BBMS + + – basic bioinformatics meta-searcher

In this paper we present a Basic Bioinformatics Meta-searcher (BBMS), a web-based service aiming to simplify and integrate biological data searching through selected biological databases. BBMS facilitates biological data searching enabling multiple sources transparently, increasing research productivity as it avoids time consuming learning and parameterization of different search engines. As a complementary service, BBMS provides insight and links to common online bioinformatics tools. Users’ feedback when evaluating BBMS in terms of usability, usefulness and efficiency was very positive

Political activism across the life course

The study of political activism has neglected people’s personal and social relationships to time. Age, life course and generation have become increasing important experiences for understanding political participation and political outcomes (e.g. Brexit), and current policies of austerity across the world are affecting people of all ages. At a time when social science is struggling to understand the rapid and unexpected changes to the current political landscape, the essay argues that the study of political activism can be enriched by engaging with the temporal dimensions of people’s everyday social experiences because it enables the discovery of political activism in mundane activities as well as in banal spaces. The authors suggest that a values-based approach that focuses on people’s relationships of concern would be a suitable way to surface contemporary political sites and experiences of activism across the life course and for different generations

Repeated Testing in Eyewitness Memory: A Means to Improve Recall of a Negative Emotional Event

Participants viewed either a violent, arousing film or a non-violent, control version of the same film. After viewing the film, they made three successive attempts to recall details of the event. Participants who were exposed to the negative emotional event were better than control participants at recalling details of the event itself, but they were worse at recalling details that preceded or followed the violence. Both groups of participants recalled significantly more information over successive recall attempts, suggesting that memory impairment due to arousal can be alleviated by repeated testing. Repeated testing was also associated with a small but reliable increase in memory intrusions. The implications of these findings for research on hypermnesia and on the relationship between arousal and memory are discussed

Look Who’s Talking:Using creative, playful arts-based methods in research with young children

Young children are often ignored or marginalised in the drive to address children’s participation and their wider set of rights. This is the case generally in social research, as well as within the field of Arts-Based Education Research. This article contributes to the growing literature on young children’s involvement in arts-based research, by providing a reflective account of our learning and playful engagement with children using creative methods. This small pilot project forms part of a larger international project titled Look Who’s Talking: Eliciting the Voices of Children from Birth to Seven, led by Professor Kate Wall at the University of Strathclyde. Visiting one nursery in Scotland, we worked with approximately 30 children from 3 to 5 years old. Seeking to connect with their play-based nursery experiences, we invited children to participate in a range of arts-based activities including drawing, craft-making, sculpting, a themed ‘play basket’ with various props, puppetry and videography. In this article, we develop reflective, analytical stories of our successes and dilemmas in the project. We were keen to establish ways of working with children that centred their own creativity and play, shaped by the materials we provided but not directed by us. However, we struggled to balance our own agenda with the more open-ended methods we had used. We argue that an intergenerational approach to eliciting voice with young children – in which adults are not afraid to shape the agenda, but do so in responsive, gradual and sensitive ways – creates the potential for a more inclusive experience for children that also meets researcher needs

Direct observation of the coherent nuclear response after the absorption of a photon.

How molecules convert light energy to perform a specific transformation is a fundamental question in photophysics. Ultrafast spectroscopy reveals the kinetics associated with electronic energy flow, but little is known about how absorbed photon energy drives nuclear motion. Here we used ultrabroadband transient absorption spectroscopy to monitor coherent vibrational energy flow after photoexcitation of the retinal chromophore. In the proton pump bacteriorhodopsin, we observed coherent activation of hydrogen-out-of-plane wagging and backbone torsional modes that were replaced by unreactive coordinates in the solution environment, concomitant with a deactivation of the reactive relaxation pathway

The nature of singlet exciton fission in carotenoid aggregates.

Singlet exciton fission allows the fast and efficient generation of two spin triplet states from one photoexcited singlet. It has the potential to improve organic photovoltaics, enabling efficient coupling to the blue to ultraviolet region of the solar spectrum to capture the energy generally lost as waste heat. However, many questions remain about the underlying fission mechanism. The relation between intermolecular geometry and singlet fission rate and yield is poorly understood and remains one of the most significant barriers to the design of new singlet fission sensitizers. Here we explore the structure-property relationship and examine the mechanism of singlet fission in aggregates of astaxanthin, a small polyene. We isolate five distinct supramolecular structures of astaxanthin generated through self-assembly in solution. Each is capable of undergoing intermolecular singlet fission, with rates of triplet generation and annihilation that can be correlated with intermolecular coupling strength. In contrast with the conventional model of singlet fission in linear molecules, we demonstrate that no intermediate states are involved in the triplet formation: instead, singlet fission occurs directly from the initial 1B(u) photoexcited state on ultrafast time scales. This result demands a re-evaluation of current theories of polyene photophysics and highlights the robustness of carotenoid singlet fission.This work was supported by the EPSRC (UK) (EP/G060738/ 1), the European Community (LASERLAB-EUROPE, grant agreement no. 284464, EC’s Seventh Framework Programme; and Marie-Curie ITN-SUPERIOR, PITN-GA-2009-238177), and the Winton Programme for the Physics of Sustainability. G.C. acknowledges support by the European Research Council Advanced Grant STRATUS (ERC-2011-AdG No. 291198). J.C. acknowledges support by the Royal Society Dorothy Hodgkin Fellowship and The University of Sheffield’s Vice- Chancellor’s Fellowship scheme.This is the final published version. It was first made available by ACS at http://pubs.acs.org/doi/abs/10.1021/jacs.5b01130

Automatic Robust Neurite Detection and Morphological Analysis of Neuronal Cell Cultures in High-content Screening

Cell-based high content screening (HCS) is becoming an important and increasingly favored approach in therapeutic drug discovery and functional genomics. In HCS, changes in cellular morphology and biomarker distributions provide an information-rich profile of cellular responses to experimental treatments such as small molecules or gene knockdown probes. One obstacle that currently exists with such cell-based assays is the availability of image processing algorithms that are capable of reliably and automatically analyzing large HCS image sets. HCS images of primary neuronal cell cultures are particularly challenging to analyze due to complex cellular morphology. Here we present a robust method for quantifying and statistically analyzing the morphology of neuronal cells in HCS images. The major advantages of our method over existing software lie in its capability to correct non-uniform illumination using the contrast-limited adaptive histogram equalization method; segment neuromeres using Gabor-wavelet texture analysis; and detect faint neurites by a novel phase-based neurite extraction algorithm that is invariant to changes in illumination and contrast and can accurately localize neurites. Our method was successfully applied to analyze a large HCS image set generated in a morphology screen for polyglutaminemediated neuronal toxicity using primary neuronal cell cultures derived from embryos of a Drosophila Huntington’s Disease (HD) model.National Institutes of Health (U.S.) (Grant

Implementing the chronic care model for frail older adults in the Netherlands: study protocol of ACT (frail older adults: care in transition)

<p>Abstract</p> <p>Background</p> <p>Care for older adults is facing a number of challenges: health problems are not consistently identified at a timely stage, older adults report a lack of autonomy in their care process, and care systems are often confronted with the need for better coordination between health care professionals. We aim to address these challenges by introducing the geriatric care model, based on the chronic care model, and to evaluate its effects on the quality of life of community-dwelling frail older adults.</p> <p>Methods/design</p> <p>In a 2-year stepped-wedge cluster randomised clinical trial with 6-monthly measurements, the chronic care model will be compared with usual care. The trial will be carried out among 35 primary care practices in two regions in the Netherlands. Per region, practices will be randomly allocated to four allocation arms designating the starting point of the intervention. <it>Participants</it>: 1200 community-dwelling older adults aged 65 or over and their primary informal caregivers. Primary care physicians will identify frail individuals based on a composite definition of frailty and a polypharmacy criterion. Final inclusion criterion: scoring 3 or more on a disability case-finding tool. <it>Intervention</it>: Every 6 months patients will receive a geriatric in-home assessment by a practice nurse, followed by a tailored care plan. Expert teams will manage and train practice nurses. Patients with complex care needs will be reviewed in interdisciplinary consultations. <it>Evaluation</it>: We will perform an effect evaluation, an economic evaluation, and a process evaluation. Primary outcome is quality of life as measured with the Short Form-12 questionnaire. Effect analyses will be based on the “intention-to-treat” principle, using multilevel regression analysis. Cost measurements will be administered continually during the study period. A cost-effectiveness analysis and cost-utility analysis will be conducted comparing mean total costs to functional status, care needs and QALYs. We will investigate the level of implementation, barriers and facilitators to successful implementation and the extent to which the intervention manages to achieve the transition necessary to overcome challenges in elderly care.</p> <p>Discussion</p> <p>This is one of the first studies assessing the effectiveness, cost-effectiveness and implementation process of the chronic care model for frail community-dwelling older adults.</p> <p>Trial registration</p> <p>The Netherlands National Trial Register NTR2160.</p

Two-Dimensional Impulsively Stimulated Resonant Raman Spectroscopy of Molecular Excited States

Monitoring the interactions between electronic and vibrational degrees of freedom in molecules is critical to our understanding of their structural dynamics. This is typically hampered by the lack of spectroscopic probes able to detect different energy scales with high temporal and frequency resolution. Coherent Raman spectroscopy can combine the capabilities of multidimensional spectroscopy with structural sensitivity at ultrafast timescales. Here, we develop a three-color-based 2D impulsive stimulated Raman technique that can selectively probe vibrational mode couplings between different active sites in molecules by taking advantage of resonance Raman enhancement. Three temporally delayed pulses generate nuclear wave packets whose evolution reports on the underlying potential energy surface, which we decipher using a diagrammatic approach enabling us to assign the origin of the spectroscopic signatures. We benchmark the method by revealing vibronic couplings in the ultrafast dynamics following photoexcitation of the green fluorescent protein.C. S. acknowledges financial support by the Royal Commission for the Exhibition of 1851. G. Bat. acknowledges the “Avvio Alla Ricerca 2018” grant by Sapienza Universitá di Roma. T. W. acknowledges the Marie Curie Intra-European Fellowship (PIEF-GA-2013-623651) within the 7th European Community Framework Programme. S. M. gratefully acknowledges the support of the National Science Foundation Grant No. CHE-1663822