Abstract: The present disclosure provides systems and methods for machine learning classification of lung nodules based on gene expression data and clinical characteristics data. The method can include, a) obtaining a data set containing gene expression measurements of a biological sample from a patient of at least two lung disease-associated genes, and clinical characteristics data of one or more clinical characteristics of the patient; b) providing the data set as an input to a machine-learning model trained to generate an inference of whether the data set is indicative of a malignant lung nodule or a benign lung nodule; c) receiving, as an output of the machine-learning model, the inference indicating whether the data set is indicative of the malignant lung nodule or the benign lung nodule; and d) electronically outputting a report classifying the lung nodule of the patient as the malignant lung nodule or the benign lung nodule.

Abstract: The present disclosure provides systems and methods for machine learning classification and assessment of COVID-19 disease based on gene expression data. In an aspect, a method for determining a COVID-19 disease state of a subject may comprise: (a) assaying a biological sample obtained or derived from the subject to produce a data set comprising gene expression measurements of the biological sample at each of a plurality of COVID-19 disease-associated genomic loci; (b) computer processing the data set to determine the COVID-19 disease state of the subject; and (c) electronically outputting a report indicative of the COVID-19 disease state of the subject.

Abstract: Described are machine learning methods of identifying one or more records having a specific phenotype to enable proper correlation between genetic records and phenotypes. In an aspect, a method of identifying one or more records having a specific phenotype may comprise: (a) receiving a plurality of first records, each associated with one or more of a plurality of phenotypes; (b) receiving a plurality of second records, each associated with one or more of the phenotypes, wherein the first and second records are non-overlapping; (c) applying a machine learning algorithm to at least one first record and at least one second record to determine a classifier; (d) receiving a plurality of third records, distinct from the first and second records; and (e) applying the classifier to the third records to identify one or more third records associated with the specific phenotype.

Abstract: The invention relates to the field of medicine. The invention provides methods for generating glatiramer-acetate-specific human T-cell lines, and assays that use these T-cell lines for demonstrating immunological identity between glatiramer acetate preparations. These assays allow sensitive and accurate comparison of glatiramer acetate preparations, and find utility as lot-release assays.

Abstract: Disclosed are computer-implemented methods, systems, and media for clustering cells using gene differential expression of single cells. In an aspect, a method may comprise: mapping RNA-Seq data of a plurality of cells onto a sphere (e.g., a hypersphere); calculating a plurality of distances, each of which is associated with an angle between two different cells mapped onto the sphere; clustering the plurality of cells into two clusters based on the plurality of distances; evaluating each of the two clusters using a pre-determined stopping criterion; and repeating the clustering and evaluating on each of the two clusters until the pre-determined stopping criterion or a second stopping criterion is met.

Abstract: The invention describes assays for determining the potency of a test lot of glatiramer acetate (GA) by quantitating and comparing the levels of mRNA response biomarkers produced in mouse T-cells in response to stimulation with the test lot or a reference standard lot of GA, wherein the T-cells are obtained from mice immunized with the test lot or the reference standard lot of GA. Methods for identifying mRNA response biomarkers useful in the assays of the invention also are described.

Abstract: The invention relates to the field of medicine. The invention provides methods for generating glatiramer-acetate-specific human T-cell lines, and assays that use these T-cell lines for demonstrating immunological identity between glatiramer acetate preparations. These assays allow sensitive and accurate comparison of glatiramer acetate preparations, and find utility as lot-release assays.

Abstract: The invention relates to the field of medicine. The invention provides methods for generating glatiramer-acetate-specific human T-cell lines, and assays that use these T-cell lines for demonstrating immunological identity between glatiramer acetate preparations. These assays allow sensitive and accurate comparison of glatiramer acetate preparations, and find utility as lot-release assays.

Abstract: The invention relates to the field of medicine. The invention provides methods for generating glatiramer-acetate-specific human T-cell lines, and assays that use these T-cell lines for demonstrating immunological identity between glatiramer acetate preparations. These assays allow sensitive and accurate comparison of glatiramer acetate preparations, and find utility as lot-release assays.

Abstract: The invention describes assays for determining the potency of a test lot of glatiramer acetate (GA) by quantitating and comparing the levels of mRNA response biomarkers produced in mouse T-cells in response to stimulation with the test lot or a reference standard lot of GA, wherein the T-cells are obtained from mice immunized with the test lot or the reference standard lot of GA. Methods for identifying mRNA response biomarkers useful in the assays of the invention also are described.

Abstract: The invention provides a method for promoting differentiation of a mature naïve B cell or a B cell progenitor into a memory B cell or a plasma cell. The method comprises (a) contacting a population of cells comprising a mature naïve B cell or a B cell progenitor with an agent that activates at least one of JAK1, JAK3, STAT3, STAT5A or STAT5B; wherein the population of cells optionally is contacted with an antigen, and (b) isolating the memory B cell or plasma cell.

Abstract: The present invention relates to a method of diagnosing and/or predicting joint destruction, early joint destruction and/or accelerated joint destruction in particular, in rheumatoid arthritis, comprising determining in a sample obtained from an individual the presence of at least one nucleic acid sequence encoding an IL-4 receptor (IL-4R) which contains a mutation in position 465 of the nucleotide sequence of the wild-type IL4R as shown in SEQ ID NO: 1, whereby at said position the nucleotide A is replaced or a nucleic acid sequence encoding an IL-4 receptor (IL-4R), said IL-4R comprising at position 75 as shown in SEQ ID NO: 2 a valine instead of an isoleucine.

Abstract: A method is disclosed herein for inducing differentiation of a B cell progenitor into a memory B cells and/or a plasma cell. The method includes contacting a population of cells including a mature B cell or a B cell progenitor with an effective amount of IL-21, and isolating memory B cells or plasma cells. In one embodiment, the B cell progenitor is an immature B cell. A method is also disclosed for enhancing an immune response. The method includes contacting a population of cells including a B cell progenitor with an effective amount of IL-21, and isolating memory B cells or plasma cells. The memory B cells and/or the plasma cell are then introduced into the subject to enhance the immune response. A method is also disclosed for treating a subject with a condition comprising a specific deficiency of at least one of memory B cells and plasma cells. A method is disclosed for identifying an agent with a physiological effect on one or more of a memory B cell and a plasma cell differentiation.

Abstract: A transgenic mouse is disclosed herein whose somatic and germ cells comprise a disrupted IL-21 receptor gene, the disruption being sufficient to inhibit the binding of IL-21 to an IL-21 receptor, and a disrupted IL-4 gene, the disruption being sufficient to inhibit the production of IL-4 or the binding of IL-4 to the IL-4 receptor. A mouse homozygous for the disrupted IL-21 receptor gene and homozygous for the disrupted IL-4 gene has diminished B cell function. A method is disclosed for altering a B cell activity. The method includes administering a therapeutically effective amount of an agent that interferes with the interaction of IL-21 with an IL-21 receptor, thereby altering the B cell activity. A method is also disclosed for of treating a subject with Job's disorder or atopic disease. A method is also disclosed for treating or preventing an allergic reaction in a subject. A method is also disclosed for treating a subject with an autoimmune or antibody mediated disorder.

Abstract: A method is disclosed herein for inducing differentiation of a B cell progenitor into a memory B cells and/or a plasma cell. The method includes contacting a population of cells including a mature B cell or a B cell progenitor with an effective amount of IL-21, and isolating memory B cells or plasma cells. In one embodiment, the B cell progenitor is an immature B cell. A method is also disclosed for enhancing an immune response. The method includes contacting a population of cells including a B cell progenitor with an effective amount of IL-21, and isolating memory B cells or plasma cells. The memory B cells and/or the plasma cell are then introduced into the subject to enhance the immune response. A method is also disclosed for treating a subject with a condition comprising a specific deficiency of at least one of memory B cells and plasma cells. A method is disclosed for identifying an agent with a physiological effect on one or more of a memory B cell and a plasma cell differentiation.

Abstract: The present invention involves the use of Tripterygium Wilfordii Hook F extracts in the treatment of rheumatoid arthritis. An alcohol extract of this plant (T2) inhibited antigen- and mitogen-stimulated proliferation of T cells and B cells, cell cycle progression, interleukin-2 (IL-2) production by T cells, immunoglobulin production by B cells and interleukin-2 mRNA production. T2 did not affect IL-2 receptor expression by T cells, IL-1 production by monocytes, the capacity of monocytes to present antigen, or signaling pathways. Inhibition could not be accounted for by nonspecific toxicity. These results support the conclusion that T2 exerts a powerful suppressive effect on human immune responses. Suppressing autoimmune disease is a most preferred embodiment of this invention.

Abstract: The present invention provides for the use of Tripterygium wilfordii Hook F extracts and purified components thereof in the treatment of inflammation or an immune disorder with concomitant lack of steroidal effect. Extracts of this plant (T2) bound to the glucocorticoid receptor and competitively inhibited glucocorticoid mediated cellular processes, such as dexamethasone binding to the glucocorticoid receptor, glucocorticoid mediated activation of target genes, dexamethasone dependent cellular growth, with concomitant inhibition of cyclooxygenase-2 induction and inflammatory processes such as the production of prostaglandin E.sub.2. The T2 extract components triptolide and tripdiolide were effective inhibitors. The particular advantage provided by the methods herein is the treatment or prevention of inflammation and the concomitant lack of steroidal agonist effects and NSAID side effects. Conditions treatable by the present methods include inflammation and immune disorders including autoimmune disease.

Abstract: Compositions that include as an active ingredient an effective concentration of a halogenated mevalonate preparation, particularly, Fmev (fluoromevalonate) are provided. The pharmacological activity of halogenated mevalonate for inhibiting ras-dependent cell growth, particularly ras-dependent tumor cell growth, is described. Methods for using preparations including a therapeutically effective concentration of Fmev for the inhibition of ras-dependent cell growth, as well as in the treatment and inhibition of ras-dependent tumors is also disclosed. The claimed compositions may be provided in liquid, salve, tablet, or capsule form, as well as other forms suitable for administration to an animal.

Abstract: Esters or amides of a peptide, preferably a dipeptide, consisting essentially of natural or synthetic L-amino acids with hydrophobic side chains were found to have specific cellular toxicities. Preferable amino acids of the peptide are leucine, phenylalanine valine, isoleucine, alanine, proline, glycine or aspartic acid beta methyl ester. Preferable dipeptides are L leucyl L-leucine, L-leucyl L-phenylalanine, L-valyl L-phenylalanine, L-leucyl L-isoleucine, L-phenylalanyl L-phenylalanine, L-valyl L-leucine, L-leucyl L-alanine, L-valyl L-valine, L-phenylalanyl L leucine, L prolyl L-leucine, L-leucyl L-valine, L-phenylalanyl L-valine, L glycyl L-leucine, L-leucyl L-glycine, glycyl L-phenylalanine and L-aspartyl beta methyl ester L-phenylalanine. Most preferable dipeptides are L-leucyl L-leucine, L-leucyl L-phenylalanine, L-valyl L-phenylalanine, L-phenylalanyl L-leucine, L-leucyl L-isoleucine L-phenylalanyl L-phenylalanine and L-valyl L-leucine.

Abstract: The present invention provides for the use of Tripterygium wilfordii Hook F extracts and purified components thereof in the treatment of inflammation or an immune disorder with concomitant lack of steroidal effect. Extracts of this plant (T2) bound to the glucocorticoid receptor and competitively inhibited glucocorticoid mediated cellular processes, such as dexamethasone binding to the glucocorticoid receptor, glucocorticoid mediated activation of target genes, dexamethasone dependent cellular growth, with concomitant inhibition of cyclooxygenase-2 induction and inflammatory processes such as the production of prostaglandin E.sub.2. The T2 extract components triptolide and tripdiolide were effective inhibitors. The particular advantage provided by the methods herein is the treatment or prevention of inflammation and the concomitant lack of steroidal agonist effects and NSAID side effects. Conditions treatable by the present methods include inflammation and immune disorders including autoimmune disease.