.

Abstract: Technology described herein includes a method that includes obtaining an image of a fluid of a microfluidic analysis system. The microfluidic analysis system includes or receives a container that contains the fluid for measurement of analyte or quality determination. A region of interest (ROI) is identified based on the image. The ROI is a set of pixel values for use in the measurement of the analyte or the quality determination of the fluid, fluidic path, or measuring system. Identifying the ROI includes: determining an alignment of the container of the fluid with the imaging device based on the image, and identifying the ROI based on information about the measurement of the fluid or based on information about non-analyte features of the fluid. An analysis of the image of the fluid is performed using the set of pixel values of the ROI.

Abstract: Application consistent dataset recovery using a cognitive control plane is provided. Sequence and timestamp of snapshots of volumes in a consistency group across heterogenous storage components corresponding to an application are recorded to facilitate operational recovery of application consistent datasets for the application. The cognitive control plane establishes a framework to manage, monitor, analyze, and update the consistency group and metadata to facilitate application consistent data recovery. A set of snapshots needed for the operational recovery of the application consistent datasets for the application is identified by mapping the sequence and timestamp of the snapshots of the volumes in the consistency group across the heterogenous storage components corresponding to the application in response to the computer determining that the operational recovery of the application consistent datasets for the application has been requested.

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: The present invention relates to a method of spatially barcoding a given location on a substrate, and further to spatially barcoding detection probes present in a sample such as a biological tissue specimen for the purposes of analysing molecular features present in the tissue. Such analysis may include: i) the spatial expression of one or more biological molecules, specifically; ii) the spatial analysis of the transcriptome and/or iii) the spatial analysis of the proteome, including post-translational protein modifications. The invention further relates to various component products for performing such methods that include reagents kits, instrumentation and software.

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: 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: Application consistent dataset recovery using a cognitive control plane is provided. Sequence and timestamp of snapshots of volumes in a consistency group across heterogenous storage components corresponding to an application are recorded to facilitate operational recovery of application consistent datasets for the application. The cognitive control plane establishes a framework to manage, monitor, analyze, and update the consistency group and metadata to facilitate application consistent data recovery. A set of snapshots needed for the operational recovery of the application consistent datasets for the application is identified by mapping the sequence and timestamp of the snapshots of the volumes in the consistency group across the heterogenous storage components corresponding to the application in response to the computer determining that the operational recovery of the application consistent datasets for the application has been requested.

Abstract: Data is migrated from a source storage device to a destination storage device using tape media. Both the source storage device and the destination storage device utilize disk drives to store data. A portion of data is detected migrating to the tape media. Metadata of the portion of data is changed to identify the portion of data as residing on the tape media. A prefetch command for the portion of data is detected. It is determined that the portion of data is stored on the tape media. In response to determining that the portion of data is stored on the tape media, the prefetch command is executing without recalling the portion of data to the disk drives. Instead, the portion of data is read directly from the tape media.

Abstract: A method, computer system, and a computer program product for enhanced application write operations is provided. The present invention may include performing a write operation by an application node. The present invention may then include committing the write operation to a local buffer cache. The present invention may then include sending the application node an indication that the write operation was successful. The present invention may then include flushing the local buffer cache to a disk based on a buffer flush trigger, and the present invention may lastly include sending a Remote Procedure Call (RPC) to at least one gateway node, wherein functionality of the gateway node is located on different physical nodes which are separated from the application node over the network.

Abstract: Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.

Abstract: Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.

Abstract: This invention relates to the identification of modified cytosine residues, such as 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) to be distinguished from cytosine (C) in a sample nucleotide sequence. Methods may comprise oxidising or reducing a first portion of polynucleotides which comprise the sample nucleotide sequence; treating the oxidised or reduced first portion and a second portion of polynucleotides with bisulfite; sequencing the polynucleotides in the first and second portions of the population following steps ii) and iii) to produce first and second nucleotide sequences, respectively and; identifying the residue in the first and second nucleotide sequences which corresponds to a cytosine residue in the sample nucleotide sequence. These methods may be useful, for example in the analysis of genomic DNA and/or of RNA.

Abstract: Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.