Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits using DNA Strand Displacement

We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of DNA strand displacement. The design is scalable: all species of DNA strands can in principle be mixed and prepared in a single test tube, rather than requiring separate purification of each species, which is a barrier to large-scale synthesis. The design is time-responsive: the concentration of output species changes in response to the concentration of input species, so that time-varying inputs may be continuously processed. The design is digital: Boolean values of wires in the circuit are represented as high or low concentrations of certain species, and we show how to construct a single-input, single-output signal restoration gate that amplifies the difference between high and low, which can be distributed to each wire in the circuit to overcome signal degradation. This means we can achieve a digital abstraction of the analog values of concentrations. Finally, the design is energy-efficient: if input species are specified ideally (meaning absolutely 0 concentration of unwanted species), then output species converge to their ideal concentrations at steady-state, and the system at steady-state is in (dynamic) equilibrium, meaning that no energy is consumed by irreversible reactions until the input again changes. Drawbacks of our design include the following. If input is provided non-ideally (small positive concentration of unwanted species), then energy must be continually expended to maintain correct output concentrations even at steady-state. In addition, our fuel species - those species that are permanently consumed in irreversible reactions - are not "generic"; each gate in the circuit is powered by its own specific type of fuel species. Hence different circuits must be powered by different types of fuel. Finally, we require input to be given according to the dual-rail convention, so that an input of 0 is specified not only by the absence of a certain species, but by the presence of another. That is, we do not construct a "true NOT gate" that sets its output to high concentration if and only if its input's concentration is low. It remains an open problem to design scalable, time-responsive, digital, energy-efficient molecular circuits that additionally solve one of these problems, or to prove that some subset of their resolutions are mutually incompatible.Comment: version 2: the paper itself is unchanged from version 1, but the arXiv software stripped some asterisk characters out of the abstract whose purpose was to highlight words. These characters have been replaced with underscores in version 2. The arXiv software also removed the second paragraph of the abstract, which has been (attempted to be) re-inserted. Also, although the secondary subject is "Soft Condensed Matter", this classification was chosen by the arXiv moderators after submission, not chosen by the authors. The authors consider this submission to be a theoretical computer science paper

Cross reactive arrays of three-way junction sensors for steroid determination

This invention provides analyte sensitive oligonucleotide compositions for detecting and analyzing analytes in solution, including complex solutions using cross reactive arrays of analyte sensitive oligonucleotide compositions

Cut Length Distributions of Haylage Particles

Alfalfa is one of the most important crops for forage production. Traditional method of alfalfa conservation assumes hay preparation. However, nowadays it is also commonly processed in the form of silage and haylage. Physiological effects of forages that are included in diets depend on plant species, stage of maturity, method of preservation and diet composition. Physical characteristics of rations for ruminants are primarily influenced by dietary forage to concentrate ratio, type of forages and concentrates, and mean particle size of feeds. Length distribution of forage particles represents an important parameter for ruminant’s diet formulation, especially for dairy cattle. During silage production, harvest considerations should be focused to obtaining the adequate particle size distribution of the ensiling crop particles. This paper presents results of testing three contemporary types of self-propelled silage harvesters applied in the alfalfa haylage preparation: Claas Jaguar 950, Krone Big X 700 and Krone Big X 500. All machines were adapted with pick-up headers. In the study are analyzed length distributions of chopped alfalfa particles. Resulting frequency distributions of produced haylage are characterised by high mass percentage of the fraction comprehending the largest particles. It is also evident that harvester Class Jaguar 950 achieved the mean chopping length closest to preset value

An Infrastructure for acquiring high quality semantic metadata

Because metadata that underlies semantic web applications is gathered from distributed and heterogeneous data sources, it is important to ensure its quality (i.e., reduce duplicates, spelling errors, ambiguities). However, current infrastructures that acquire and integrate semantic data have only marginally addressed the issue of metadata quality. In this paper we present our metadata acquisition infrastructure, ASDI, which pays special attention to ensuring that high quality metadata is derived. Central to the architecture of ASDI is a erification engine that relies on several semantic web tools to check the quality of the derived data. We tested our prototype in the context of building a semantic web portal for our lab, KMi. An experimental evaluation omparing the automatically extracted data against manual annotations indicates that the verification engine enhances the quality of the extracted semantic metadata

Supplementary Feeding of Grazing Dairy Cows

The objective of this paper was to consider the effect of supplementary feeding of grazing dairy cows on dry matter intake (DMI), milk production and milk composition. Accurate estimations of total DMI and pasture DMI are important to the management of dairy grazing systems. The intakes of dry matter (DM) and net energy-NEL are lower on the pasture-only diet compared with cows supplementary fed with concentrate. Many pasture factors affect DMI, including pregrazing pasture mass and pasture allowance. Milk production of high producing grazing dairy cows in early lactation increases linearly as the amount of concentrate increases to 10 kg DM/day with a milk response of 1 kg milk/kg concentrate. In late lactation, increases are with a lower milk response per kilogram of supplemented concentrate. With the amount of concentrate supplementation, milk fat and protein yield increase while milk fat percentage decreases. Supplementation with rumen undegradable protein (RUP) is important for meeting requirements of grazing dairy cows, because the pasture has high ruminal crude protein (CP) degradability. Corn silage supplementation to grazing cows may increase milk production if pasture offered is restricted, but if pasture is offered ad libitum milk production does not change or can decrease. Supplementation of ruminally inert fat could have positive effect on milk production with concentrate supplemented at a lower rate

Influence of the Main Filter on QRS-amplitude and Duration in Human Electrocardiogram.

Accurate measurement of electrocardiograms (ECG) is critical for effective diagnosis of patient’s cardiac functions. Detailed examination of filters’ effects on ECG accuracy, reproducibility and robustness covering a wide range of available commercial products can provide valuable information on the relationship between quality and effectiveness of filters, and assessments of patients’ cardiac functions. In this study, ECG device with 12 leads and built-in filters used for ECG measurements was assessed on human volunteers. Results showed that with respect to measuring QRS wave duration and R-amplitude variation, there was a 4 % inaccuracy when the main filter was ON and OFF, and R-amplitude variation was most pronounced in the V4 lead. Accordingly, variability of R-amplitude and length of QRS wave can be reduced by the use of appropriate lead, and filter activation during the ECG assessment

A review of recent perspectives on biomechanical risk factors associated with anterior cruciate ligament injury

There is considerable evidence to support a number of biomechanical risk factors associated with non-contact anterior cruciate ligament (ACL) injury. This paper aimed to review these biomechanical risk factors and highlight future directions relating to them. Current perspectives investigating trunk position and relationships between strength, muscle activity and biomechanics during landing/cutting highlight the importance of increasing hamstring muscle force during dynamic movements through altering strength, muscle activity, muscle length and contraction velocity. In particular, increased trunk flexion during landing/cutting and greater hamstring strength are likely to increase hamstring muscle force during landing and cutting which have been associated with reduced ACL injury risk. Decision making has also been shown to influence landing biomechanics and should be considered when designing tasks to assess landing/cutting biomechanics. Coaches should therefore promote hamstring strength training and active trunk flexion during landing and cutting in an attempt to reduce ACL injury risk.Peer reviewe

DNA hybridization catalysts and catalyst circuits

Practically all of life's molecular processes, from chemical synthesis to replication, involve enzymes that carry out their functions through the catalysis of metastable fuels into waste products. Catalytic control of reaction rates will prove to be as useful and ubiquitous in DNA nanotechnology as it is in biology. Here we present experimental results on the control of the decay rates of a metastable DNA "fuel". We show that the fuel complex can be induced to decay with a rate about 1600 times faster than it would decay spontaneously. The original DNA hybridization catalyst [15] achieved a maximal speed-up of roughly 30. The fuel complex discussed here can therefore serve as the basic ingredient for an improved DNA hybridization catalyst. As an example application for DNA hybridization catalysts, we propose a method for implementing arbitrary digital logic circuits