Ten Quick Tips for Using a Raspberry Pi

Much of biology (and, indeed, all of science) is becoming increasingly computational. We tend to think of this in regards to algorithmic approaches and software tools, as well as increased computing power. There has also been a shift towards slicker, packaged solutions--which mirrors everyday life, from smart phones to smart homes. As a result, it's all too easy to be detached from the fundamental elements that power these changes, and to see solutions as "black boxes". The major goal of this piece is to use the example of the Raspberry Pi--a small, general-purpose computer--as the central component in a highly developed ecosystem that brings together elements like external hardware, sensors and controllers, state-of-the-art programming practices, and basic electronics and physics, all in an approachable and useful way. External devices and inputs are easily connected to the Pi, and it can, in turn, control attached devices very simply. So whether you want to use it to manage laboratory equipment, sample the environment, teach bioinformatics, control your home security or make a model lunar lander, it's all built from the same basic principles. To quote Richard Feynman, "What I cannot create, I do not understand".Comment: 12 pages, 2 figure

Sense of agency, associative learning, and schizotypy

Despite the fact that the role of learning is recognised in empirical and theoretical work on sense of agency (SoA), the nature of this learning has, rather surprisingly, received little attention. In the present study we consider the contribution of associative mechanisms to SoA. SoA can be measured quantitatively as a temporal linkage between voluntary actions and their external effects. Using an outcome blocking procedure, it was shown that training action-outcome associations under conditions of increased surprise augmented this temporal linkage. Moreover, these effects of surprise were correlated with schizotypy scores, suggesting that individual differences in higher level experiences are related to associative learning and to its impact on SoA. These results are discussed in terms of models of SoA, and our understanding of disrupted SoA in certain disorders

Impact of efavirenz pharmacokinetics and pharmacogenomics on neuropsychological performance in older HIV-infected patients

Pharmacokinetics (PK) and pharmacodynamics of efavirenz and its 8-hydroxy metabolite (8-OH-efavirenz) have not been robustly evaluated in older HIV-infected persons

Consistency and interpretation of changes in millimeter-scale cortical intrinsic curvature across three independent datasets in schizophrenia.

Several studies have sought to test the neurodevelopmental hypothesis of schizophrenia through analysis of cortical gyrification. However, to date, results have been inconsistent. A possible reason for this is that gyrification measures at the centimeter scale may be insensitive to subtle morphological changes at smaller scales. The lack of consistency in such studies may impede further interpretation of cortical morphology as an aid to understanding the etiology of schizophrenia. In this study we developed a new approach, examining whether millimeter-scale measures of cortical curvature are sensitive to changes in fundamental geometric properties of the cortical surface in schizophrenia. We determined and compared millimeter-scale and centimeter-scale curvature in three separate case-control studies; specifically two adult groups and one adolescent group. The datasets were of different sizes, with different ages and gender-spreads. The results clearly show that millimeter-scale intrinsic curvature measures were more robust and consistent in identifying reduced gyrification in patients across all three datasets. To further interpret this finding we quantified the ratio of expansion in the upper and lower cortical layers. The results suggest that reduced gyrification in schizophrenia is driven by a reduction in the expansion of upper cortical layers. This may plausibly be related to a reduction in short-range connectivity

Differential tangential expansion as a mechanism for cortical gyrification.

Gyrification, the developmental buckling of the cortex, is not a random process-the forces that mediate expansion do so in such a way as to generate consistent patterns of folds across individuals and even species. Although the origin of these forces is unknown, some theories have suggested that they may be related to external cortical factors such as axonal tension. Here, we investigate an alternative hypothesis, namely, whether the differential tangential expansion of the cortex alone can account for the degree and pattern-specificity of gyrification. Using intrinsic curvature as a measure of differential expansion, we initially explored whether this parameter and the local gyrification index (used to quantify the degree of gyrification) varied in a regional-specific pattern across the cortical surface in a manner that was replicable across independent datasets of neurotypicals. Having confirmed this consistency, we further demonstrated that within each dataset, the degree of intrinsic curvature of the cortex was predictive of the degree of cortical folding at a global and regional level. We conclude that differential expansion is a plausible primary mechanism for gyrification, and propose that this perspective offers a compelling mechanistic account of the co-localization of cytoarchitecture and cortical folds

High Energy Hadron-Nucleus Cross Sections and Their Extrapolation to Cosmic Ray Energies

Old models of the scattering of composite systems based on the Glauber model of multiple diffraction are applied to hadron-nucleus scattering. We obtain an excellent fit with only two free parameters to the highest energy hadron-nucleus data available. Because of the quality of the fit and the simplicity of the model it is argued that it should continue to be reliable up to the highest cosmic ray energies. Logarithmic extrapolations of proton-proton and proton-antiproton data are used to calculate the proton-air cross sections at very high energy. Finally, it is observed that if the exponential behavior of the proton-antiproton diffraction peak continues into the few TeV energy range it will violate partial wave unitarity. We propose a simple modification that will guarantee unitarity throughout the cosmic ray energy region.Comment: 8 pages, 9 postscript figures. This manuscript replaces a partial manuscript incorrectly submitte

Assessment, Quantification, and Management of Fracture Pain: from Animals to the Clinic

Purpose of review: Fractures are painful and disabling injuries that can occur due to trauma, especially when compounded with pathologic conditions, such as osteoporosis in older adults. It is well documented that acute pain management plays an integral role in the treatment of orthopedic patients. There is no current therapy available to completely control post-fracture pain that does not interfere with bone healing or have major adverse effects. In this review, we focus on recent advances in the understanding of pain behaviors post-fracture. Recent findings: We review animal models of bone fracture and the assays that have been developed to assess and quantify spontaneous and evoked pain behaviors, including the two most commonly used assays: dynamic weight bearing and von Frey testing to assess withdrawal from a cutaneous (hindpaw) stimulus. Additionally, we discuss the assessment and quantification of fracture pain in the clinical setting, including the use of numeric pain rating scales, satisfaction with pain relief, and other biopsychosocial factor measurements. We review how pain behaviors in animal models and clinical cases can change with the use of current pain management therapies. We conclude by discussing the use of pain behavioral analyses in assessing potential therapeutic treatment options for addressing acute and chronic fracture pain without compromising fracture healing. There currently is a lack of effective treatment options for fracture pain that reliably relieve pain without potentially interfering with bone healing. Continued development and verification of reliable measurements of fracture pain in both pre-clinical and clinical settings is an essential aspect of continued research into novel analgesic treatments for fracture pain

Superficial simplicity of the 2010 El Mayor–Cucapah earthquake of Baja California in Mexico

The geometry of faults is usually thought to be more complicated at the surface than at depth and to control the initiation, propagation and arrest of seismic ruptures. The fault system that runs from southern California into Mexico is a simple strike-slip boundary: the west side of California and Mexico moves northwards with respect to the east. However, the M_w 7.2 2010 El Mayor–Cucapah earthquake on this fault system produced a pattern of seismic waves that indicates a far more complex source than slip on a planar strike-slip fault. Here we use geodetic, remote-sensing and seismological data to reconstruct the fault geometry and history of slip during this earthquake. We find that the earthquake produced a straight 120-km-long fault trace that cut through the Cucapah mountain range and across the Colorado River delta. However, at depth, the fault is made up of two different segments connected by a small extensional fault. Both segments strike N130° E, but dip in opposite directions. The earthquake was initiated on the connecting extensional fault and 15 s later ruptured the two main segments with dominantly strike-slip motion. We show that complexities in the fault geometry at depth explain well the complex pattern of radiated seismic waves. We conclude that the location and detailed characteristics of the earthquake could not have been anticipated on the basis of observations of surface geology alone

Reconstruction for Time-Domain In Vivo EPR 3D Multigradient Oximetric Imaging—A Parallel Processing Perspective

Three-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23 × 23 × 23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet). The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time