Abstract: A functionally graded material is formed by pipetting individual micro-or-nano-litter droplets with a variety of materials including multi-nanostructured material (nanowires, carbon nanotubes, enzymes, multi-element and/or multi-color, multi-biomolecules) and UV polymerization of the flat hydrogel meniscus surface formed at the carrier fluid interface. After step-by-step droplet pipetting and subsequent layer-by-layer UV polymerization via a digital mask, the complete fabricated part without supporting layers is taken out of the carrier fluid while the un-cured micro-litter residue is conveniently suctioned out of the carrier fluid.

Abstract: The present invention provides a method for providing a diagnosis or prognosis of a non-alcoholic fatty liver disease (NAFLD) in a subject by detecting expression level of the Squalene Epoxidase (SQLE) gene. A kit and device useful for such methods are also provided. In addition, the present invention provides a method for treating NAFLD by suppressing SQLE gene expression or activity.

Abstract: Disclosed are methods and tools for rapidly aligning reads to a reference sequence. These methods and tools employ Bloom filters or similar set membership testers to perform the alignment. The reads may be short sequences of nucleic acids or other biological molecules and the reference sequences may be sequences of genomes, chromosomes, etc. The Bloom filters include a collection of hash functions, a bit array, and associated logic for applying reads to the filter. Each filter, and there may be multiple of these used in a particular application, is used to determine whether an applied read is present in a reference sequence. Each Bloom filter is associated with a single reference sequence such as the sequence of a particular chromosome. In one example, chromosomal abundance is determined by aligning reads from a sequencer to multiple chromosomes, each having an associated Bloom filter or other set membership tester.

Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the present method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.

Abstract: Improved methods and systems for diagnosing and for treating Cushing's syndrome and Cushing's Disease are provided herein, including methods and systems for concurrently treating Cushing's syndrome and differentially diagnosing Cushing's Disease from Ectopic Cushing's Syndrome in a patient with an established diagnosis of ACTH-dependent Cushing's syndrome. Treatment methods can use glucocorticoid receptor antagonists (GRAs), which differentially affect the ratio of cortisol to ACTH levels in patients having Cushing's Disease versus patients having Ectopic Cushing's Syndrome.

Abstract: The present disclosure describes baseline and on treatment blood-based gene signature biomarkers that are predictive of tumor sensitivity to therapy with a PD-1 antagonist. The on-treatment biomarkers comprise a PD-L1 gene signature or an interferon gamma gene signature and the baseline gene signature biomarker comprises genes associated with the oxidative phosphorylation pathway. The disclosure also provides methods and kits for testing tumor samples for these biomarkers, as well as methods for treating subjects with a PD-1 antagonist based on the test results.

Abstract: A method and apparatus for determining a presence of a microorganism in a sample is provided. The method includes storing electrophysiological and/or impedance signatures of a plurality of microorganisms in a memory of a processor. The method also includes obtaining a sample and generating an electrophysiological and/or impedance signature of the sample. The electrophysiological and/or impedance signature of the sample is compared with the electrophysiological and/or impedance signatures in the memory. A presence of one of the plurality of microorganisms in the sample is then identified based on a correlation between the electrophysiological and/or impedance signature of the sample and the electrophysiological and/or impedance signature of the one of the plurality of microorganisms. A method is also provided for determining a growth stage of a microorganism in a sample.

Abstract: The present invention relates to a variant of oleaginous yeast of the species Trichosporon oleaginosus characterized by mutations affecting cell wall synthesis that change the morphology thereof with respect to the wild-type strain of the same species. In particular, thanks to said mutations, cell aggregates are formed which, with respect to the wild-type strain of the same species, lower the viscosity of the culture broth, are more easily separable therefrom and thus make their recovery easier. Said variant of oleaginous yeast of the species Trichosporon oleaginosus is also characterized by yields of oleaginous cellular biomass and intracellular accumulation of lipids that are similar or even higher than those of the wild-type strain. Further, the present invention relates to a process for the production of lipids through said variant of oleaginous yeast of the species Trichosporon oleaginosus.

Abstract: Provided herein is a method for distinguishing an aberrant methylation level for DNA from a first cell type, including steps of (a) providing a test data set that includes (i) methylation states for a plurality of sites from test genomic DNA from at least one test organism, and (ii) coverage at each of the sites for detection of the methylation states; (b) providing methylation states for the plurality of sites in reference genomic DNA from one or more reference individual organisms, (c) determining, for each of the sites, the methylation difference between the test genomic DNA and the reference genomic DNA, thereby providing a normalized methylation difference for each site; and (d) weighting the normalized methylation difference for each site by the coverage at each of the sites, thereby determining an aggregate coverage-weighted normalized methylation difference score.

Abstract: A method for determining a risk score that indicates a risk that a clinical event will occur within a certain period of time. The risk score is based at least in part on a combination of inferred activities of two or more cellular signaling pathways in a tissue and/or cells and/or a body fluid of a subject. The cellular signaling pathways comprise a Wnt pathway, an ER pathway, an HH pathway, and/or an AR pathway. The risk score is defined such that the indicated risk that the clinical event will occur within the certain period of time decreases with an increasing PER and increases with an increasing max(PWnt, PHH), wherein PER, PWnt, and PHH denote the inferred activity of the ER pathway, the Wnt pathway, and the HH pathway, respectively.

Abstract: There are provided, inter alia, methods for reacting an enzyme and its substrate, methods for purifying a protein and an enzyme reactor and its use thereof.

Abstract: Disclosed are methods of treating an individual at risk for a negative outcome associated with a treatment for a disease, in particular a proliferative disorder such as cancer. The method may include the steps of creating a predictive assay that includes both a biomarker and a genetic mutation. The predictive assay indicates the likelihood of a negative outcome associated with a particular treatment in a particular individual, such that an individual may be administered a treatment less likely to be associated with a negative outcome.

Abstract: This invention relates to a binomial calculation of copy number of data obtained from a mixed sample having a first source and a second source.

Abstract: Disclosed is a method of designing a valid primer pair satisfying a specificity condition. The method includes searching for an identifier of a base sequence from a genetic information index based on a query language associated with a gene, searching for a candidate primer from a provided candidate primer set index to satisfy the specificity condition based on the identifier of the base sequence, filtering the candidate primer based on primer-related filtering conditions, and providing information about a primer pair satisfying the query language and the filtering conditions based on a result of the filtering.

Abstract: A method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions.

Abstract: A layered material suitable as substrate for a three-dimensional cell culture includes a transparent carrier layer and a transparent conductive layer as well as a photoconductive layer comprising titanium oxide phthalocyanine. A method for producing the layered material and an article comprising it and a receiving unit are disclosed. A mold-free method is provided for forming a three-dimensional hydrogel as well as for forming a three-dimensional cell culture by using the layered material or article. Uses of the layered material and of the three-dimensional hydrogel and three-dimensional cell culture are also disclosed.

Abstract: Provided is a novel Lactobacillus acidophilus YTI strain (deposition number: KCCM 11808P); and a composition for preventing, alleviating, or treating menopause, comprising, as an active ingredient, Lactobacillus acidophilus comprising the novel strain.

Abstract: Values for tumor mutation burden from different samples can be made more comparable to each other or control standards by a normalization regime that takes into account the minor allele fraction of highly rated mutations in a sample. Such analysis can provide an indication where the tumor mutation burden of a test sample lies on a distribution of tumor mutation burdens in a control population, and thus, whether the individual providing the test sample is likely to be amenable to immunotherapy to treat cancer.

Abstract: Systems and methods of genomic analysis are presented that provide a framework to determine a tumor's clonality, the number and proportion of all major clones, and the variants that distinguish them. Contemplated systems and methods also allow phasing mutations to parental alleles to so time their emergence within the population of tumor cells, and provide an accurate estimate of the amount of contaminating normal tissue that was present in the tumor biopsy.

Abstract: Methods for preparing a personalized cancer vaccine and a method to train a machine-learning HLA-peptide presentation prediction model.