Genome-Wide Survey of MicroRNA - Transcription Factor Feed-Forward Regulatory Circuits in Human

In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops (FFL), in which a master transcription factor regulates a microRNA, and together with it, a set of joint target protein coding genes. The circuits were assembled with a two step procedure. We first constructed separately the transcriptional and post-transcriptional components of the human regulatory network by looking for conserved over-represented motifs in human and mouse promoters, and 3'-UTRs. Then, we combined the two subnetworks looking for mixed feed-forward regulatory interactions, finding a total of 638 putative (merged) FFLs. In order to investigate their biological relevance, we filtered these circuits using three selection criteria: (I) GeneOntology enrichment among the joint targets of the FFL, (II) independent computational evidence for the regulatory interactions of the FFL, extracted from external databases, and (III) relevance of the FFL in cancer. Most of the selected FFLs seem to be involved in various aspects of organism development and differentiation. We finally discuss a few of the most interesting cases in detail.Comment: 51 pages, 5 figures, 4 tables. Supporting information included. Accepted for publication in Molecular BioSystem

Lattice Boltzmann simulations of soft matter systems

This article concerns numerical simulations of the dynamics of particles immersed in a continuum solvent. As prototypical systems, we consider colloidal dispersions of spherical particles and solutions of uncharged polymers. After a brief explanation of the concept of hydrodynamic interactions, we give a general overview over the various simulation methods that have been developed to cope with the resulting computational problems. We then focus on the approach we have developed, which couples a system of particles to a lattice Boltzmann model representing the solvent degrees of freedom. The standard D3Q19 lattice Boltzmann model is derived and explained in depth, followed by a detailed discussion of complementary methods for the coupling of solvent and solute. Colloidal dispersions are best described in terms of extended particles with appropriate boundary conditions at the surfaces, while particles with internal degrees of freedom are easier to simulate as an arrangement of mass points with frictional coupling to the solvent. In both cases, particular care has been taken to simulate thermal fluctuations in a consistent way. The usefulness of this methodology is illustrated by studies from our own research, where the dynamics of colloidal and polymeric systems has been investigated in both equilibrium and nonequilibrium situations.Comment: Review article, submitted to Advances in Polymer Science. 16 figures, 76 page

Quantum control of hybrid nuclear-electronic qubits

Pulsed magnetic resonance is a wide-reaching technology allowing the quantum state of electronic and nuclear spins to be controlled on the timescale of nanoseconds and microseconds respectively. The time required to flip either dilute electronic or nuclear spins is orders of magnitude shorter than their decoherence times, leading to several schemes for quantum information processing with spin qubits. We investigate instead the novel regime where the eigenstates approximate 50:50 superpositions of the electronic and nuclear spin states forming "hybrid nuclear-electronic" qubits. Here we demonstrate quantum control of these states for the first time, using bismuth-doped silicon, in just 32 ns: this is orders of magnitude faster than previous experiments where pure nuclear states were used. The coherence times of our states are five orders of magnitude longer, reaching 4 ms, and are limited by the naturally-occurring 29Si nuclear spin impurities. There is quantitative agreement between our experiments and no-free-parameter analytical theory for the resonance positions, as well as their relative intensities and relative Rabi oscillation frequencies. In experiments where the slow manipulation of some of the qubits is the rate limiting step, quantum computations would benefit from faster operation in the hybrid regime.Comment: 20 pages, 8 figures, new data and simulation

Controlling spin relaxation with a cavity

Spontaneous emission of radiation is one of the fundamental mechanisms by which an excited quantum system returns to equilibrium. For spins, however, spontaneous emission is generally negligible compared to other non-radiative relaxation processes because of the weak coupling between the magnetic dipole and the electromagnetic field. In 1946, Purcell realized that the spontaneous emission rate can be strongly enhanced by placing the quantum system in a resonant cavity -an effect which has since been used extensively to control the lifetime of atoms and semiconducting heterostructures coupled to microwave or optical cavities, underpinning single-photon sources. Here we report the first application of these ideas to spins in solids. By coupling donor spins in silicon to a superconducting microwave cavity of high quality factor and small mode volume, we reach for the first time the regime where spontaneous emission constitutes the dominant spin relaxation mechanism. The relaxation rate is increased by three orders of magnitude when the spins are tuned to the cavity resonance, showing that energy relaxation can be engineered and controlled on-demand. Our results provide a novel and general way to initialise spin systems into their ground state, with applications in magnetic resonance and quantum information processing. They also demonstrate that, contrary to popular belief, the coupling between the magnetic dipole of a spin and the electromagnetic field can be enhanced up to the point where quantum fluctuations have a dramatic effect on the spin dynamics; as such our work represents an important step towards the coherent magnetic coupling of individual spins to microwave photons.Comment: 8 pages, 6 figures, 1 tabl

Relationship between eating behaviors and physical activity of preschoolers and their peers: a systematic review

Abstract: Objectives: Children learn by observing and imitating others, meaning that their eating behaviors and physical activity may be influenced by their peers. This paper systematically reviews how preschoolers’ eating behaviors and physical activity relate to their peers’ behaviors, and discusses avenues for future research. Methods: Six databases were searched for quantitative, peer-reviewed studies published up to July 2015 reporting on the correlates, predictors or effectiveness of peers on eating behaviors and physical activity in preschoolers. Risk of bias was independently assessed by two evaluators using the Quality Assessment Tool for Quantitative Studies. Results: Thirteen articles were included: six measured physical activity, and seven assessed eating behaviors. Four of the six physical activity studies reported that children were more active when peers were present, while large peer group size was negatively associated with physical activity in two cross-sectional studies. All nutrition interventions reported that children’s eating behaviors may be influenced by their peers. Conclusions: Although supported by weak evidence, peers appear to influence children’s eating behaviors and physical activity. However, this influence may be moderated by the number of peers, gender, age and the perceived status of the role models. Future obesity prevention interventions should consider involving peers as agents for positive eating behaviors and physical activity in preschoolers

Responsibility Ascriptions in Technology Development and Engineering: Three Perspectives

In the last decades increasing attention is paid to the topic of responsibility in technology development and engineering. The discussion of this topic is often guided by questions related to liability and blameworthiness. Recent discussions in engineering ethics call for a reconsideration of the traditional quest for responsibility. Rather than on alleged wrongdoing and blaming, the focus should shift to more socially responsible engineering, some authors argue. The present paper aims at exploring the different approaches to responsibility in order to see which one is most appropriate to apply to engineering and technology development. Using the example of the development of a new sewage water treatment technology, the paper shows how different approaches for ascribing responsibilities have different implications for engineering practice in general, and R&D or technological design in particular. It was found that there was a tension between the demands that follow from these different approaches, most notably between efficacy and fairness. Although the consequentialist approach with its efficacy criterion turned out to be most powerful, it was also shown that the fairness of responsibility ascriptions should somehow be taken into account. It is proposed to look for alternative, more procedural ways to approach the fairness of responsibility ascriptions

Electron spin coherence exceeding seconds in high purity silicon

Silicon is undoubtedly one of the most promising semiconductor materials for spin-based information processing devices. Its highly advanced fabrication technology facilitates the transition from individual devices to large-scale processors, and the availability of an isotopically-purified $^{28}$Si form with no magnetic nuclei overcomes what is a main source of spin decoherence in many other materials. Nevertheless, the coherence lifetimes of electron spins in the solid state have typically remained several orders of magnitude lower than what can be achieved in isolated high-vacuum systems such as trapped ions. Here we examine electron spin coherence of donors in very pure $^{28}$Si material, with a residual $^{29}$Si concentration of less than 50 ppm and donor densities of $10^{14-15}$ per cm$^3$. We elucidate three separate mechanisms for spin decoherence, active at different temperatures, and extract a coherence lifetime $T_2$ up to 2 seconds. In this regime, we find the electron spin is sensitive to interactions with other donor electron spins separated by ~200 nm. We apply a magnetic field gradient in order to suppress such interactions and obtain an extrapolated electron spin $T_2$ of 10 seconds at 1.8 K. These coherence lifetimes are without peer in the solid state by several orders of magnitude and comparable with high-vacuum qubits, making electron spins of donors in silicon ideal components of a quantum computer, or quantum memories for systems such as superconducting qubits.Comment: 18 pages, 4 figures, supplementary informatio

Evaluation of serum CEA, CYFRA21-1 and CA125 for the early detection of colorectal cancer using longitudinal preclinical samples

Blood-borne biomarkers for early detection of colorectal cancer (CRC) could markedly increase screening uptake. The aim of this study was to evaluate serum carcinoembryonic antigen (CEA), CYFRA21-1 and CA125 for the early detection of CRC in an asymptomatic cohort

Psychometric Properties of the Parent and Teacher Versions of the Strengths and Difficulties Questionnaire for 4- to 12-Year-Olds: A Review

Since its development, the Strengths and Difficulties Questionnaire (SDQ) has been widely used in both research and practice. The SDQ screens for positive and negative psychological attributes. This review aims to provide an overview of the psychometric properties of the SDQ for 4- to 12-year-olds. Results from 48 studies (N = 131,223) on reliability and validity of the parent and teacher SDQ are summarized quantitatively and descriptively. Internal consistency, test–retest reliability, and inter-rater agreement are satisfactory for the parent and teacher versions. At subscale level, the reliability of the teacher version seemed stronger compared to that of the parent version. Concerning validity, 15 out of 18 studies confirmed the five-factor structure. Correlations with other measures of psychopathology as well as the screening ability of the SDQ are sufficient. This review shows that the psychometric properties of the SDQ are strong, particularly for the teacher version. For practice, this implies that the use of the SDQ as a screening instrument should be continued. Longitudinal research studies should investigate predictive validity. For both practice and research, we emphasize the use of a multi-informant approach