Provided herein are methods and compositions related to Prevotella bacteria for the reduction of IL-8, IL-6, IL-Iβ, and/C or TNFα expression and/or for the treatment of viral infections.

A method of identifying a subject who is likely to be responsive to a treatment comprising an inhibitor of IL1α, or predicting the responsiveness of a subject to a treatment comprising an inhibitor of IL1α, comprising providing a sample from a subject; administering the inhibitor of IL1α to the sample; measuring levels of one or more biomarkers in the sample; and determining the pharmacodynamic or the pharmacokinetic effect of the inhibitor of IL1α based on the levels of the one or more biomarkers.

A method for assessing a suicidal severity in a depressed patient according to an embodiment includes measuring a concentration of a suicidal behavior prediction biomarker contained in a biological sample of the depressed patient, wherein the suicidal behavior prediction biomarker is one or more markers selected from the group consisting of cortisol, interleukin-1 beta (IL-1β), homocysteine, total cholesterol, and folate, and determining a probability of an increased suicidal severity by comparing the measured concentration of the suicidal behavior prediction biomarker with a preset cutoff level thereof.

A method for predicting antidepressant treatment response and acute prognosis for depressed patients according to an embodiment of the present disclosure includes measuring a concentration of an antidepressant treatment response prediction biomarker contained in a biological sample of a depressed patient at baseline and determining whether there is an acute phase remission, depending on the measured concentration of the antidepressant treatment response prediction marker.

The invention provides methods and systems for detecting a biomarker in a synovial fluid wherein the system also includes a control to ensure that the test sample is indeed synovial fluid. The biomarkers and the control for synovial fluid can be identified using proteomic methods, including but not limited to antibody based methods, such as an enzyme-linked immunosorbant assay (ELISA), a radioimmunoassay (RIA), or a lateral flow immunoassay.

The invention provides methods and systems for detecting a biomarker in a synovial fluid wherein the system also includes a control to ensure that the test sample is indeed synovial fluid. The biomarkers and the control for synovial fluid can be identified using proteomic methods, including but not limited to antibody based methods, such as an enzyme-linked immunosorbant assay (ELISA), a radioimmunoassay (RIA), or a lateral flow immunoassay.

The present invention provides a method for providing information for diagnosis of metastasis of radiotherapy-treated lung cancer, the method comprising the steps of: (a) measuring an expression level of receptor-interacting protein kinase 1 (RIP1) in a sample from a lung cancer patient who has undergone radiotherapy; (b) measuring an expression level of RIP1 in a normal control sample; and (c) comparing the expression levels of step (a) and step (b).

Methods and kits for screening, diagnosing, detecting or predicting a patient outcome/risk in a patient with a respiratory illness, the method comprising: a. obtaining a sample obtained from the patient; b. quantitatively measuring in the sample a polypeptide level of one or more biomarkers selected from: IL-6, CXCL8, IL-10, IL-IRA, IL-2, IL-4, IL-7, IL-9, IL-13, IL-17, IFN-g, IP-10, MCP-1, G-CSF, GM-CSF, FGF-basic, SCGF-β, GRO-α, MIP1-α, MIP1-β, CK-18, PDGF-bb, caspase 3, HMGB-1, TNF α, VEGF, sTNFR1 and sTREM1; and c. i) comparing the level of the one or more biomarkers in the sample with a control or cut-off level, wherein the differential level is indicative of patient outcome risk; or ii) using the polypeptide level of several of the biomarkers in combination, as inputs for an algebraic calculation or machine learning model of patient outcome risk.

Methods and kits for screening, diagnosing, detecting or predicting a patient outcome/risk variable for a lung transplant recipient after transplant or an EVLP outcome by measuring biomarker levels of at least three biomarkers selected from IL-6, IL-8, IL-10 and IL-1β optionally in combination with one or both of sTNFR1 and sTREM1 in EVLP perfusate are described. The methods involve for example, i. obtaining one or more test EVLP perfusate samples of a donor lung; ii. determining in one or more test EVLP perfusate sample of a donor lung, a polypeptide level of the at least three biomarkers selected from IL-8, IL-6, IL-10 and IL-1β and optionally one or both of sTNFR1 and sTREM1 i; and iii. a) comparing the one or more parameter values related to a level of the at least three biomarkers in the perfusate sample with control EVLP data or a cut-off level, wherein the differential level is indicative of outcome/risk of after transplant or of an EVLP outcome; or b) using the one or more parameter values related to a level of the at least three biomarkers in combination, as part of an algebraic calculation or model of outcome/risk.

The present invention provides methods for using surgical drainage waste fluid as a means for diagnosing disease, assessing disease progression, predicting metastatic disease, assessing cancer metastasis, disease staging, molecular staging, and assessing metastatic disease. During surgery, suction is used to drain fluids such as blood, tissue fluids, and other bodily fluids away from the surgery site. The suction drainage fluid waste, also called drain fluid, is removed from the patient during the surgical procedure. Because surgical drain fluid is typically viewed as something that is not useful, it is disregarded and thrown away during the surgery. Instead, the invention provides that drain fluid, which is mostly lymphatic fluid and interstitial fluid, is diagnostically rich and contains important information for assessing, diagnosing, and treating disease. The methods of the invention use this waste fluid for the valuable data it contains. Therefore, while a patient is already undergoing surgery for a medical condition, the waste drain fluid is sampled and analyzed for biomarkers or other molecular indicia of disease.