Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.

Abstract: Antibodies that bind the tumor (T) antigen of the Merkel cell polyomavirus are disclosed. The antibodies can be use used in cell-based immunotherapies, antibody-based therapies, diagnostics, and detection assays, among other uses.

Abstract: The present disclosure provides for the treatment of cardiac diseases and disorders using in vitro-differentiated cardiomyocytes. Such methods can take advantage of both autologous and allogeneic pluripotent stem cells.

Abstract: N-oxide and monomers, N-oxide polymers and copolymers, methods for making the N-oxide monomers, polymers, and copolymers, compositions and materials that include N-oxide polymers and copolymers, and methods for using the N-oxide monomers, N-oxide polymers, and N-oxide copolymers.

Abstract: The disclosure provides methods and related kits, reagents, and systems for selectively deaminating unmethylated cytosine residues in nucleic acid molecules. In some embodiments, the methods and related kits, reagents, and systems are applied for methods of detecting and/or mapping methylated cytosine residues in nucleic acids. The nucleic can be RNA or DNA. Some embodiments include contacting the polynucleic acid with a bacterial cytosine deaminase, for example DddA or SsdA, or functional fragments or derivatives thereof. Representative DddA and SsdA have sequences set forth in SEQ ID NOS:1 and 2, respectively. The bacterial cytosine deaminases of the disclosure are sensitive to methylation and, thus, deaminate only unmethylated cytosines to provide a cytosine to uracil conversion. The conversion can be detected as a C•G-to-T•A transitions in subsequent sequencing analysis.

Abstract: Provided herein are Mycobacterium smegmatis porin nanopores, systems that comprise these nanopores, and methods of using and making these nanopores. Such nanopores may be wild-type MspA porins, mutant MspA porins, wild-type MspA paralog porins, wild-type MspA homolog porins, mutant MspA paralog porins, mutant MspA homolog porins, or single-chain Msp porins. Also provided are bacterial strains capable of inducible Msp porin expression.

Abstract: Examples of biomimetic codecs and biomimetic coding techniques are described herein. Morphologically-adaptive coding networks can be developed in accordance with energy dissipation driven “heat” generated by application of training data. The morphologically-adaptive coding networks may be representative of common features expected in an input signal or data stream. Decoding may proceed using the morphologically-adaptive coding network. Morphologically-adaptive coding networks may be used as a cortex that can be shared for boosting multimedia data compression rates and/or increasing the encode-decode fidelity of information content while the features remain queryable in encoded form. Examples of the biomimetic codecs and biomimetic coding techniques provide a broad-based technology platform that can be used in context-IDed multimedia storage, pattern recognition, and high-performance computing/big data management, the hallmarks of web- and cloud-based systems.

Abstract: The present disclosure generally relates to the methods and compositions to efficiently analyze polymer characteristics using nanopore-based assays. Specifically disclosed is a method for generating reference signals for polymer analysis in a nanopore system, wherein the nanopore system has a multi-subunit output signal resolution. The method comprises translocating a reference sequence through a nanopore to generate a plurality of reference output signals, wherein each possible multi-subunit sequence that can determine an output signal appears only once in the reference sequence. The output signals are compiled into a reference map for nanopore analysis of an analyte polymer. Also provided are methods and compositions for calibrating the nanopore system for optimized polymer analysis.

Abstract: Nucleotide sequences including a micro-dystrophin gene are provided. The micro-dystrophin genes may be operatively linked to a regulatory cassette. Methods of treating a subject having, or at risk of developing, muscular dystrophy, sarcopenia, heart disease, or cachexia are also provided. The methods may include administering a pharmaceutical composition including the micro-dystrophin gene and a delivery vehicle to a subject. Further, the methods may include administering the pharmaceutical composition a subject having Duchenne muscular dystrophy or Becker muscular dystrophy.

Abstract: A capacitive sensor system configured to measure capacitance, including a sample volume, a sample capacitive sensor configured to measure the capacitance of the sample volume without physical contact between the sample capacitive sensor and the sample volume, a control capacitive sensor, a differential sensing subsystem configured to measure a control sensor volume using the control capacitive sensor, and electrical circuitry connected to both the control capacitive sensor and the sample capacitive sensor.

Abstract: Methods of uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are provided. Kits for uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are also provided. The molecules to be labeled may include, but are not limited to, RNAs, cDNAs, DNAs, proteins, peptides, and/or antigens.

Abstract: Methods of uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are provided. Kits for uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are also provided. The molecules to be labeled may include, but are not limited to, RNAs, cDNAs, DNAs, proteins, peptides, and/or antigens.

Abstract: An example method for detecting stability of a medical implant is provided. The method includes (a) applying a force to the medical implant with a probe, (b) based on the applied force, determining a response signal associated with a vibration of the medical implant, (c) comparing the determined response signal with a computer model of the medical implant, and (d) based on the comparison, determining an angular stiffness coefficient of the medical implant, wherein the angular stiffness coefficient indicates a stability of the medical implant.

Abstract: Methods of uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are provided. Kits for uniquely labeling or barcoding molecules within a cell, a plurality of cells, and/or a tissue are also provided. The molecules to be labeled may include, but are not limited to, RNAs, cDNAs, DNAs, proteins, peptides, and/or antigens.

Abstract: Methods, devices, and systems for performing digital assays are provided. In certain aspects, the methods, devices, and systems can be used for the amplification and detection of nucleic acids. In certain aspects, the methods, devices, and systems can be used for the recognition, detection, and sizing of droplets in a volume. Also provided are compositions and kits suitable for use with the methods and devices of the present disclosure.

Abstract: The present disclosure provides a method of analyzing the structure of a glycan sample, the method including: receiving data indicative of one or more spectra of mass-to-charge ratio (m/z) versus relative abundance of the glycan sample from a mass spectrometer (MS) instrument; generating a ratio according to the following Equation: a a + b wherein a is a magnitude of one or more first peaks in the one or more spectra and b is the magnitude of one or more second peaks in the one or more spectra; determining that the ratio is within a range of a predetermined ratio; based on determining that the ratio is within the range of the predetermined ratio, determining that a predetermined structural characteristic is present in the glycan sample; and outputting an indication of the predetermined structural characteristic in the glycan sample.

Abstract: Methods for nanopore-based protein analysis are provided. The methods address the characterization of a target protein analyte, which has a dimension greater than an internal diameter of the nanopore tunnel, and which is also physically associated with a polymer. The methods further comprise applying an electrical potential to the nanopore system to cause the polymer to interact with the nanopore tunnel. The ion current through the nanopore is measured to provide a current pattern reflective of the structure of the portion of the polymer interacting with the nanopore tunnel. This is used as a metric for characterizing the associated protein that does not pass through the nanopore.

Abstract: A microperifusion system includes at least one perifusate reservoir module having N receptacles and at least one port to communicate a pressurizing gas into or out from the respective perifusate reservoir module. A corresponding perifusion chamber module having M microperifusion channels is mechanically coupleable to at least one perifusate reservoir module to thereby form, when coupled, a sealed fluid communication between a selected first number of the N receptacles and a selected second number of the microperifusion channels. A control system module is coupleable to each perifusate reservoir and each perifusion chamber to control a flow of pressuring gas communicated into or out from the perifusate reservoir sense an effect of a microperifusion test operation occurring in each microperifusion channel.

Abstract: A biological cement including algal biomatter, cement, and water. The present disclosure also provides methods of preparing the biological cement. The biological cement can be used in place of traditional cement, for instance by being incorporated into mortar or concrete for structural or other applications. The algal biomatter may include one or more of biomass from Chlorella, Spirulina (Arthrospira platensis), Saccharina latissima, Ulva spp. (such as U. lactuca or U. expensa), Agarophyton, Sargassum, Gracilaria parvispora, Halymenia hawaiiana or Caulerpa lentillifera.

Abstract: Bioplastic compositions and methods of making are described herein. The various mechanical and physical properties of the bioplastic may be varied by altering the thermoforming or incorporating an additive depending on the desired mechanical and physical properties of the end product. The bioplastic may be made entirely of biomatter and be backyard compostable.