Abstract: A card reader can include a card insertion slot, a conveyor member, a card-reading head, and a pendulum sensor assembly. The card insertion slot can receive a card from a user. The conveyor member can be configured to move the card along a transport path extending at least partially within the card reader. The card-reading head can be positioned along the transport path, directed toward the transport path. The card-reading head can be configured to read data held on a magnetic strip or held on an embedded chip. The pendulum sensor assembly can include a pendulum and a first sensor. The pendulum can extend into the transport path and can be freely-pivotable about a pivot axis. The first sensor can be configured to detect an angular position of the pendulum about the pivot axis.

Abstract: The present disclosure provides compositions comprising nucleic acid single-stranded splint strands, including kits, and methods that employ the single-stranded splint strands. The single-stranded splint strands can hybridize to portions of linear library molecules to form circularized library-splint complexes having a nick, where the nick can be ligated to form covalently closed circular molecules which can be subjected to downstream amplification and sequencing workflows.

Abstract: Described herein are systems, apparatus, methods, and/or computer program product embodiments, and/or combinations and sub-combinations thereof which enables automated determination of index sequence(s) during DNA sequencing data analysis. As a particular application of such, embodiments of methods, systems, and media for automatically determining index sequences are disclosed herein so that sequencing results from multiple samples can be sorted and separated accurately for downstream analysis, such as secondary analysis.

Abstract: Image data analysis, particularly identifying cluster locations for performing base-calling in a digital flow cell image during DNA sequencing, is described. Each nucleic acid template molecule immobilized on a support may include an insert sequence and a sample index sequence. The sample index sequence may include a k-mer sequence. A sequencing system may conduct k cycles of sequencing reactions of the k-mer sequence before conducting one or more cycles of the insert sequence sequencing reactions and generate a first plurality of flow cell images. Pixel intensities may be determined for pixels of the first plurality of flow cell images. A base calling template may be determined and include base calling locations based on the pixel intensities and respective color purities of the pixel intensities. The base calling template may register a second plurality of flow cell images of the support in one or more cycles subsequent to the k cycles.

Abstract: Disclosed embodiments concern novel interleukin receptor associated kinases (IRAK) inhibitors and compositions comprising such inhibitors. Also disclosed are methods of making and using the compounds and compositions. The disclosed compounds and/or compositions may be used to treat or prevent an IRAK-associated disease or condition.

Abstract: The present disclosure includes methods, systems, and media for performing a phasing and prephasing correction in sequencing analysis, comprising: determining corrected image intensities of a plurality of polonies, Ipc(N), based on a cycle N?1 phasing coefficient, pN?1, a cycle N?1 prephasing coefficient, ppN?1, or both; obtaining base calls in the cycle N based on the corrected image intensities of the plurality of polonies in the cycle N, Ipc(N); selecting, by the processor, polonies from the plurality of polonies based on the base calls; determining a cycle N phasing coefficient, pN, a cycle N prephasing coefficient, ppN, or both; and updating image intensities of the plurality of polonies in cycle N, I(N), using updated and corrected image intensities, Ipc_n(N), wherein Ipc_n(N) is obtained based on the cycle N phasing coefficient, pN, the cycle N prephasing coefficient, ppN, or both.

Abstract: Aspects of the present disclosure relate to a method for predicting quality of base calling in sequencing. A plurality of predictors may be selected and a corresponding value for each of the plurality of predictors may be determined from one or more flow cell images. A quality score may be determined from a look-up table based on the corresponding value for each of the plurality of predictors, wherein the look-up table comprises a plurality of dimensions corresponding to the plurality of predictors and is generated based on a training data set.

Abstract: The present disclosure provides compositions comprising nucleic acid single-stranded splint strands, including kits, and methods that employ the single-stranded splint strands. The single-stranded splint strands can hybridize to portions of linear library molecules to form circularized library-splint complexes having a nick, where the nick can be ligated to form covalently closed circular molecules which can be subjected to downstream amplification and sequencing workflows.

Abstract: A dome lens extending upwardly about a center axis A and outwardly in a radial direction R, having: a first portion forming a first annular ring about the center axis A that includes a first inner surface that is convex, and being oriented so that a first tangent to the first inner surface is at a first angle to the center axis A that is less than forty-five degrees; a second portion being continuous with the first portion and forming a second annular ring about the center axis A and including a second inner surface that is convex, and being oriented so a second tangent to the second inner surface is canted toward the center axis A; a third portion being continuous with the second portion to enclose the lens, forming an annular solid disk about the center axis A, and including a third inner surface that is convex.

Abstract: A card reader can include a card insertion slot, a conveyor member, a card-reading head, and a pendulum sensor assembly. The card insertion slot can receive a card from a user. The conveyor member can be configured to move the card along a transport path extending at least partially within the card reader. The card-reading head can be positioned along the transport path, directed toward the transport path. The card-reading head can be configured to read data held on a magnetic strip or held on an embedded chip. The pendulum sensor assembly can include a pendulum and a first sensor. The pendulum can extend into the transport path and can be freely-pivotable about a pivot axis. The first sensor can be configured to detect an angular position of the pendulum about the pivot axis.

Abstract: A card reader can include a card insertion slot, a conveyor member, a card-reading head, and a pendulum sensor assembly. The card insertion slot can receive a card from a user. The conveyor member can be configured to move the card along a transport path extending at least partially within the card reader. The card-reading head can be positioned along the transport path, directed toward the transport path. The card-reading head can be configured to read data held on a magnetic strip or held on an embedded chip. The pendulum sensor assembly can include a pendulum and a first sensor. The pendulum can extend into the transport path and can be freely-pivotable about a pivot axis. The first sensor can be configured to detect an angular position of the pendulum about the pivot axis.

Abstract: Disclosed embodiments concern interleukin receptor associated kinases (IRAK) inhibitors, such as oxazole compounds, and compositions comprising such inhibitors. Also disclosed are methods of making and using the compounds and compositions. The disclosed compounds and/or compositions may be used to treat or prevent an IRAK-associated disease or condition.

Abstract: The present disclosure provides compositions comprising reagents employed in a nucleic acid library preparation workflow for removing deaminated bases, and methods for using the reagents. The compositions and methods described herein reduce base call errors, such as C:G to T:A transitions, in nucleic acid sequencing workflows.

Abstract: The disclosed embodiments concern index oligonucleotides configured to identify sources of samples of nucleic acids and methods, apparatus, systems and computer program products for identifying and making the index oligonucleotides. In some implementations, the index oligonucleotides include a set of index sequences, a Hamming distance between any two index sequences of the set of index sequences meeting one or more criteria. System, apparatus, and computer program products are also provided for determining a sequence of interest using the index oligonucleotides.

Abstract: The disclosed embodiments concern index oligonucleotides configured to identify sources of samples of nucleic acids and methods, apparatus, systems and computer program products for identifying and making the index oligonucleotides. In some implementations, the index oligonucleotides include a set of index sequences, a Hamming distance between any two index sequences of the set of index sequences meeting one or more criteria. System, apparatus, and computer program products are also provided for determining a sequence of interest using the index oligonucleotides.

Abstract: The present disclosure provides compositions comprising nucleic acid single-stranded splint strands, including kits, and methods that employ the single-stranded splint strands. The single-stranded splint strands can hybridize to portions of linear library molecules to form circularized library-splint complexes having a nick, where the nick can be ligated to form covalently closed circular molecules which can be subjected to downstream amplification and sequencing workflows.

Abstract: A card reader can include a card insertion slot, a conveyor member, a card-reading head, and a pendulum sensor assembly. The card insertion slot can receive a card from a user. The conveyor member can be configured to move the card along a transport path extending at least partially within the card reader. The card-reading head can be positioned along the transport path, directed toward the transport path. The card-reading head can be configured to read data held on a magnetic strip or held on an embedded chip. The pendulum sensor assembly can include a pendulum and a first sensor. The pendulum can extend into the transport path and can be freely-pivotable about a pivot axis. The first sensor can be configured to detect an angular position of the pendulum about the pivot axis.

Abstract: A modular surgical retractor including a handle and a blade. The handle includes a base and a neck. The neck projects from an end of the base to a tail region. The blade includes a head section and a blade member. The head section includes opposing side walls and a floor combining to define a slot sized to receive the neck. The blade member projects from the head section. The blade is removably attached to the handle. In some embodiments, a light source, such as an LED, is disposed within the neck and arranged to emit light along a face of the blade member. Two or more additional blades are provided, each additional blade including the head section and a differently configured blade member.

Abstract: Disclosed embodiments concern interleukin receptor associated kinases (IRAK) inhibitors, such as oxazole compounds, and compositions comprising such inhibitors. Also disclosed are methods of making and using the compounds and compositions. The disclosed compounds and/or compositions may be used to treat or prevent an IRAK-associated disease or condition.

Abstract: Provided are methods, systems, and computer products for genotyping polyploid organisms, as well as diploid organisms. The provided methods use an allele-intensity model to generate cluster definitions. The allele-intensity model relates allele counts of different genotypes to signal intensities generated by the genotyping platform. The model also includes a capability to update cluster positions obtained from a maximum likelihood model using a Bayesian method.