Abstract: An iterative process for optimizing one or more parameters used by a k-mer based de novo genome assembler program to assemble a set of sequenced nucleic acids is described. The method utilizes quality metrics whose desired values are initially specified. Computed values of the quality metrics are calculated during the assembly process and compared to the desired values. The assembly process stops when the computed values are not desired values. After modification of one or more of the parameters (e.g., k-mer value), the assembly process re-initiates using the modified parameter set. This process repeats until the computed values of the quality metrics meet the desired values. The final parameter set is then used to generate or complete one or more final assembled genomes.

Abstract: A large collection of sample genomes containing misclassified k-mers and metadata errors from a reference taxonomy was converted to a self-consistent k-mer database comprising a self-consistent taxonomy. The self-consistent taxonomy was based on genetic distances calculated using the MinHash method or the Meier-Koltoff method. An agglomerative clustering algorithm was used to calculate the self-consistent taxonomy. Each k-mer of the sample genomes was assigned to only one node of the self-consistent taxonomy. In another step, each node of the self-consistent taxonomy was mapped to the reference taxonomy, thereby preserving in the self-consistent taxonomy links to the reference taxonomy while correcting for the misclassification errors therein. The self-consistent k-mer database can be used to taxonomically profile sequenced nucleic acids with greater specificity compared to systems relying on the reference taxonomy.

Abstract: Methods are disclosed for reducing the size of a k-mer reference database used for queries and/or taxonomic classifications when available computer storage and/or memory are inadequate. The k-mers of the reference database have been previously classified to a taxonomy, preferably based on genetic distances. In one method, the k-mers are separated into one or more groups followed by removing k-mers common to the groups. In another method, k-mers are removed based on a selected taxonomic threshold level. A third method combines the features of the previous two methods. The methods are adaptable to machine learning.

Abstract: A method is described for automatically correcting metadata errors in a k-mer database. A k-mer database having a self-consistent taxonomy based on genome-genome distance was constructed from a set of sample and reference genomes whose metadata included taxonomic labeling from a reference taxonomy (the standard NCBI taxonomy), which is not based on genetic distance. As a result, genomes of a given taxonomic ID of the self-consistent taxonomy could be separated into clusters based on the differences in the metadata. Genomes of the clusters less than a minimum cluster size Cmin were removed and profiled against the remaining genomes, correcting metadata automatically for those genomes that could be mapped back. The resulting k-mer database showed improved specificity for genetic profiling. Another method is described for identifying and handling chimeric genomes using the self-consistent taxonomy. Another method is described for correcting a classification database.

Abstract: For each unique pair of a complete set of data items, a computing device determines a distance between the data items of the unique pair. The computing device repeats the following until no data items remain in the complete set. For each data item remaining in the complete set, the computing device determines a similarity subset including each other data item that the distance between the data item and the other data item is less than a target difference threshold. The computing device moves a selected data item from a largest similarity subset to a reference database that is a subset of the complete set. The computing device removes each data item from the complete set that the distance between the selected data item and the data item is less than the threshold. A new data item can be classified using the reference database.

Abstract: Methods are disclosed for reducing the size of a k-mer reference database used for queries and/or taxonomic classifications when available computer storage and/or memory are inadequate. The k-mers of the reference database have been previously classified to a taxonomy, preferably based on genetic distances. In one method, the k-mers are separated into one or more groups followed by removing k-mers common to the groups. In another method, k-mers are removed based on a selected taxonomic threshold level. A third method combines the features of the previous two methods. The methods are adaptable to machine learning.

Abstract: A lighting fixture can comprise a substantially flat sheet of metal supporting a circuit that comprises one or more light emitting diodes with one or more associated optics for manipulating emitted light. The circuit can be attached to, mounted next to, or integrated with the sheet of metal. In some examples, a layer of dielectric material adheres to the sheet of metal, and circuit elements adhere to the layer of dielectric material. Such circuit elements may comprise electrical traces, light emitting diodes, and/or a light emitting diode driver. The sheet of metal can provide a substrate for the circuit or a support for a freestanding circuit board that may be rigid or flexible.

Abstract: An iterative process for optimizing one or more parameters used by a k-mer based de novo genome assembler program to assemble a set of sequenced nucleic acids is described. The method utilizes quality metrics whose desired values are initially specified. Computed values of the quality metrics are calculated during the assembly process and compared to the desired values. The assembly process stops when the computed values are not desired values. After modification of one or more of the parameters (e.g., k-mer value), the assembly process re-initiates using the modified parameter set. This process repeats until the computed values of the quality metrics meet the desired values. The final parameter set is then used to generate or complete one or more final assembled genomes.

Abstract: A method of electronically separating host and non-host sequence data (sequenced DNA, RNA, and/or proteins) utilizes electronic host filters, which can be generated on a just-in-time basis by a cloud-based software service. Host reads and non-host reads of a given sample are separated and stored in separate data repositories. Also disclosed is a cloud-based software service utilizing the method. The non-host reads resulting from the host filtration process can then be profiled more accurately for the microorganism content therein.

Abstract: A method is described for automatically correcting metadata errors in a k-mer database. A k-mer database having a self-consistent taxonomy based on genome-genome distance was constructed from a set of sample and reference genomes whose metadata included taxonomic labeling from a reference taxonomy (the standard NCBI taxonomy), which is not based on genetic distance. As a result, genomes of a given taxonomic ID of the self-consistent taxonomy could be separated into clusters based on the differences in the metadata. Genomes of the clusters less than a minimum cluster size Cmin were removed and profiled against the remaining genomes, correcting metadata automatically for those genomes that could be mapped back. The resulting k-mer database showed improved specificity for genetic profiling. Another method is described for identifying and handling chimeric genomes using the self-consistent taxonomy. Another method is described for correcting a classification database.

Abstract: A large collection of sample genomes containing misclassified k-mers and metadata errors from a reference taxonomy was converted to a self-consistent k-mer database comprising a self-consistent taxonomy. The self-consistent taxonomy was based on genetic distances calculated using the MinHash method or the Meier-Koltoff method. An agglomerative clustering algorithm was used to calculate the self-consistent taxonomy. Each k-mer of the sample genomes was assigned to only one node of the self-consistent taxonomy. In another step, each node of the self-consistent taxonomy was mapped to the reference taxonomy, thereby preserving in the self-consistent taxonomy links to the reference taxonomy while correcting for the misclassification errors therein. The self-consistent k-mer database can be used to taxonomically profile sequenced nucleic acids with greater specificity compared to systems relying on the reference taxonomy.

Abstract: For each unique pair of a complete set of data items, a computing device determines a distance between the data items of the unique pair. The computing device repeats the following until no data items remain in the complete set. For each data item remaining in the complete set, the computing device determines a similarity subset including each other data item that the distance between the data item and the other data item is less than a target difference threshold. The computing device moves a selected data item from a largest similarity subset to a reference database that is a subset of the complete set. The computing device removes each data item from the complete set that the distance between the selected data item and the data item is less than the threshold. A new data item can be classified using the reference database.

Abstract: A lighting fixture can comprise a substantially flat sheet of metal supporting a circuit that comprises one or more light emitting diodes with one or more associated optics for manipulating emitted light. The circuit can be attached to, mounted next to, or integrated with the sheet of metal. In some examples, a layer of dielectric material adheres to the sheet of metal, and circuit elements adhere to the layer of dielectric material. Such circuit elements may comprise electrical traces, light emitting diodes, and/or a light emitting diode driver. The sheet of metal can provide a substrate for the circuit or a support for a freestanding circuit board that may be rigid or flexible.

Abstract: A luminaire can comprise a lightguide, a substrate to which an array of light emitting diodes is mounted, and a cover that extends over the substrate. A light-receiving edge of the lightguide can be positioned adjacent the array of light emitting diodes so that emitted light couples into the lightguide via that edge. The lightguide can guide the coupled light from the light-receiving edge to an opposing, light-emitting edge that emits the coupled light to provide illumination. The cover can comprise an aperture through which the lightguide extends, so that the cover may enclose the light-receiving edge while the light emitting edge may protrude through the aperture.

Abstract: A lighting fixture can comprise a substantially flat sheet of metal supporting a circuit that comprises one or more light emitting diodes with one or more associated optics for manipulating emitted light. The circuit can be attached to, mounted next to, or integrated with the sheet of metal. In some examples, a layer of dielectric material adheres to the sheet of metal, and circuit elements adhere to the layer of dielectric material. Such circuit elements may comprise electrical traces, light emitting diodes, and/or a light emitting diode driver. The sheet of metal can provide a substrate for the circuit or a support for a freestanding circuit board that may be rigid or flexible.

Abstract: A ballistic resistant armor plate assembly includes an armor plate which includes a strike side and a back side and a solid foam material positioned in overlying relationship with respect to the strike side and the back side of the armor plate.

Abstract: A measurement apparatus includes a body suit for a body that includes an appendage having a pivotable joint, the body suit comprising a sleeve to cover the appendage, wherein a first portion of the sleeve is configured to cover the pivotable joint. One or more multi-core optical fiber sensors is/are within or on the sleeve in a routing pattern that is substantially aligned with a longitudinal axis of the sleeve except within the first portion and that is at least partially transverse to the longitudinal axis within the first portion. An optical shape sensing system coupled to the one or more multi-core optical fiber sensors sends light into the one or more multi-core optical fiber sensors and determines a position of each of the multiple appendages based on reflected optical signal measurements detected from one or more multi-core optical fiber sensors.

Abstract: A lighting fixture can comprise a substantially flat sheet of metal supporting a circuit that comprises one or more light emitting diodes with one or more associated optics for manipulating emitted light. The circuit can be attached to, mounted next to, or integrated with the sheet of metal. In some examples, a layer of dielectric material adheres to the sheet of metal, and circuit elements adhere to the layer of dielectric material. Such circuit elements may comprise electrical traces, light emitting diodes, and/or a light emitting diode driver. The sheet of metal can provide a substrate for the circuit or a support for a freestanding circuit board that may be rigid or flexible.