Abstract: A method of detecting Enterovirus D68 is provided. The method may include adding to a mixture containing the sample from the subject, (a) a first forward primer comprising SEQ ID NO: 1, (b) a second forward primer comprising SEQ ID NO: 2, (c) a third forward primer comprising SEQ ID NO: 3, (d) a first reverse primer comprising SEQ ID NO: 4, and (e) a second reverse primer comprising SEQ ID NO: 5, subjecting the mixture to conditions that allow nucleic acid amplification, and detecting the presence or absence of Enterovirus D68 by analyzing the nucleic acid amplification products. The forward primers may include a first universal tail sequence and reverse primers may include a second universal tail sequence. The nucleic acid amplification products may be sequenced using next-generation sequencing.

Abstract: The present invention relates to method of detecting and characterizing one or more Borrelia species causing Lyme Disease or tick-borne relapsing fever within a sample from a subject, the method comprising: a) subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting at least one region of Borrelia 16S rRNA and at least one region of flaB, ospA, ospB, ospC, glpQ, 16S-23S intergenic spacer (IGS1), 5S-23S intergenic spacer (IGS2), bbk32, dbpA, dbpB, and/or p66; and b) analyzing amplification products resulting from the PCR amplification reaction to detect the one or more Borrelia species.

Abstract: The present invention provides a method of detecting one or more Klebsiella species within a sample from a subject, the method comprising: subjecting DNA and/or RNA from the sample to a PCR amplification reaction using primer pairs targeting species-specific canonical single nucleotide polymorphisms (canSNPs); and analyzing amplification products resulting from the PCR amplification reaction to detect the one or more Klebsiella species. The present invention also provides a kit for detection of one or more Klebsiella species, Klebsiella clonal groups, AMR genes, and/or virulence genes, the kit comprising primer pairs targeting species-specific canSNPs, K. pneumoniae genes M1 and M2, clonal group-specific canSNPs, AMR genes, and/or virulence genes.

Abstract: Various embodiments provide compositions and methods for detecting cancers containing an NRG1 fusion event and treating a patient with a therapeutic agent that is targeted to the NRG1 fusion. Exemplary compositions for treating cancers containing the NRG1 fusion may comprise therapeutic agents inhibiting Epidermal Growth Factor Receptor and/or ERBB2 such as cetuximab, panitumumab, Sym004, MM-151, mAb 806, mAb 528, MEHD794A, gefitinib, erlotinib, lapatinib, afatinib, PD153035, AG1478, trastuzumab, and pertuzumab. In some embodiments, the therapeutic agent may be a combination of trastuzumab, and pertuzumab.

Abstract: The present disclosure includes a multiplexed peptide assay to generate an epitope-resolved view of antibody reactivity across all human coronaviruses (CoVs). PepSeq accurately classifies SARS-CoV-2 exposure status and reveals epitopes across the Spike and Nucleocapsid proteins. Two of these represent recurrent reactivities to conserved, functionally-important sites in the S2 subunit of Spike, regions that we show are also targeted for the endemic CoVs in pre-pandemic controls. At one of these sites, we demonstrate that the SARS-CoV-2 response strongly and recurrently cross-reacts with the endemic virus hCoV-OC43. The disclosed epitope-resolved analysis reveals new CoV targets for the development of diagnostics, vaccines and therapeutics, including a site that may have broad neutralizing potential.

Abstract: The invention provides a method for validating patient-specific oligos using spike-in sequences.

Abstract: Various embodiments provide compositions and methods for detecting cancers containing an NRG1 fusion event and treating a patient with a therapeutic agent that is targeted to the NRG1 fusion. Exemplary compositions for treating cancers containing the NRG1 fusion may comprise therapeutic agents inhibiting Epidermal Growth Factor Receptor and/or ERBB2 such as cetuximab, panitumumab, Sym004, MM-151, mAb 806, mAb 528, MEHD794A, gefitinib, erlotinib, lapatinib, afatinib, PD153035, AG1478, trastuzumab, and pertuzumab. In some embodiments, the therapeutic agent may be a combination of trastuzumab, and pertuzumab.

Abstract: Embodiments of the invention provide a method of detecting one or more strains of Klebsiella pneumoniae. The method may include forming a plurality of mixtures for nucleic amplification. The method can include amplification of specific sequences within the K. pneumonia genome that can provide definitive information to distinguish between one or more types or strains of K. pneumonia.

Abstract: Embodiments of the invention include methods of identifying microorganisms and/or diagnosing infections in subjects cause by microorganisms. Embodiments of the invention may also include further characterizing (e.g., determining the presence of one or more antibiotic resistance markers) the microorganisms and determining a strain identity of the microorganisms.

Abstract: Embodiments of the invention provide a method of treating cancer, the method comprising providing a subject having cancer cells, and contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising the steps of: (a) receiving a sample of the cancer cells from the subject; (b) determining if at least a portion of the sample of the cancer cells is LKB1 deficient; and (c) contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising contacting the cancer cells with a therapeutically effective amount of a Wee1 inhibitor and a therapeutically effective amount of a second pharmaceutical composition.

Abstract: The invention provides microRNA markers and methods for determining the risk a subject has for developing mild traumatic brain injuries (mTBI). In some aspects, the methods further include determine the fitness of a subject for participating in an activity with increased chances of receiving a head impact. Certain embodiments are directed to kits designed for these purposes.

Abstract: The present technology provides a method of determining whether a subject with cancer is likely to experience one or more metastases. The method may include determining a methylation level of at least one gene selected from the group consisting of BEND4, CDH4, C1QL3, ERG, GP5, GSC, HTR1B, LMX1B, MCF2L2, PENK, REC8, RUNX3, PAX5, PCDHIO, SP8, SP9, STAC2, ULBP1, UNC13A, VIM, VWC2 in a subject-derived sample and then comparing the subject-derived methylation level determined in step a) with a normal control level obtained from a normal sample. Thereafter, the method may include correlating an increase of said subject-derived methylation level as compared to the normal control level to a diagnosis the subject as likely to experience one or more metastases.

Abstract: Embodiments of the invention provide a method of treating cancer, the method comprising providing a subject having cancer cells, and contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising the steps of: (a) receiving a sample of the cancer cells from the subject; (b) determining if at least a portion of the sample of the cancer cells is LKB1 deficient; and (c) contacting the cancer cells with a therapeutically effective amount of a G2/M checkpoint inhibitor. Embodiments of the invention also provide a method of treating cancer in a subject, the method comprising contacting the cancer cells with a therapeutically effective amount of a Wee1 inhibitor and a therapeutically effective amount of a second pharmaceutical composition.

Abstract: Methods are provided for diagnosing and treating idiopathic pulmonary fibrosis (IPF) in humans and canine idiopathic pulmonary fibrosis (CIPF) in canines. The methods include detecting expression of genes found to indicate a predisposition, a risk, or a presence of IPF: SDHAF2, CPSF7, and MUC5B. One variant, rs22669389, corresponding to position 54992254 on canine (CanFam3.1) chromosome 18, was identified at a suggestive level of significance to be associated with CIPF. The methods further comprise performing whole genome sequencing (WGS) of DNA in the sample to confirm detection of a variant indicating a predisposition, a risk, or a diagnosis of IPF or CIPF. The method further includes treating a subject for IPF or CIPF, based on the diagnosis of IPF or CIPF.

Abstract: The present invention relates to a method of creating a biomarker profile, the method comprising the steps of: obtaining a sample of biofluid from a subject, wherein the sample is stored on a sample collection apparatus; removing the sample from the sample collection apparatus; extracting nucleic acids from the sample; sequencing the extracted nucleic acids to generate sequence data; and analyzing the sequence data using a two-step analytical methodology to create the biomarker profile. The present invention athletic performance in a subject.

Abstract: The invention provides biomarkers and methods for determining the risk of a subject for developing mild traumatic brain injuries (mTBI). In some aspects, the methods of the invention also determine the fitness of a subject for participating in an activity with increased chances of receiving a head impact. Some embodiments of the invention are directed to kits for determining the risk of a subject for developing mTBI or the fitness of a subject for participating in an activity with increased chances of receiving a head impact.

Abstract: The present invention provides method of classifying a subject into a necrotizing meningoencephalitis (NME) disease risk group. The method may include assessing the presence of one or more marker (e.g., SNPs or risk loci) in a sample from the subject. For example, detection of the presence of one or more markers that are associated with an increased risk of NME can indicate that the subject should be classified into a risk group.

Abstract: This invention is in the field of medicinal chemistry. In particular, the invention relates to a new class of small-molecules having a benzimidazole or imidazopyridine structure which function as inhibitors of DYRK1A protein, and their use as therapeutics for the treatment of Alzheimer's disease, Down syndrome, glioblastoma, autoimmune diseases, inflammatory disorders (e.g., airway inflammation), and other diseases.

Abstract: The present invention comprises methods of treating an infection using a pharmaceutical composition comprising an active ingredient selected from Table 1. In some aspects, the infection can be caused by one or more pathogens, including fungal pathogens. For example, the infection may be Valley Fever.

Abstract: The present invention provides a method of diagnosing a breast cancer central nervous system (CNS) metastasis in a subject, comprising determining the expression level of at least one biomarker in a subject-derived brain or breast tissue comparing the subject-derived expression level with a normal control level obtained from normal brain or breast cells; and correlating an increase or decrease of the subject-derived expression level as compared to the normal control level to a diagnosis of a breast cancer CNS metastasis. The present invention also provides a method for the treatment of a breast cancer CNS metastasis in a subject comprising administering to the subject an inhibitor of an overexpressed gene associated with CNS metastasis.