Probabilistic reasoning with a bayesian DNA device based on strand displacement

We present a computing model based on the DNA strand displacement technique which performs Bayesian inference. The model will take single stranded DNA as input data, representing the presence or absence of a specific molecular signal (evidence). The program logic encodes the prior probability of a disease and the conditional probability of a signal given the disease playing with a set of different DNA complexes and their ratios. When the input and program molecules interact, they release a different pair of single stranded DNA species whose relative proportion represents the application of Bayes? Law: the conditional probability of the disease given the signal. The models presented in this paper can empower the application of probabilistic reasoning in genetic diagnosis in vitro

Non-Typhi Salmonella gastroenteritis in children presenting to the emergency department: characteristics of patients with associated bacteraemia

ABSTRACTThe records of children with Salmonella gastroenteritis only (n = 97), and those with associated bacteraemia (n = 64), seen in one medical centre during a 12-year period, were analysed retrospectively. Mean patient age was 2.24 ± 2.8 years (range, 0.05–16 years), and 49% were male. Children with bacteraemia presented after a longer duration of symptoms (7.0 ± 6.9 vs. 3.9 ± 4.6 days, p 0.0002), and had higher erythrocyte sedimentation rates (45 ± 22 vs. 33 ± 22 mm/h, p < 0.02) and lactate dehydrogenase values (924 ± 113 vs. 685 ± 165 IU/L, p 0.001). There was a trend in bacteraemic children towards immunosuppression (6.3% vs. 1.0%, p 0.08) and a lower number of siblings (2.9 ± 1.9 vs. 3.8 ± 2.7, p 0.063). Non-bacteraemic children had a more severe clinical appearance, and a higher percentage had a moderate to bad general appearance (51.5 vs. 29.7%, p < 0.01), with dehydration (37.1 vs. 18.8%, p 0.02) and vomiting (58.8 vs. 39.0%, p 0.02). Laboratory dehydration indicators were also markedly worse in non-bacteraemic children, with urine specific gravity of 1020 ± 9.4 vs. 1013 ± 9.0 (p 0.0002), base excess of −4.2 ± 3.0 vs. −2.5 ± 3.4 mEq/L (p 0.01), and blood urea nitrogen of 10.1 ± 7.0 vs. 7.4 ± 4.5 mg% (p 0.002). Thus, the clinical presentation of bacteraemic children was more gradual, and associated gastroenteritis and dehydration was less pronounced. These findings may contribute in part to the inadvertent discharge of bacteraemic children from the emergency department

A mechanical Turing machine: blueprint for a biomolecular computer

We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and control by molecular recognition unleashing allosteric conformational changes. Logically, the device is not more complicated than biomolecular machines of the living cell, and all its operations are part of the standard repertoire of these machines; hence, a biomolecular embodiment of the device is not infeasible. If implemented, such a biomolecular device may operate in vivo, interacting with its biochemical environment in a program-controlled manner. In particular, it may ‘compute’ synthetic biopolymers and release them into its environment in response to input from the environment, a capability that may have broad pharmaceutical and biological applications

A Fast Algorithm Finding the Shortest Reset Words

In this paper we present a new fast algorithm finding minimal reset words for finite synchronizing automata. The problem is know to be computationally hard, and our algorithm is exponential. Yet, it is faster than the algorithms used so far and it works well in practice. The main idea is to use a bidirectional BFS and radix (Patricia) tries to store and compare resulted subsets. We give both theoretical and practical arguments showing that the branching factor is reduced efficiently. As a practical test we perform an experimental study of the length of the shortest reset word for random automata with $n$ states and 2 input letters. We follow Skvorsov and Tipikin, who have performed such a study using a SAT solver and considering automata up to $n=100$ states. With our algorithm we are able to consider much larger sample of automata with up to $n=300$ states. In particular, we obtain a new more precise estimation of the expected length of the shortest reset word $\approx 2.5\sqrt{n-5}$.Comment: COCOON 2013. The final publication is available at http://link.springer.com/chapter/10.1007%2F978-3-642-38768-5_1

Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotype

<p>Abstract</p> <p>Background</p> <p>A finite state machine manipulating information-carrying DNA strands can be used to perform autonomous molecular-scale computations at the cellular level.</p> <p>Results</p> <p>We propose a new finite state machine able to detect and correct aberrant molecular phenotype given by mutated genetic transcripts. The aberrant mutations trigger a cascade reaction: specific molecular markers as input are released and induce a spontaneous self-assembly of a wild type protein or peptide, while the mutational disease phenotype is silenced. We experimentally demostrated in <it>in vitro </it>translation system that a viable protein can be autonomously assembled.</p> <p>Conclusion</p> <p>Our work demostrates the basic principles of computational genes and particularly, their potential to detect mutations, and as a response thereafter administer an output that suppresses the aberrant disease phenotype and/or restores the lost physiological function.</p

Coulomb Effect: A Possible Probe for the Evolution of Hadronic Matter

Electromagnetic field produced in high-energy heavy-ion collisions contains much useful information, because the field can be directly related to the motion of the matter in the whole stage of the reaction. One can divide the total electromagnetic field into three parts, i.e., the contributions from the incident nuclei, non-participating nucleons and charged fluid, the latter consisting of strongly interacting hadrons or quarks. Parametrizing the space-time evolution of the charged fluid based on hydrodynamic model, we study the development of the electromagnetic field which accompanies the high-energy heavy-ion collisions. We found that the incident nuclei bring a rather strong electromagnetic field to the interaction region of hadrons or quarks over a few fm after the collision. On the other hand, the observed charged hadrons' spectra are mostly affected (Coulomb effect) by the field of the charged fluid. We compare the result of our model with experimental data and found that the model reproduces them well. The pion yield ratio pi^-/pi+ at a RHIC energy, Au+Au 100+100 GeV/nucleon, is also predicted.Comment: 23 pages, RevTex, 19 eps figures, revised versio

Towards Real-Time Head Pose Estimation: Exploring Parameter-Reduced Residual Networks on In-the-wild Datasets

Head poses are a key component of human bodily communication and thus a decisive element of human-computer interaction. Real-time head pose estimation is crucial in the context of human-robot interaction or driver assistance systems. The most promising approaches for head pose estimation are based on Convolutional Neural Networks (CNNs). However, CNN models are often too complex to achieve real-time performance. To face this challenge, we explore a popular subgroup of CNNs, the Residual Networks (ResNets) and modify them in order to reduce their number of parameters. The ResNets are modifed for different image sizes including low-resolution images and combined with a varying number of layers. They are trained on in-the-wild datasets to ensure real-world applicability. As a result, we demonstrate that the performance of the ResNets can be maintained while reducing the number of parameters. The modified ResNets achieve state-of-the-art accuracy and provide fast inference for real-time applicability.Comment: 32nd International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems (IEA/AIE 2019

Synchronizing Objectives for Markov Decision Processes

We introduce synchronizing objectives for Markov decision processes (MDP). Intuitively, a synchronizing objective requires that eventually, at every step there is a state which concentrates almost all the probability mass. In particular, it implies that the probabilistic system behaves in the long run like a deterministic system: eventually, the current state of the MDP can be identified with almost certainty. We study the problem of deciding the existence of a strategy to enforce a synchronizing objective in MDPs. We show that the problem is decidable for general strategies, as well as for blind strategies where the player cannot observe the current state of the MDP. We also show that pure strategies are sufficient, but memory may be necessary.Comment: In Proceedings iWIGP 2011, arXiv:1102.374

Massively parallel computing on an organic molecular layer

Current computers operate at enormous speeds of ~10^13 bits/s, but their principle of sequential logic operation has remained unchanged since the 1950s. Though our brain is much slower on a per-neuron base (~10^3 firings/s), it is capable of remarkable decision-making based on the collective operations of millions of neurons at a time in ever-evolving neural circuitry. Here we use molecular switches to build an assembly where each molecule communicates-like neurons-with many neighbors simultaneously. The assembly's ability to reconfigure itself spontaneously for a new problem allows us to realize conventional computing constructs like logic gates and Voronoi decompositions, as well as to reproduce two natural phenomena: heat diffusion and the mutation of normal cells to cancer cells. This is a shift from the current static computing paradigm of serial bit-processing to a regime in which a large number of bits are processed in parallel in dynamically changing hardware.Comment: 25 pages, 6 figure