Abstract: Compositions and methods for highly specific nucleic acid probes and primers are provided. The probe system comprises a complement strand and a protector stand that form a partially double-stranded probe. The reaction standard free energy of hybridization between the probe and target nucleic acid as determined by Expression 1 (?G°rxn=?G°t-TC??G°nh-PC+(?G°v-TC??G°h-PC)) is from about ?4 kcal/mol to about +4 kcal/mol. Alternatively, the reaction standard free energy of hybridization between the probe and target nucleic acid is determined by Expression 1 to be within 5 kcal/mol of the standard free energy as determined by Expression 2 (?R? ln(([P]0?[C]0)/[C]0)]), where the [P]0 term of Expression 2 equals the concentration of the protector strand and the [C]0 term of Expression 2 equals the concentration of the complement strand. In addition, a method for on-the-fly fine tuning of a reaction using the present probe is provided.

Abstract: A gas engine is disclosed. The gas engine may include a combustion cylinder. The combustion cylinder may include an intake with an intake valve. The combustion cylinder may include an exhaust with an exhaust valve. The gas engine may include a gas admission valve assembly coupled to the intake. The gas admission assembly may include a trimmable electro-hydraulically actuatable gas admission valve to control a gas flow into the intake.

Abstract: The present disclosure provides, in various aspects and embodiments, methods and compositions for selectively amplifying a rare target nucleic acid and/or suppressing amplification of non-target nucleic acids with sequences similar to the rare target nucleic acid. The methods and composition are useful, for example, for detecting rare alleles among a population of wild-type alleles.

Abstract: An ignition system for a gaseous fuel engine includes an igniter and an actuator structured to apply an actuating force to a piston within the igniter, to autoignite an ignition charge of fuel and air within the igniter. A housing of the igniter includes a gas orifice having a flow area that is increased between a combustion pre-chamber in the igniter and a main combustion chamber in the engine, to limit velocity of outgoing combustion gases to below a threshold velocity for engine mis-fire.

Abstract: Systems, methods, and non-transitory computer readable media can receive a request to upload a file from a user. A server of a plurality of servers can be determined to process the request to upload the file. An indication of an amount of the file that has been received by the server prior to the request to upload the file can be provided. At least a portion of the file that has not been received by the server prior to the request to upload the file can be received.

Abstract: Provided are methods for characterizing nucleotide accessibility and nucleic acid structure at single nucleotide resolution, using a combination of low-yield bisulfite conversion and next-generation sequencing (NGS). Cytosine (C) nucleotides that are in base-paired states or bound to proteins, etc. are less accessible to chemical reactions and thus exhibit lower bisulfite conversion yields. Analysis of NGS results of a low-yield bisulfite conversion product can thus inform nucleotide accessibility and nucleic acid structure. Compared to other methods for chemical probing of nucleic acid structure, the present methods provide higher information throughput, because each NGS read simultaneously reports on the base pair status of multiple nucleotides.

Abstract: Provided herein are primers and primer systems having improved specificity and kinetics over existing primers, and methods of use thereof.

Abstract: A piston for an engine is provided. The piston includes a body having a crown disposed about a central axis. The crown includes an inner circumference and an outer circumference. The piston includes a central chamber transversely disposed within the body and recessed with respect to the crown. The piston includes a central mound disposed within the central chamber about the central axis. The piston also includes a bowl extending from the central mound towards the crown. The piston further includes a passageway provided on the inner circumference of the crown. The passageway includes a slot defined by a first surface inclined at a first angle with respect to the central axis. The slot is adapted to allow flow of a fuel from the central chamber towards the outer circumference of the crown.

Abstract: Provided herein are primers and primer systems having improved specificity and kinetics over existing primers, and methods of use thereof.

Abstract: Systems, methods, and non-transitory computer readable media can receive a request to upload a file from a user. A server of a plurality of servers can be determined to process the request to upload the file. An indication of an amount of the file that has been received by the server prior to the request to upload the file can be provided. At least a portion of the file that has not been received by the server prior to the request to upload the file can be received.

Abstract: This invention describes a method of controlling the hybridization yield of nucleic acid probes by adjusting the relative concentrations of auxiliary oligonucleotides to the probes and the targets. The auxiliary oligonucleotide is partially or fully complementary to either the probe or the target, and is released upon hybridization of the probe to the target.

Abstract: A piston for an engine is provided. The piston includes a body having a crown disposed about a central axis. The crown includes an inner circumference and an outer circumference. The piston includes a central chamber transversely disposed within the body and recessed with respect to the crown. The piston includes a central mound disposed within the central chamber about the central axis. The piston also includes a bowl extending from the central mound towards the crown. The piston further includes a passageway provided on the inner circumference of the crown. The passageway includes a slot defined by a first surface inclined at a first angle with respect to the central axis. The slot is adapted to allow flow of a fuel from the central chamber towards the outer circumference of the crown.

Abstract: Aspects of the present disclosure relate to systems, kits and methods that comprise a nucleic acid capture strand linked to a first dye molecule, a nucleic acid trigger strand longer than the capture strand and comprising (a) a capture domain that is complementary to the capture strand and (b) at least two concatenated domains, each of which comprises two subdomains, and a partially double-stranded nucleic acid comprising a single-stranded toehold domain having a nucleotide sequence complementary to one of the subdomains of the two subdomains of the concatenated domains, a double-stranded region linked to a second dye molecule and having a nucleotide sequence complementary to the other of the two subdomains of the concatenated domains, and a single-stranded hairpin loop having a nucleotide sequence that is complementary to the single-stranded toehold domain.

Abstract: The invention provides systems and methods for spatial sequestration of elements in nucleic acid circuits.

Abstract: The invention provides compositions and methods relating to self-assembly of structures of various size and shape complexity. The composition include synthetic single-stranded polymers having a backbone and pre-determined linear arrangement of monomers.

Abstract: The present invention provides an oligonucleotide composition including a blocker and a first primer oligonucleotide. The blocker oligonucleotide includes a first sequence having a target-neutral subsequence and a blocker variable subsequence. The non-target specific subsequence is flanked on its 3? and 5? ends by the target-neutral subsequence and is continuous with the target-neutral subsequence. The first primer oligonucleotide is sufficient to induce enzymatic extension; herein the first primer oligonucleotide includes a second sequence. The second sequence overlaps with the 5? end of the target-neutral subsequence by at least 5 nucleotides; herein the second sequence includes an overlapping subsequence and a non-overlapping subsequence. The second sequence does not include the non-target specific subsequence.

Abstract: The present disclosure describes the thermodynamic design and concentrations necessary to design probe compositions with desired optimal specificity that enable enrichment, detection, quantitation, purification, imaging, and amplification of rare-allele-bearing species of nucleic acids (prevalence <1%) in a large stoichiometric excess of a dominant-allele-bearing species (wildtype). Being an enzyme-free and homogeneous nucleic acid enrichment composition, this technology is broadly compatible with nearly all nucleic acid-based biotechnology, including plate reader and fluorimeter readout of nucleic acids, microarrays, PCR and other enzymatic amplification reactions, fluorescence barcoding, nanoparticle-based purification and quantitation, and in situ hybridization imaging technologies.

Abstract: Compositions and methods for highly specific nucleic acid probes and primers are provided. The probe system comprises a complement strand and a protector stand that form a partially double-stranded probe. The reaction standard free energy of hybridization between the probe and target nucleic acid as determined by Expression 1 (?G°rxn=?G°t-TC??G°nh-PC+(?G°v-TC??G°h-PC)) is from about ?4 kcal/mol to about +4 kcal/mol. Alternatively, the reaction standard free energy of hybridization between the probe and target nucleic acid is determined by Expression 1 to be within 5 kcal/mol of the standard free energy as determined by Expression 2 (?R? ln(([P]0?[C]0)/[C]0)]), where the [P]0 term of Expression 2 equals the concentration of the protector strand and the [C]0 term of Expression 2 equals the concentration of the complement strand. In addition, a method for on-the-fly fine tuning of a reaction using the present probe is provided.

Abstract: Nucleic acid probes are described comprising a universal component and a target dependent component. The universal component provides an economical advantage in that the universal component can retain any desired functional moiety, such as a fluorophore or other label which can be used with any target dependent component. Thus, the cost of designing target specific functionalized probes is significantly reduced with this probe system by limiting de novo synthesis to only the target dependent component of the probe for each desired target nucleic acid. Furthermore, the probe design of the present disclosure provides high target specificity demonstrating selective binding of the target in a 1% target load sample.

Abstract: The present disclosure provides, in various aspects and embodiments, methods and compositions for selectively amplifying a rare target nucleic acid and/or suppressing amplification of non-target nucleic acids with sequences similar to the rare target nucleic acid. The methods and composition are useful, for example, for detecting rare alleles among a population of wild-type alleles.