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 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: Identified herein are sperm ligand proteins located in the membrane of sperm, which proteins interact with the membrane of oocytes. Methods of using these proteins, or fragments or derivatives or analogs thereof, are also described. These include methods of increasing (or reducing) successful fertilization, for instance through improved sperm-oocyte binding, fusion or activation (or the blocking thereof); methods of preventing fertilization of an oocyte, for instance by inducing an immune response to at least one sperm ligand that promotes sperm-oocyte binding, sperm-oocyte fusion or oocyte activation; and methods for enhancing assisted reproductive technologies, for instance through stimulation of activation with nuclear transfer, stimulation of inactive or weak sperm, and so forth.

Abstract: The present invention provides a therapeutic composition having at least one syringopeptin and at least one rhamnolipid so that the composition has one or more of the following activities: antibacterial; antifungal; and antitumor activity. The therapeutic composition includes the following: a therapeutically effective amount of a syringopeptin; a therapeutically effective amount of a rhamnolipid; and a pharmaceutically acceptable carrier. Additionally, the present invention provides a method for inhibiting or treating cancer or a microbial infection in a subject, wherein the method includes the following: providing a subject in need of inhibition or treatment of cancer or a microbial infection; and administering a therapeutic amount of a therapeutic composition to the subject so as to inhibit or treat the cancer or microbial infection.

Abstract: Identified herein are sperm ligand proteins located in the membrane of sperm, which proteins interact with the membrane of oocytes. Methods of using these proteins, or fragments or derivatives or analogs thereof, are also described. These include methods of increasing (or reducing) successful fertilization, for instance through improved sperm-oocyte binding, fusion or activation (or the blocking thereof); methods of preventing fertilization of an oocyte, for instance by inducing an immune response to at least one sperm ligand that promotes sperm-oocyte binding, sperm-oocyte fusion or oocyte activation; and methods for enhancing assisted reproductive technologies, for instance through stimulation of activation with nuclear transfer, stimulation of inactive or weak sperm, and so forth.

Abstract: Antigens can be captured and detected from complex samples, such as food and environmental samples, in about 30 minutes using apparatus and methods that include flow of the samples through a module containing antibodies coupled to beads. The samples flow through the modified beads at about 0.2 to 1.2 liters/minute, which fluidizes the bead bed. The antigens are captured by the antibodies, and then detection of the captured antibodies is carried out with chemiluminescence, fluorescence, or spectrophotometric techniques.

Abstract: Antigens can be captured and detected from complex samples, such as food and environmental samples, in about 30 minutes using apparatus and methods that include flow of the samples through a module containing antibodies coupled to beads. The samples flow through the modified beads at about 0.2 to 1.2 liters/minute, which fluidizes the bead bed. The antigens are captured by the antibodies, and then detection of the captured antibodies is carried out with chemiluminescence, fluorescence, or spectrophotometric techniques.

Abstract: A modified bead having a structure represented by the formula B—X—A is disclosed, wherein B is a solid support preferably in the form of a bead, X is a spacer selected from the group consisting of poly(threonine), poly(serine), dextran, and poly(ethylene glycol), and A is an antibody. Using such modified beads in an immunoflow module, antigens can be captured and detected from food and environmental samples in about 30 minutes.

Abstract: A method for removing a selected contaminant from a liquid food product is disclosed. A special application of the method is for removing an antibiotic from milk. The method comprises the steps of contacting the milk with a matrix-antibody composition, wherein the antibody has a specific affinity for the selected contaminant, for a time and at a temperature sufficient for the contaminant to bind to the antibody to form a complex, and separating the complex from the food product. The matrix-antibody composition is regenerable by treating the complex with high ionic strength solution to release bound contaminants from the antibodies.