Design and analysis of DNA strand displacement devices using probabilistic model checking

Designing correct, robust DNA devices is difficult because of the many possibilities for unwanted interference between molecules in the system. DNA strand displacement has been proposed as a design paradigm for DNA devices, and the DNA strand displacement (DSD) programming language has been developed as a means of formally programming and analysing these devices to check for unwanted interference. We demonstrate, for the first time, the use of probabilistic verification techniques to analyse the correctness, reliability and performance of DNA devices during the design phase. We use the probabilistic model checker prism, in combination with the DSD language, to design and debug DNA strand displacement components and to investigate their kinetics. We show how our techniques can be used to identify design flaws and to evaluate the merits of contrasting design decisions, even on devices comprising relatively few inputs. We then demonstrate the use of these components to construct a DNA strand displacement device for approximate majority voting. Finally, we discuss some of the challenges and possible directions for applying these methods to more complex designs

Electromagnetically Induced Transparency and Slow Light with Optomechanics

Controlling the interaction between localized optical and mechanical excitations has recently become possible following advances in micro- and nano-fabrication techniques. To date, most experimental studies of optomechanics have focused on measurement and control of the mechanical subsystem through its interaction with optics, and have led to the experimental demonstration of dynamical back-action cooling and optical rigidity of the mechanical system. Conversely, the optical response of these systems is also modified in the presence of mechanical interactions, leading to strong nonlinear effects such as Electromagnetically Induced Transparency (EIT) and parametric normal-mode splitting. In atomic systems, seminal experiments and proposals to slow and stop the propagation of light, and their applicability to modern optical networks, and future quantum networks, have thrust EIT to the forefront of experimental study during the last two decades. In a similar fashion, here we use the optomechanical nonlinearity to control the velocity of light via engineered photon-phonon interactions. Our results demonstrate EIT and tunable optical delays in a nanoscale optomechanical crystal device, fabricated by simply etching holes into a thin film of silicon (Si). At low temperature (8.7 K), we show an optically-tunable delay of 50 ns with near-unity optical transparency, and superluminal light with a 1.4 microseconds signal advance. These results, while indicating significant progress towards an integrated quantum optomechanical memory, are also relevant to classical signal processing applications. Measurements at room temperature and in the analogous regime of Electromagnetically Induced Absorption (EIA) show the utility of these chip-scale optomechanical systems for optical buffering, amplification, and filtering of microwave-over-optical signals.Comment: 15 pages, 9 figure

Prognostic model to predict postoperative acute kidney injury in patients undergoing major gastrointestinal surgery based on a national prospective observational cohort study.

Background: Acute illness, existing co-morbidities and surgical stress response can all contribute to postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery. The aim of this study was prospectively to develop a pragmatic prognostic model to stratify patients according to risk of developing AKI after major gastrointestinal surgery. Methods: This prospective multicentre cohort study included consecutive adults undergoing elective or emergency gastrointestinal resection, liver resection or stoma reversal in 2-week blocks over a continuous 3-month period. The primary outcome was the rate of AKI within 7 days of surgery. Bootstrap stability was used to select clinically plausible risk factors into the model. Internal model validation was carried out by bootstrap validation. Results: A total of 4544 patients were included across 173 centres in the UK and Ireland. The overall rate of AKI was 14·2 per cent (646 of 4544) and the 30-day mortality rate was 1·8 per cent (84 of 4544). Stage 1 AKI was significantly associated with 30-day mortality (unadjusted odds ratio 7·61, 95 per cent c.i. 4·49 to 12·90; P < 0·001), with increasing odds of death with each AKI stage. Six variables were selected for inclusion in the prognostic model: age, sex, ASA grade, preoperative estimated glomerular filtration rate, planned open surgery and preoperative use of either an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker. Internal validation demonstrated good model discrimination (c-statistic 0·65). Discussion: Following major gastrointestinal surgery, AKI occurred in one in seven patients. This preoperative prognostic model identified patients at high risk of postoperative AKI. Validation in an independent data set is required to ensure generalizability

Software-aided design of idealised programmable nucleic acid circuits

The idea to use nucleic acid as a substrate for design of programmable biomolecular circuits was first introduced almost four decades ago; however, up till now, the field of DNA computing holds many challenges and uncertainties to be discovered. This chapter describes the historical evolution of DNA programming along with its most noticeable breakthroughs till the current days, describes the basics of such important theoretical concepts as DNA strand displacement and Abstract Chemical Reaction Networks, and finally, familiarises the reader with various platforms for in silico synthesis and simulation of genetic circuits

Computation of ratios using chemical reactions and DNA strand displacements

Recent researches has focused on nucleic acids as a substrate for designing biomolecular circuits for in situ monitoring and control. A common approach is to express them by a set of idealised abstract chemical reaction networks (ACRNs). Here, we present new results on how abstract chemical reactions, viz., catalysis, annihilation and degradation, can be used to implement circuits that accurately compute ratio of two input signals. The input signals can be either constant-valued scalars or time-varying scalars or polynomials. We also characterise the robustness of our circuits to parameter variations, as would be encountered in wet-lab implementations

The role of explicit and implicit self-esteem in peer modeling of palatable food intake: A study on social media interaction among youngsters

Contains fulltext : 116712.pdf (publisher's version ) (Open Access)Objective: This experimental study investigated the impact of peers on palatable food intake of youngsters within a social media setting. To determine whether this effect was moderated by self-esteem, the present study examined the roles of global explicit self-esteem (ESE), body esteem (BE) and implicit self-esteem (ISE). Methods: Participants (N = 118; 38.1% boys; M age 11.14 +/-.79) were asked to play a computer game while they believed to interact online with a same-sex normal-weight remote confederate (i.e., instructed peer) who ate either nothing, a small or large amount of candy. Results: Participants modeled the candy intake of peers via a social media interaction, but this was qualified by their self-esteem. Participants with higher ISE adjusted their candy intake to that of a peer more closely than those with lower ISE when the confederate ate nothing compared to when eating a modest (beta = .26, p = .05) or considerable amount of candy (kcal) (beta = .32, p = .001). In contrast, participants with lower BE modeled peer intake more than those with higher BE when eating nothing compared to a considerable amount of candy (kcal) (beta = .21, p = .02); ESE did not moderate social modeling behavior. In addition, participants with higher discrepant or "damaged" self-esteem (i.e., high ISE and low ESE) modeled peer intake more when the peer ate nothing or a modest amount compared to a substantial amount of candy (kcal) (beta = -.24, p = .004; beta= -.26, p < .0001, respectively). Conclusion: Youngsters conform to the amount of palatable food eaten by peers through social media interaction. Those with lower body esteem or damaged self-esteem may be more at risk to peer influences on food intake.11 p

The role of explicit and implicit self-esteem in peer modeling of palatable food intake: A study on social media interaction among youngsters

Contains fulltext : 116712.pdf (publisher's version ) (Open Access)Objective: This experimental study investigated the impact of peers on palatable food intake of youngsters within a social media setting. To determine whether this effect was moderated by self-esteem, the present study examined the roles of global explicit self-esteem (ESE), body esteem (BE) and implicit self-esteem (ISE). Methods: Participants (N = 118; 38.1% boys; M age 11.14 +/-.79) were asked to play a computer game while they believed to interact online with a same-sex normal-weight remote confederate (i.e., instructed peer) who ate either nothing, a small or large amount of candy. Results: Participants modeled the candy intake of peers via a social media interaction, but this was qualified by their self-esteem. Participants with higher ISE adjusted their candy intake to that of a peer more closely than those with lower ISE when the confederate ate nothing compared to when eating a modest (beta = .26, p = .05) or considerable amount of candy (kcal) (beta = .32, p = .001). In contrast, participants with lower BE modeled peer intake more than those with higher BE when eating nothing compared to a considerable amount of candy (kcal) (beta = .21, p = .02); ESE did not moderate social modeling behavior. In addition, participants with higher discrepant or "damaged" self-esteem (i.e., high ISE and low ESE) modeled peer intake more when the peer ate nothing or a modest amount compared to a substantial amount of candy (kcal) (beta = -.24, p = .004; beta= -.26, p < .0001, respectively). Conclusion: Youngsters conform to the amount of palatable food eaten by peers through social media interaction. Those with lower body esteem or damaged self-esteem may be more at risk to peer influences on food intake.11 p