Abstract: Methods, devices, and kits for performing rapid, highly sensitive, high throughput, accurate, and flexible detection and quantification of nucleic acids based on highly optimized rolling circle amplification are provided. The methods, devices, and kits can be used to detect and track an emergent virus or other pathogen, including SARS-CoV-2, to test and diagnose individual patients with respect to a specific pathogen or disease, including COVID-19, and to detect and analyze cellular nucleic acids. The methods and devices also can be used to detect fragments and variants of DNA or RNA, including those present in cancer cells. The methods, devices, and kits are suitable for use in both high throughput screening carried out in centralized testing laboratories and in point-of-care testing devices used in the field, at home, in the workplace, or at public facilities for rapid detection and diagnosis.

Abstract: The present invention provides a new methodology combining MD simulations and database-guided high-throughput screening to rationally design pore forming membrane-active peptides. The present inventive methodology is able to allow tuning of a range of structural and functional properties such as pore size and selectively targeting membranes with specific lipid compositions. The present inventive methods will ultimately allow de novo design of membrane-active peptides for a wide range of biomedical applications, including for example, antimicrobial agents.

Abstract: The present invention is directed to SH3 domain derivatives having a specific binding affinity to a target molecule. In this respect, the invention provides SH3 domain derivatives of nephrocystin (NPHP1) and the Tec kinase. The invention also provides a method for the production of a library comprising recombinant derivatives of NPHP1 or the Tec kinase SH3 domains and a method for selecting from the library one or more derivatives of the SH3 domain of nephrocystin (NPHP1) or the Tec kinase having a specific binding affinity to a target molecule.

Abstract: The present disclosure describes various improved methods for imaging at least one target in a sample, including methods employing an adapter strand oligonucleotide and a bridge strand oligonucleotide. Some methods also employ bouncer oligonucleotides and/or blocker oligonucleotides. Some methods also use two partial docking strands to detect proximity of the partial docking strands to each other.

Abstract: Disclosed herein are peptoids and related compounds, including peptoid affinity ligands, and hybrid peptoids, for binding and/or purifying immunoglobulins, immunoglobulin fragments or immunoglobulin fusion proteins thereof. Methods of making peptoid affinity ligands and using the same to bind, purify and/or isolate immunoglobulins and related compounds are also disclosed. Such peptoid affinity ligands comprise a peptoid compound consisting of sequentially coupled peptoid residues forming a peptoid backbone, with one or more functional groups appended to a Nitrogen of the peptoid residues of the peptoid backbone configured to provide the desired binding affinity. The peptoids can further comprise a peptoid backbone with at least one functional group coupled to an alpha carbon (C) of a peptide bond in the peptoid backbone thereby forming a hybrid peptoid.

Abstract: The present invention provides a device for assaying living cells comprising a substrate, wherein the substrate comprises one or more tethering molecules which adhere to the substrate and are capable of interacting with cell membranes of the cells, wherein the cells maintain a free-floating, non-adherent character when bound to the one or more tethering molecules.

Abstract: A dielectrophoresis-based in-droplet cell concentrator is disclosed herein. The concentrator can include a concentration microchannel having an input port and two or more outlet ports. The input port introduces cell-encapsulated droplets or particle-encapsulated droplets into the microchannel; a first outlet port receives droplets including most of the cells or particles and a second output port receives droplets including few cells or particles. The concentrator also can include a pair of electrodes. When voltage is applied, the electrodes will create an electric field across the microchannel. The concentrator adds new capabilities to droplet microfluidics operations, such as adjusting concentrations of cells in droplets, separating cells of different properties from inside droplets, and solution exchange.

Abstract: Disclosed herein are peptoids and related compounds, including peptoid affinity ligands for binding and/or purifying immunoglobulins, immunoglobulin fragments or immunoglobulin fusion proteins thereof. Methods of making peptoid affinity ligands and using the same to bind, purify and/or isolate immunoglobulins and related compounds are also disclosed. Such peptoid affinity ligands comprise a peptoid compound consisting of sequentially coupled peptoid residues forming a peptoid backbone, with one or more functional groups appended to a nitrogen of the peptoid residues of the peptoid backbone configured to provide the desired binding affinity.

Abstract: Methods for display of recombinant whole immunoglobulins or immunoglobulin libraries on the surface of eukaryote host cells, including yeast and filamentous fungi, are described. The methods are useful for screening libraries of recombinant immunoglobulins in eukaryote host cells to identify immunoglobulins that are specific for an antigen of interest.

Abstract: The present invention relates to a method for producing renal cells, comprising overexpressing Hnf1b and Pax8, and optionally Hnf4a and/or Emx2 in differentiated cells.

Abstract: The present invention provides a three-dimensional bioprinter for fabricating cellular constructs such as tissues and organs using electromagnetic radiation (EMR) at or above 405 nm. The bioprinter includes a material deposition device comprising a cartridge for receiving and holding a composition which contains biomaterial that cures after exposure to EMR. The bioprinter also includes an EMR module that emits EMR at a wavelength of about 405 nm or higher. Also provided is a bioprinter cartridge which contains cells and a material curable at a wavelength of about 405 nm or greater. The cells are present in a chamber and are extruded through an orifice to form the cellular construct.

Abstract: The present invention relates to methods and systems for testing for the presence of a material such as one or more analyte types within a sample and more particularly, for improved single enzyme-linked immunosorbent assay (sELISA) testing as well as other variants of single-enzyme linked molecular analysis (SELMA). Background and false positives are reduced due to the presence of at least two detection cycles where each detection cycle comprises the steps of a) triggering a signal from captured and labelled analyte(s), b) recording of the number and positions of capture sites exhibiting a signal from the captured and labelled analyte(s), c) and before a further detection cycle is performed, deactivation of signal(s).

Abstract: The present invention describes methods for performing higher multiplexed real-time PCR for detection and quantitation of target nucleic acids using tagged hydrolysis probes.

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: Methods of detecting and amplifying short RNAs are provided.

Abstract: Embodiments facilitate predicting a patient prostate cancer (PCa) DECIPHER risk group. A first set of embodiments relates to training of a machine learning classifier to compute a probability that a patient is a member of a DECIPHER low/intermediate risk group based on radiomic features extracted from bi-parametric magnetic resonance imaging (bpMRI) images. A second set of embodiments relates to classifying a patient as a member of DECIPHER low/intermediate risk group, or DECIPHER high-risk group, based on radiomic features extracted from bpMRI imagery of the patient.

Abstract: The invention generally relates to methods and devices for transferring a sample into a cartridge for processing. Methods of the invention include providing a vessel containing a sample, coupling the sample to a cartridge configured to process the sample at an interface, in which the interface is configured to provide communication between the vessel and the cartridge, introducing a fluid, capture particles, or both from the cartridge into the vessel, and transferring the sample, fluid, and capture particles from the vessel and into the cartridge for processing.

Abstract: Kits and methods are provided for performing multiplex LAMP reactions. These kits and methods are directed to specific and sensitive methods of target nucleic acid detection and more specifically pathogen diagnostics such as detection of Coronavirus. The kits and methods utilize a plurality of sets of oligonucleotide primers for targeting the viral nucleic acid target.

Abstract: Embodiments facilitate stratification of a patient according to prostate cancer (PCa) risk. A first set of embodiments relates to training of a machine learning classifier to compute a probability that a patient has a low-risk of PCa progression based on intratumoral radiomic features and peritumoral radiomic features extracted from multi-parametric magnetic resonance imaging (mpMRI) images. A second set of embodiments relates to classifying a patient as low-risk of PCa progression, or high-risk of PCa progression, based on radiomic features extracted from mpMRI imagery of the patient.

Abstract: Methods of forming a chip with fluidic channels include forming (e.g., milling) at least one nanofunnel with a wide end and a narrow end into a planar substrate, the nanofunnel having a length, with width and depth dimensions that both vary over its length and forming (e.g., milling) at least one nanochannel into the planar substrate at an interface adjacent the narrow end of the nanofunnel.

Abstract: Kits and methods providing measurement of tumor burden in a patient derived xenograft (PDX) mouse are described. Exemplary embodiments contemplate taking a sample, typically a blood sample, from a PDX mouse and using a real-time polymerase chain reaction (PCR) system to quantitate both human patient circulating tumor DNA (ctDNA) and mouse DNA. In preferred embodiments, both PCR amplifications are done simultaneously in a multiplex, and a highly polymorphic human DNA target sequence is amplified for high sensitivity, allowing for small volume samples, typically 50-100 ?L, of mouse blood. Serial evaluations are possible because the mouse can survive withdrawal of these small volumes of blood. A related method allows for quantitation of ctDNA in the presence of human immune cells added to a “humanized” mouse. These relatively quick and easy methods of determining tumor burden in PDX mice can have predictive value for the efficacy of cancer treatments in human patients.

Abstract: The present invention addresses the problem of providing a novel method for classifying cancer cells by an analysis method in which measurement of the activity of two types of protein kinase is used. Cancer cells are newly classified and drug sensitivity is predicted on the basis of the ratio of the activity of two types of protein kinase derived from the same sample.

Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

Abstract: Compositions and methods are provided for diagnosis and/or prognosis of cardiovascular diseases or events in a subject. In some embodiments, the method includes measuring and comparing the level of particular proteins to other proteins. In other embodiments, the method includes comparison with clinical variable information.

Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

Abstract: Cells and methods for producing polyhydroxyalkanoates. The cells comprise one or more recombinant genes selected from an R-specific enoyl-CoA hydratase gene, a PHA polymerase gene, a thioesterase gene, and an acyl-CoA-synthetase gene. The cells further have one or more genes functionally deleted. The functionally deleted genes include such genes as an enoyl-CoA hydratase gene, a 3-hydroxyacyl-CoA dehydrogenase, and a 3-ketoacyl-CoA thiolase gene. The recombinant cells are capable of using producing polyhydroxyalkanoates with a high proportion of monomers having the same carbon length from non-lipid substrates, such as carbohydrates.

Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.

Abstract: The present application provides a means for differential diagnosis of Parkinson's disease and the clinically similar Parkinsonian disorders multiple system atrophy with predominantly Parkinsonian features (MSA-P) and progressive supranuclear palsy (PSP).

Abstract: This application provides a kit or a device for detection of ovarian tumor, comprising a nucleic acid(s) for detecting a miRNA(s) in a sample from a subject, and a method for detecting ovarian tumor, comprising measuring the miRNA(s) in vitro.

Abstract: Kits and methods are provided for performing multiplex LAMP reactions. These kits and methods are directed to specific and sensitive methods of target nucleic acid detection and more specifically pathogen diagnostics such as detection of Coronavirus. The kits and methods utilize a plurality of sets of oligonucleotide primers for targeting different template sequences in a single nucleic acid target. The kits and methods also include guanidium salts that enhance the sensitivity of the assay.

Abstract: A signal of fluorescence emitted from a fluorescent particle of a pathological specimen can be increased in sensitivity and be stabilized, thereby resulting in an enhancement in retrieval accuracy of information from a fluorescence image. A pathological specimen including a tissue section subjected to a treatment (immunostaining/FISH staining treatment) for fluorescence-labeling of an objective biomaterial with a fluorescent particle observable in a dark field, based on an immunostaining or FISH method; a packed layer with which the tissue section is covered; and a protection layer with which the packed layer is covered; wherein the refractive indexes of the fluorescent particle, the packed layer and the protection layer (measurement wavelength: 589 nm; measurement temperature: 20° C.; in all) satisfy the conditions of Expressions (1) and (2): |n1?n2|?0.20??Expression (1) |n2?n3|?0.

Abstract: Haploid human embryonic stem cells and cell lines, haploid multipotent human cells, and haploid differentiated human cells are provided. In addition, methods of making and using the haploid human cells are provided.

Abstract: A detector is provided including a plurality of nanofiber chemical sensors, each having an electrical characteristic; and a processing and alarm circuit in electrical communication with the plurality of nanofiber chemical sensors; wherein the electrical characteristics of at least one of the plurality of nanofiber chemical sensors changes in the presence of a first airborne material; wherein the electrical characteristics of at least one of the plurality of nanofiber chemical sensors changes in the presence of a second airborne material; and wherein the changes in the electrical characteristics of at least one of the plurality of nanofiber chemical sensors in the presence of the first airborne material are different from the changes in the electrical characteristics of at least one of the plurality of nanofiber chemical sensors in the presence of the second airborne material.

Abstract: This invention relates to ?1-microglobulin (A1M) for use in the diagnosis or treatment of malignancies requiring radionuclide diagnostics (RD), radionuclide therapy (RNT) or radioimmunotherapy (RIT), respectively, wherein A1M is used as a co-treatment to RD, RNT or RIT.

Abstract: The present invention relates to methods, kits and means for diagnosing Parkinson's disease in a blood sample from a subject. Further, the present invention relates to a set of polynucleotides for detecting sets of miRNAs for diagnosing Parkinson's disease in a blood sample from a subject.

Abstract: Embodiments described herein provide methods of determining a risk of progression of Barrett's esophagus in a subject, classifying Barrett's esophagus in a subject, and detecting a field effect associated with malignant transformation of an esophagus of a subject suffering from Barrett's esophagus. The disclosure also provides kits for determining a risk of progression of Barrett's esophagus in a subject and classifying Barrett's esophagus in a subject.

Abstract: The disclosure provides for methods, compositions, and kits for multiplex nucleic acid analysis of single cells. The methods, compositions and systems may be used for massively parallel single cell sequencing. The methods, compositions and systems may be used to analyze thousands of cells concurrently. The thousands of cells may comprise a mixed population of cells (e.g., cells of different types or subtypes, different sizes).

Abstract: Methods, apparatus, and other embodiments predict response to immunotherapy from computed tomography (CT) images of a region of tissue demonstrating non-small cell lung cancer (NSCLC). One example apparatus includes a set of circuits that includes an image acquisition circuit that accesses a CT image of a region of tissue demonstrating cancerous pathology, a tumoral definition circuit that generates a tumoral surface boundary that defines a tumoral volume, a peritumoral segmentation circuit that generates a peritumoral region based on the tumoral surface boundary, and that segments the peritumoral region into a plurality of annular bands, a radiomics circuit that extracts a set of discriminative features from the tumoral volume and at least one of the plurality of annular bands, and a classification circuit that classifies the ROI as a responder or a non-responder, based, at least in part, on the set of discriminative features.

Abstract: The present invention provides a method for determining increased risk of premature birth in a pregnant woman by detecting altered expression level of one or more marker genes in the woman's blood. A kit and device useful for such a method are also provided. In addition, the present invention provides a method for preventing or reducing the likelihood of premature birth.

Abstract: The present invention relates to panels of methylation and mi RNA marker as well as their use in the prognosing, diagnosing and/or treatment of cancer, means for detecting said marker, kits comprising said means, and devices for analysing the marker panel.

Abstract: A method for real-time quantitative detection of single-type, target nucleic acid sequences amplified using a PCR in a microwell, comprising introducing in the microwell a sample comprising target nucleic acid sequences, magnetic primers, and labelling probes; performing an amplification cycle to form labelled amplicons; attracting the magnetic primers to a surface through a magnetic field to form a layer including labelled amplification products and free magnetic primers; and detecting the labelled amplification products in the layer with a surface-specific reading method.

Abstract: Provided herein are multiplex assays for detecting antibodies indicative of presence and stage of syphilis infection in an individual. Individuals infected with syphilis produce antibodies directed to syphilis components and the lipid cellular debris associated with the infection. The present disclosure represents the first combination of these diverse antibody targets in a single assay.

Abstract: The present invention relates to a simultaneous analysis method for a target using a plurality of metal nano-tags and, more particularly, to a simultaneous analysis method for a target using a plurality of metal nano-tags, wherein the method fuses a nano-particle technology on the basis of an antigen-antibody reaction, which is a conventional biological immune response, and simultaneously diagnoses a plurality of target materials by using a plurality of antigen-antibody reactions and a plurality of metal nano-tags, thereby enhancing diagnostic effect.

Abstract: Methods and apparatus that mix a plurality of individual capture reagents for the diagnostic assays are described herein. In an embodiment, a system for optically analyzing a patient sample includes an automated immunochemistry analyzer storing a plurality of capture reagents and a plurality of paramagnetic particles, a user interface configured to allow a selection of a combination of two or more of the capture reagents, and a logic implementer configured to cause the automated immunochemistry analyzer to (i) mix together each capture reagent of the combination of two or more of the capture reagents; (ii) bind the mixture of the combination of two or more of the capture reagents to the paramagnetic particles; (iii) bind the patient sample to the bound mixture of the combination of two or more of the capture reagents; and (iv) optically analyze the patient sample.

Abstract: In an example of the method, a functionalized coating layer is applied in depressions of a patterned flow cell substrate. The depressions are separated by interstitial regions. A primer is grafted to the functionalized coating layer to form a grafted functionalized coating layer in the depressions. A hydrogel is applied on at least the grafted functionalized coating layer.

Abstract: A MNase-Sequence Capture method, mTSS-seq, was developed herein to map genome-wide nucleosome distribution in cancer, for example primary human lung and colon adenocarcinoma tissue. Here, it was confirmed that nucleosome redistribution is an early, widespread event in lung adenocarcinoma (LAC) and colon adenocarcinoma (CRC). These altered nucleosome architectures are consistent between LAC and CRC patient samples indicating that they can serve as important early adenocarcinoma markers. As such, this consistency would be expected in other adenocarcinomas, as well as other carcinomas. It was demonstrated that the nucleosome alterations are driven by the underlying DNA sequence and potentiate transcription factor binding. DNA-directed nucleosome redistributions are widespread early in cancer progression, thus providing a methodology for early detection of cancer in grade one patients.

Abstract: A textured substrate comprising: a first side comprising discrete regions and a continuous region extending between the discrete regions and a second side comprising discrete portions corresponding to the discrete regions and a continuous portion corresponding to the continuous region and a second side comprising discrete portions corresponding to the discrete regions and a continuous portion corresponding to the continuous region. Each discrete region comprises an outer section and sidewall sections extending outwardly from the adjacent continuous region to the outer section. Polymer particles are deposited on at least one of the first side or the second side. At least a section of each polymer particle defines a raised edge.

Abstract: The present invention provides a method for evaluating a protrusion-forming ability of cell spheroids, comprising step (a) of imaging a cell spheroid labeled with a fluorescent substance using a fluorescence microscope at a resolution capable of identifying individual cells, and acquiring a plane tomographic image of a fluorescence emitted from the fluorescent substance, step (b) of analyzing the plane tomographic image acquired in step (a) to determine a protrusion part of the cell spheroid, and step (c) of evaluating a protrusion-forming ability of the cell spheroid based on the protrusion part determined in step (b).

Abstract: Disclosed herein are methods for the generation of highly accurate nucleic acid libraries encoding for predetermined variants of a nucleic acid sequence. The nucleic acid sequence may encode for all or part of a TCR or a TCR-binding antigen. The degree of variation may be complete, resulting in a saturated variant library, or less than complete, resulting in a non-saturating library of variants. The variant nucleic acid libraries described herein may designed for further processing by transcription or translation. The variant nucleic acid libraries described herein may be designed to generate variant RNA, DNA and/or protein populations. Further provided herein are method for identifying variant species with increased or decreased activities, with applications in regulating biological functions and the design of therapeutics for treatment or reduction of a disease, such as cancer.

Abstract: Provided is a highly multiplex approach to disease condition diagnostics that combines nanopore sensing and nucleic acid nanoparticle (NANP) design and synthesis to detect multiple biomarkers to diagnose diseases. The system works by taking a sample containing biomarkers that is mixed with a plurality of nucleic acid nanoparticle (NANP) populations, with each population designed and synthesized to be able to detect a particular biomarker. Upon incubation, the mixture is used with nanopore measurements, with recordings of the ionic current through the nanopore. The ionic current recordings are analyzed, which determines the presence and/or concentration of biomarkers in the sample.