spFRET Using Alternating Excitation and FCS Reveals Progressive DNA Unwrapping in Nucleosomes

AbstractAccessibility to DNA wrapped in nucleosomes is essential for nuclear processes such as DNA transcription. Large conformational changes in nucleosome structure are required to facilitate protein binding to target sites within nucleosomal DNA. Transient unwrapping of DNA from nucleosome ends can provide an intrinsic exposure of wrapped DNA, allowing proteins to bind DNA that would otherwise be occluded in the nucleosome. The molecular details underlying these mechanisms remain to be resolved. Here we show how DNA unwrapping occurs progressively from both nucleosome ends. We performed single-pair fluorescence resonance energy transfer (spFRET) spectroscopy with alternating laser excitation (ALEX) on nucleosomes either in free solution or confined in a gel after PAGE separation. We combined ALEX-spFRET with a correlation analysis on selected bursts of fluorescence, to resolve a variety of unwrapped nucleosome conformations. The experiments reveal that nucleosomes are unwrapped with an equilibrium constant of ∼0.2–0.6 at nucleosome ends and ∼0.1 at a location 27 basepairs inside the nucleosome, but still remain stably associated. Our findings, obtained using a powerful combination of single-molecule fluorescence techniques and gel electrophoresis, emphasize the delicate interplay between DNA accessibility and condensation in chromatin

Flipping the classroom:an effective approach to deal with diversity at higher education

Even though the flipped classroom is an increasingly popular method in education, a literature search shows a gap in research on this method in higher education. This article describes an experiment with two central questions: (1) How do students and lecturers assess the effectiveness of the FC method? And (2) What are crucial design elements? To be able to answer these questions we designed an experiment within a large-size, interdisciplinary, course. For three years we carefully monitored and evaluated the course. A mixed-method approach was used to collect data. Our findings show a positive contribution of the FC approach to the learning experience of students. We also found that a strong link between theory and practice is essential in the course design; combined with active learning we were able to involve students and stimulate them to reach a deeper level of understanding. Moreover, we believe that the FC approach offers opportunities to have a large interdisciplinary group, with different learning needs, work together on higher attainment levels

High-Lift Propeller Noise Prediction for a Distributed Electric Propulsion Flight Demonstrator

Over the past several years, the use of electric propulsion technologies within aircraft design has received increased attention. The characteristics of electric propulsion systems open up new areas of the aircraft design space, such as the use of distributed electric propulsion (DEP). In this approach, electric motors are placed in many different locations to achieve increased efficiency through integration of the propulsion system with the airframe. Under a project called Scalable Convergent Electric Propulsion Technology Operations Research (SCEPTOR), NASA is designing a flight demonstrator aircraft that employs many "high-lift propellers" distributed upstream of the wing leading edge and two cruise propellers (one at each wingtip). As the high-lift propellers are operational at low flight speeds (take-off/approach flight conditions), the impact of the DEP configuration on the aircraft noise signature is also an important design consideration. This paper describes efforts toward the development of a mulit-fidelity aerodynamic and acoustic methodology for DEP high-lift propeller aeroacoustic modeling. Specifically, the PAS, OVERFLOW 2, and FUN3D codes are used to predict the aerodynamic performance of a baseline high-lift propeller blade set. Blade surface pressure results from the aerodynamic predictions are then used with PSU-WOPWOP and the F1A module of the NASA second generation Aircraft NOise Prediction Program to predict the isolated high-lift propeller noise source. Comparisons of predictions indicate that general trends related to angle of attack effects at the blade passage frequency are captured well with the various codes. Results for higher harmonics of the blade passage frequency appear consistent for the CFD based methods. Conversely, evidence of the need for a study of the effects of increased azimuthal grid resolution on the PAS based results is indicated and will be pursued in future work. Overall, the results indicate that the computational approach is acceptable for fundamental assessment of low-noise high-lift propeller designs. The extent to which the various approaches may be used in a complementary manner will be further established as measured data becomes available for validation. Ultimately, it is anticipated that this combined approach may be used to provide realistic incident source fields for acoustic shielding/scattering studies on various aircraft configurations

Predictors of outcome for severely emotionally disturbed children in treatment

Despite general agreement that severely emotionally disturbed children and adolescents are an "at risk" group, and that ongoing evaluation and research into the effectiveness of services provided for them is important, very little outcome evaluation actually takes place. The absence of well-conducted and appropriately interpreted studies is particularly notable for day or residential treatment programs, which cater for the most severely emotionally disturbed youths. This thesis outlines the main areas of conceptual, pragmatic and methodological confusion and neglect which impede progress in research in this area. It argues for plurality of data analytic strategies and research designs. It then critically reviews the reported findings about the effectiveness of day and residential treatment in specialist facilities, and the predictors of good outcomes for this treatment type. This review confirms that there is very little to guide practice. Having argued for the legitimacy of its methods and the necessity to address basic questions, the thesis reports the results of a naturalistic study based on data accumulated during a decade-long evaluative research program taking place at Arndell Child and Adolescent Unit, Sydney. The study addresses the question of what child, family and treatment variables predict outcome for 159 children and adolescents treated at this facility from 1990 to 1999. Statistically significant results with large effect size were obtained. Among the most disturbed subgroup of forty three children, (a) psychodynamic milieu-based treatment was shown to be more effective than the “empirically-validated” cognitive-behavioural treatment which superseded it in 1996, and (b) children from step-families showed better outcome than those from other family structures. Furthermore, it was found for the study sample as a whole that severe school-based problem behaviours were associated with a limited trajectory of improvement in home-based problem behaviour. These results are discussed with regard to implications for treatment, research methodology, policy and further studies

Denken over dieren : dier en ding, zegen en zorg

Dit rapport, dat in opdracht van het ministerie van Economische zaken, Landbouw en Innovatie is opgesteld, beschrijft een eerste trendanalyse (nulmeting) van (verwachte) morele opvattingen in Nederland over de omgang met dieren, nu en in de toekomst ten behoeve van het dierbeleid. In dit onderzoek is gestreefd naar de volgende inzichten: 1) de hedendaagse publieke opvattingen over de omgang met dieren; 2) de thema's die in de verschillende dierpraktijken spelen; 3) de verwachte ontwikkeling van deze thema's in de komende 20 jaar

On QBF Proofs and Preprocessing

QBFs (quantified boolean formulas), which are a superset of propositional formulas, provide a canonical representation for PSPACE problems. To overcome the inherent complexity of QBF, significant effort has been invested in developing QBF solvers as well as the underlying proof systems. At the same time, formula preprocessing is crucial for the application of QBF solvers. This paper focuses on a missing link in currently-available technology: How to obtain a certificate (e.g. proof) for a formula that had been preprocessed before it was given to a solver? The paper targets a suite of commonly-used preprocessing techniques and shows how to reconstruct certificates for them. On the negative side, the paper discusses certain limitations of the currently-used proof systems in the light of preprocessing. The presented techniques were implemented and evaluated in the state-of-the-art QBF preprocessor bloqqer.Comment: LPAR 201

Opening the GATE : systems thinking from the global assistive technology alliance

Purpose: This paper describes international actions to collaborate in the assistive technology (AT) arena and provides an update of programmes supporting AT globally. Methods: The World Health Organisation (WHO) identifies the severe global uneven distribution of resources, expertise and extensive unmet need for AT, as well the optimistic substantial capability for innovations and developments in appropriate and sustainable AT design, development and delivery. Systems thinking and market shaping are identified as means to address these challenges and leverage the ingenuity and expertise of AT stakeholders. Results: This paper is a ‘call to action’, showcasing emerging AT networks as exemplars of a distributed, but integrated mechanism for addressing AT needs globally, and describing the Global Alliance of Assistive Technology Organisations (GAATO) as a vehicle to facilitate this global networking. Conclusion: Partners in this Global Alliance aim to advance the field of assistive technology by promoting shared research, policy advocacy, educating people and organisations within and outside the field, teaching, training and knowledge transfer by pulling together broad-based membership organisations

Experimental validation of the quadratic constitutive relation in supersonic streamwise corner flows

The quadratic constitutive relation is a simple extension to the linear eddy-viscosity hypothesis and has shown some promise in improving the computation of flow along streamwise corner geometries. In order to further investigate these improvements, the quadratic model is validated by comparing RANS simulations of a Mach 2.5 wind tunnel flow with high-quality experimental velocity data. Careful set up and assessment of computations using detailed characterisation data of the overall flow field suggests a minimum expected discrepancy of approximately 3% for any experimental–computational velocity comparisons. The corner regions of the rectangular cross-section wind tunnel exhibit velocity differences of 7% between experimental data and computations with linear eddy-viscosity models, but these discrepancies are reduced to 4–5% when the quadratic constitutive relation is used. This improvement can be attributed to a better prediction of the corner boundary-layer structure, due to computations reproducing the stress-induced streamwise vortices which are known to exist in this flow field. However, the strength and position of these vortices do not correspond exactly with those in the measured flow. A further observation from this study is the appearance of additional, non-physical vortices when the value of the quadratic coefficient in the relation exceeds the recommended value of 0.3.This material is based upon work supported by the US Air Force Office of Scientific Research under award number FA9550–16–1–0430

A surface-patterned chip as a strong source of ultracold atoms for quantum technologies

Laser-cooled atoms are central to modern precision measurements. They are also increasingly important as an enabling technology for experimental cavity quantum electrodynamics, quantum information processing and matter–wave interferometry. Although significant progress has been made in miniaturizing atomic metrological devices, these are limited in accuracy by their use of hot atomic ensembles and buffer gases. Advances have also been made in producing portable apparatus that benefits from the advantages of atoms in the microkelvin regime. However, simplifying atomic cooling and loading using microfabrication technology has proved difficult. In this Letter we address this problem, realizing an atom chip that enables the integration of laser cooling and trapping into a compact apparatus. Our source delivers ten thousand times more atoms than previous magneto-optical traps with microfabricated optics and, for the first time, can reach sub-Doppler temperatures. Moreover, the same chip design offers a simple way to form stable optical lattices. These features, combined with simplicity of fabrication and ease of operation, make these new traps a key advance in the development of cold-atom technology for high-accuracy, portable measurement devices

Harm–benefit analysis – what is the added value?:A review of alternative strategies for weighing harms and benefits as part of the assessment of animal research

Animal experiments are widely required to comply with the 3Rs, to minimise harm to the animals and to serve certain purposes in order to be ethically acceptable. Recently, however, there has been a drift towards adding a so-called harm-benefit analysis as an additional requirement in assessing experiments. According to this, an experiment should only be allowed if there is a positive balance when the expected harm is weighed against the expected benefits. This paper aims to assess the added value of this requirement. Two models, the discourse model and the metric model, are presented. According to the former, the weighing of harms and benefits must be conducted by a committee in which different stakeholders engage in a dialogue. Research into how this works in practice, however, shows that in the absence of an explicit and clearly defined methodology, there are issues about transparency, consistency and fairness. According to the metric model, on the other hand, several dimensions of harms and benefits are defined beforehand and integrated in an explicit weighing scheme. This model, however, has the problem that it makes no real room for ethical deliberation of the sort committees undertake, and it has therefore been criticised for being too technocratic. Also, it is unclear who is to be held accountable for built-in ethical assumptions. Ultimately, we argue that the two models are not mutually exclusive and may be combined to make the most of their advantages while reducing the disadvantages of how harm-benefit analysis in typically undertaken