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

Survey on Vision-based Path Prediction

Path prediction is a fundamental task for estimating how pedestrians or vehicles are going to move in a scene. Because path prediction as a task of computer vision uses video as input, various information used for prediction, such as the environment surrounding the target and the internal state of the target, need to be estimated from the video in addition to predicting paths. Many prediction approaches that include understanding the environment and the internal state have been proposed. In this survey, we systematically summarize methods of path prediction that take video as input and and extract features from the video. Moreover, we introduce datasets used to evaluate path prediction methods quantitatively.Comment: DAPI 201

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

On the discovery of doubly-magic 48^{48}Ni

The paper reports on the first observation of doubly-magic Nickel-48 in an experimental at the SISSI/LISE3 facility of GANIL. Four Nickel-48 isotopes were identified. In addition, roughly 100 Nickel-49, 50 Iron-45, and 290 Chromium-42 isotopes were observed. This opens the possibility to search for two-proton emission from these nuclei.Comment: 4 pages, 3 figures, accepted for publication in Phys. Rev. Let

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

Dynamics of Transformation from Segregation to Mixed Wealth Cities

We model the dynamics of the Schelling model for agents described simply by a continuously distributed variable - wealth. Agents move to neighborhoods where their wealth is not lesser than that of some proportion of their neighbors, the threshold level. As in the case of the classic Schelling model where segregation obtains between two races, we find here that wealth-based segregation occurs and persists. However, introducing uncertainty into the decision to move - that is, with some probability, if agents are allowed to move even though the threshold level condition is contravened - we find that even for small proportions of such disallowed moves, the dynamics no longer yield segregation but instead sharply transition into a persistent mixed wealth distribution. We investigate the nature of this sharp transformation between segregated and mixed states, and find that it is because of a non-linear relationship between allowed moves and disallowed moves. For small increases in disallowed moves, there is a rapid corresponding increase in allowed moves, but this tapers off as the fraction of disallowed moves increase further and finally settles at a stable value, remaining invariant to any further increase in disallowed moves. It is the overall effect of the dynamics in the initial region (with small numbers of disallowed moves) that shifts the system away from a state of segregation rapidly to a mixed wealth state. The contravention of the tolerance condition could be interpreted as public policy interventions like minimal levels of social housing or housing benefit transfers to poorer households. Our finding therefore suggests that it might require only very limited levels of such public intervention - just sufficient to enable a small fraction of disallowed moves, because the dynamics generated by such moves could spur the transformation from a segregated to mixed equilibrium.Comment: 12 pages, 7 figure

Routine testing for IgG antibodies against hepatitis A virus in Israel

BACKGROUND: Viral hepatitis is highly endemic in Israel, with the hepatitis A virus (HAV) responsible for most cases. Improved socioeconomic factors, as well as the universal vaccination of infants (introduced in 1999) has resulted in a decline in infection rates in Israel. This study examines the benefits of routine testing for anti-HAV IgG in high-risk population. METHODS: A retrospective examination of the files of teenage and adult patients (aged 16–99 years; mean 33.9) in two primary care clinics found 1,017 patients who had been tested for anti-HAV IgG antibodies for either general healthcare screening or ongoing follow-up for chronic illness. Seropositive patients were then asked regarding recall of past hepatitis (i.e. jaundice, regardless of viral etiology); post-exposure prophylaxis with immune serum immunoglobulin (ISG); and active immunization with inactivated virus. Seronegative patients were subsequently sent for active immunization. RESULTS: Of the1,017 patient records studied (503 male, 514 female), a total of 692 were seropositive (354 males, 338 females; P = 0.113). Seropositivity rates increased with age (p < 0.005), and were highest among those born in Middle Eastern countries other than Israel (91.3%) and lowest among immigrants from South America (44.1%; P < 0.005). 456 of the seropositive patients were interviewed, of whom only 91 recalled past illness while 103 remembered receiving post-exposure prophylaxis (ISG) and 8 active vaccination. Those who were unaware of past infection were more likely to have been vaccinated with ISG than those who were aware (26.3% vs. 7.7%; p < 0.005). CONCLUSION: The relatively high prevalence rate of anti-HAV seropositivity in our study may me due to the fact that the study was conducted in a primary care clinic or that it took place in Jerusalem, a relatively poor and densely populated Israeli city. Most of the seropostive patients had no recollection of prior infection, which can be explained by the fact that most hepatitis A infections occur during childhood and are asymptomatic. Routine testing for anti-HAV IgG in societies endemic for HAV would help prevent seropositive patients from receiving either post-exposure or preventive immunization and target seronegative patients for preventive vaccination

Excitation and decay of projectile-like fragments formed in dissipative peripheral collisions at intermediate energies

Projectile-like fragments (PLF:15<=Z<=46) formed in peripheral and mid-peripheral collisions of 114Cd projectiles with 92Mo nuclei at E/A=50 MeV have been detected at very forward angles, 2.1 deg.<=theta_lab<=4.2 deg. Calorimetric analysis of the charged particles observed in coincidence with the PLF reveals that the excitation of the primary PLF is strongly related to its velocity damping. Furthermore, for a given V_PLF*, its excitation is not related to its size, Z_PLF*. For the largest velocity damping, the excitation energy attained is large, approximately commensurate with a system at the limiting temperatureComment: 5 pages, 6 figure

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