Abstract: Clinical management of human cancer is dependent on the accurate monitoring of residual and recurrent tumors. We have developed a method, called personalized analysis of rearranged ends (PARE), which can identify translocations in solid tumors. Analysis of four colorectal and two breast cancers revealed an average of nine rearranged sequences (range 4 to 15) per tumor. Polymerase chain reaction with primers spanning the breakpoints were able to detect mutant DNA molecules present at levels lower than 0.001% and readily identified mutated circulating DNA in patient plasma samples. This approach provides an exquisitely sensitive and broadly applicable approach for the development of personalized biomarkers to enhance the clinical management of cancer patients.

Abstract: Embodiments in accordance with the present disclosure are directed to polymer beads and uses thereof, including forming libraries of compounds for screening and assay purposes. A polymer bead, in accordance with embodiments, has an interior surface and an exterior surface that are topologically segregated from one another. The interior surface includes a protecting group and the exterior surface includes a deprotected group, which can also be referred to as a deprotected functional group. The protecting group can includes a nitrobenzenesulfonamide group that protects an amine group.

Abstract: Certain embodiments are directed to paper and its hybrid microfluidic devices integrated with nucleic acid amplification for simple, cost-effective, rapid, and sensitive pathogen detection, especially in low-resource settings.

Abstract: The present invention provides a method of solid-phase synthesis of DNA-encoded compound library. The method includes following steps: a) reacting solid carrier G-1 with linker molecule L-1 to prepare L-G-1; b) reacting DNA with linker molecule L-0 to prepare L-2; c) reacting L-G-1 with L-2 to prepare L-G-2; d) removing protection group of the L-G-2 and obtaining L-G-2-1; e) reacting the L-G-2-1 with synthetic building block and performing DNA encoding; and f) removing the solid carrier and obtaining the DNA-encoded compound library. Compared with the prior art, the present invention can complete post-treatment purification of the reaction only by filtration and irrigation processes for several times. The present invention is simple to operate, can shorten the production cycle of DNA encoded compound library with more than 50%, significantly increases the production efficiency and the unicity as well as the purity of the final products.

Abstract: Cells produce electrophilic products with the potential to modify and affect the function of proteins. Chemoproteomic methods have provided a means to qualitatively inventory proteins targeted by endogenous electrophiles; however, ascertaining the potency and specificity of these reactions to identify the most sensitive sites in the proteome to electrophilic modification requires more quantitative methods. Here, we describe a competitive activity-based profiling method for quantifying the reactivity of electrophilic compounds against 1000+ cysteines in parallel in the human proteome. Using this approach, we identify a select set of proteins that constitute hot spots for modification by various lipid-derived electrophiles, including the oxidative stress product 4-hydroxnonenal (HNE).

Abstract: The present invention provides a rapid, sensitive method for forensic drug testing in a post-mortem subject or a live or a post-mortem animal using oral fluid collected from the post-mortem subject or live or post-mortem animal. The method comprises collecting a sample of oral fluid from a post-mortem subject or a live or a post-mortem animal, analyzing the oral fluid sample qualitatively to detect the presence of one or more non-naturally occurring drugs, analyzing the oral fluid sample quantitatively to determine concentration of the one or more non-naturally occurring drugs in the post-mortem subject or in the live or the post-mortem animal, and identifying the one or more non-naturally occurring drugs in the post-mortem subject or in the live or the post-mortem animal. The detection and quantification in oral fluid is more sensitive and faster than detection and quantification of the non-naturally occurring drugs in blood, urine, bile, and liver tissue collected from the same post-mortem subject.

Abstract: A method for validating quantification of biomarkers, the biomarkers being quantified using a quantification technique of a selected type, and the method including determining a plurality of biomarker values, each biomarker value being indicative of a value measured or derived from a measured value, for at least one corresponding biomarker of the biological subject and being at least partially indicative of a concentration of the biomarker in a sample taken from the subject, determining at least one control value by determining a combination of biomarker values, comparing each control value to a respective control reference and determining if the biomarker values are valid using results of the comparison.

Abstract: Disclosed herein are methods, compositions, probes, polypeptides, assays, and kits for identifying a cysteine containing protein as a binding target for a small molecule fragment. Also disclosed herein are methods, compositions, and probes for mapping a biologically active cysteine site on a protein and screening a small molecule fragment for interaction with a cysteine containing protein.

Abstract: Certain embodiments are directed to paper/polymer hybrid microfluidic devices integrated with nano-biosensors for pathogen detection and infectious disease diagnosis.

Abstract: A method is for the simultaneous identification of one or more chemical compounds contained in a sample, from an analytical measurement of a pool of two or more of the samples. A measured intensity of a first and second signal is representative of an abundance of respectively the first and second chemical compound in the first sample, and a measured intensity of a third and fourth second signal is representative of an abundance of respectively a third and fourth chemical compound in the second sample. The first and third, and the second and fourth compound may be the same or different. The signal intensities are organized in a matrix aij of m columns and n rows, in which n is ?2 and corresponds to the number of chemical compounds in the pool, and m?2 and corresponds to the number of samples in the pool.

Abstract: The present invention relates to a method for screening a molecule of interest by means of nanoparticles comprising a candidate molecule, a tracer, and a single DNA tag specific to said molecule. The present invention also relates to a method for screening biomarkers of a disease and/or of a phenotype feature, more particularly of a cancer or an infection, by means of said nanoparticles. The invention finally relates to the nanoparticles as such as well as to a library of said nanoparticles.

Abstract: Disclosed are methods and systems concerning flow cells for sequencing a nucleic acid sample that may be characterized by the following components: (a) a substrate having an inner surface facing a library sequencing region, and an outer surface; (b) a plurality of a plurality of forward and reverse amplification primers immobilized over the inner surface and providing a nucleic acid library capture surface of the library sequencing region; (c) a plurality of electrodes disposed along the inner surface directly under at least some of the forward and reverse amplification primers, and configured to provide, when charged, an electric field through the library capture surface and into the library sequencing region; (d) electrical leads connected to the plurality of electrodes to permit the electrodes to be independently addressable; and (e) fluidic couplings configured to deliver a plurality of nucleic acid libraries to the flow cell during different time periods.

Abstract: This disclosure relates to libraries of oligosaccharides comprising multiple individual oligosaccharides derived from cells that contain a tag or detectable marker. In certain embodiments, the tag or detectable marker is an oxygen linked to the oligosaccharides through the first carbon of a sugar ring. In certain embodiments, the disclosure relates to methods of generating the libraries of oligosaccharides using saccharides, e.g., monosaccharides, or a disaccharide, in which hydroxyl groups are chemically acetylated.

Abstract: Devices and methods for detecting a target molecule are provided herein. The methods entail contacting a sample with a polymer scaffold, the polymer comprising at least one association site configured to associate with the target molecule. The sample is brought into contact with the polymer to determine whether the target molecule is present in the sample under conditions allowing the target molecule, if present, to associate with the polymer scaffold. The methods further involve loading the polymer into a device comprising a pore or channel that connects two volumes, configuring the device to pass the polymer through the pore or channel from one volume to the other volume, and determining, with a sensor configured to detect objects passing through the pore or channel, whether the target molecule is associated with the association site, and thereby detecting the presence or absence of the target molecule in the sample.

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: A method and reagent for constructing a nucleic acid double-linker single-strand cyclic library.

Abstract: The present disclosure provides for microbial testing devices, methods for making microbial testing devices, methods for growing and testing microbial cultures and methods for testing compounds for antimicrobial activity.

Abstract: The invention provides arrays of compound for use in profiling samples. The arrays include compounds bind to components of the samples at relatively low affinities. The avidity of compounds binding to components of the samples can be increased by forming arrays such that multivalent components of the samples (e.g., antibodies or cells) can bind to more than one molecule of a compound at the same time. When a sample is applied to an array under such conditions, the compounds of the array bind to component(s) of the sample with significantly different avidities generating a profile characteristic of the sample.

Abstract: Device for use in a biosensor comprising a multisite array of test sites, the device being useful for modulating the binding interactions between a (biomolecular) probe or detection agent and an analyte of interest from a biological by modulating the pH or ionic gradient near the electrodes in such biosensor. The device provides a biosensor which is more accurate, reliable and the results of which are more reproducible. Analytic methods for more accurately measuring an analyte of interest in a biological sample are also provided.

Abstract: Compositions and methods determines post-transfusion survival of platelets and the suitability of platelet units for transfusion by measuring the levels of one or more markers in a platelet sample. A method determines post-transfusion survival of platelets (PL T) prior to transfusion, the method comprising the steps of: a) measuring the levels of one or more markers in a PL T sample selected from the group consisting of adenine, 13-HODE/9-HODE, Caprylate, Laurate, C-glycosyltryptophan, andro steroid monsulfate 2, and Unelucidated Compounds (UC) 1-4; b) comparing the level of the one or more markers in the PLT sample with the level of the one or more markers present in a control sample, wherein a higher or lower level of the one or more markers in the PL T sample is indicative of post-transfusion survival of platelets.