Neo: an object model for handling electrophysiology data in multiple formats

Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. However, incompatible data models and file formats make it difficult to exchange data between these tools. This reduces scientific productivity, renders potentially useful analysis methods inaccessible and impedes collaboration between labs. A common representation of the core data would improve interoperability and facilitate data-sharing. To that end, we propose here a language-independent object model, named “Neo,” suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. As a concrete instantiation of this object model we have developed an open source implementation in the Python programming language. In addition to representing electrophysiology data in memory for the purposes of analysis and visualization, the Python implementation provides a set of input/output (IO) modules for reading/writing the data from/to a variety of commonly used file formats. Support is included for formats produced by most of the major manufacturers of electrophysiology recording equipment and also for more generic formats such as MATLAB. Data representation and data analysis are conceptually separate: it is easier to write robust analysis code if it is focused on analysis and relies on an underlying package to handle data representation. For that reason, and also to be as lightweight as possible, the Neo object model and the associated Python package are deliberately limited to representation of data, with no functions for data analysis or visualization. Software for neurophysiology data analysis and visualization built on top of Neo automatically gains the benefits of interoperability, easier data sharing and automatic format conversion; there is already a burgeoning ecosystem of such tools. We intend that Neo should become the standard basis for Python tools in neurophysiology.EC/FP7/269921/EU/Brain-inspired multiscale computation in neuromorphic hybrid systems/BrainScaleSDFG, 103586207, GRK 1589: Verarbeitung sensorischer Informationen in neuronalen SystemenBMBF, 01GQ1302, Nationaler Neuroinformatik Knote

Inter-species variation in colour perception

Inter-species variation in colour perception poses a serious problem for the view that colours are mind-independent properties. Given that colour perception varies so drastically across species, which species perceives colours as they really are? In this paper, I argue that all do. Specifically, I argue that members of different species perceive properties that are determinates of different, mutually compatible, determinables. This is an instance of a general selectionist strategy for dealing with cases of perceptual variation. According to selectionist views, objects simultaneously instantiate a plurality of colours, all of them genuinely mind-independent, and subjects select from amongst this plurality which colours they perceive. I contrast selectionist views with relationalist views that deny the mind-independence of colour, and consider some general objections to this strategy

Experiences of refugees and asylum seekers in general practice: a qualitative study

Background: There has been much debate regarding the refugee health situation in the UK. However most of the existing literature fails to take account of the opinions of refugees themselves. This study was established to determine the views of asylum seekers and refugees on their overall experiences in primary care and to suggest improvements to their care. Methods: Qualitative study of adult asylum seekers and refugees who had entered the UK in the last 10 years. The study was set in Barnet Refugee Walk in Service, London. 11 Semi structured interviews were conducted and analysed using framework analysis. Results: Access to GPs may be more difficult for failed asylum seekers and those without support from refugee agencies or family. There may be concerns amongst some in the refugee community regarding the access to and confidentiality of professional interpreters. Most participants stated their preference for GPs who offered advice rather than prescriptions. The stigma associated with refugee status in the UK may have led to some refugees altering their help seeking behaviour. Conclusion: The problem of poor access for those with inadequate support may be improved by better education and support for GPs in how to provide for refugees. Primary Care Trusts could also supply information to newly arrived refugees on how to access services. GPs should be aware that, in some situations, professional interpreters may not always be desired and that instead, it may be advisable to reach a consensus as to who should be used as an interpreter. A better doctor-patient experience resulting from improvements in access and communication may help to reduce the stigma associated with refugee status and lead to more appropriate help seeking behaviour. Given the small nature of our investigation, larger studies need to be conducted to confirm and to quantify these results

Hsp21potentiates antifungal drug tolerance in Candida albicans

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Humanities for medical students? A qualitative study of a medical humanities curriculum in a medical school program

BACKGROUND: Today, there is a trend towards establishing the medical humanities as a component of medical education. However, medical humanities programs that exist within the context of a medical school can be problematic. The aim of this study was to explore problems that can arise with the establishment of a medical humanities curriculum in a medical school program. METHODS: Our theoretical approach in this study is informed by derridean deconstruction and by post-structuralist analysis. We examined the ideology of the Humanities and Medicine program at Lund University, Sweden, the practical implementation of the program, and how ideology and practice corresponded. Examination of the ideology driving the humanities and medicine program was based on a critical reading of all available written material concerning the Humanities and Medicine project. The practice of the program was examined by means of a participatory observation study of one course, and by in-depth interviews with five students who participated in the course. Data was analysed using a hermeneutic editing approach. RESULTS: The ideological language used to describe the program calls it an interdisciplinary learning environment but at the same time shows that the conditions of the program are established by the medical faculty's agenda. In practice, the "humanities" are constructed, defined and used within a medical frame of reference. Medical students have interesting discussions, acquire concepts and enjoy the program. But they come away lacking theoretical structure to understand what they have learned. There is no place for humanities students in the program. CONCLUSION: A challenge facing cross-disciplinary programs is creating an environment where the disciplines have equal standing and contribution

Hyperspectral imaging of cuttlefish camouflage indicates good color match in the eyes of fish predators

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 108 (2011):9148-9153, doi:10.1073/pnas.1019090108.Camouflage is a widespread phenomenon throughout nature and an important anti-predator tactic in natural selection. Many visual predators have keen color perception, thus camouflage patterns should provide some degree of color matching in addition to other visual factors such as pattern, contrast, and texture. Quantifying camouflage effectiveness in the eyes of the predator is a challenge from the perspectives of both biology and optical imaging technology. Here we take advantage of Hyperspectral Imaging (HSI), which records full-spectrum light data, to simultaneously visualize color match and pattern match in the spectral and the spatial domains, respectively. Cuttlefish can dynamically camouflage themselves on any natural substrate and, despite their colorblindness, produce body patterns that appear to have high-fidelity color matches to the substrate when viewed directly by humans or with RGB images. Live camouflaged cuttlefish on natural backgrounds were imaged using HSI, and subsequent spectral analysis revealed that most reflectance spectra of individual cuttlefish and substrates were similar, rendering the color match possible. Modeling color vision of potential di- and tri-chromatic fish predators of cuttlefish corroborated the spectral match analysis and demonstrated that camouflaged cuttlefish show good color match as well as pattern match in the eyes of fish predators. These findings (i) indicate the strong potential of HSI technology to enhance studies 3 of biological coloration, and (ii) provide supporting evidence that cuttlefish can produce color-coordinated camouflage on natural substrates despite lacking color vision.We gratefully acknowledge financial support from the National Science Council of Taiwan NSC-98-2628-B-007-001-MY3 to CCC, from the Network Science Center at West Point and the Army Research Office to JKW, from the NDSEG Fellowship to JJA, and from ONR grant N000140610202 to RTH

Small but crucial : the novel small heat shock protein Hsp21 mediates stress adaptation and virulence in Candida albicans

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