Enhanced pinning and proliferation of matching effects in a superconducting film with a Penrose array of magnetic dots

The vortex dynamics in superconducting films deposited on top of a five-fold Penrose array of magnetic dots is studied by means of transport measurements. We show that in the low pinning regime (demagnetized dots) a few periodic and aperiodic matching features coexist. In the strong pinning regime (magnetized dots) a richer structure of unforeseen periodic and aperiodic vortex patterns appear giving rise to a clear enhancement of the critical current in a broader field range. Possible stable vortex configurations are determined by molecular dynamics simulations

Layering, freezing and re-entrant melting of hard spheres in soft confinement

Confinement can have a dramatic effect on the behavior of all sorts of particulate systems and it therefore is an important phenomenon in many different areas of physics and technology. Here, we investigate the role played by the softness of the confining potential. Using grand canonical Monte Carlo simulations, we determine the phase diagram of three-dimensional hard spheres that in one dimension are constrained to a plane by a harmonic potential. The phase behavior depends strongly on the density and on the stiffness of the harmonic confinement. Whilst we find the familiar sequence of confined hexagonal and square-symmetric packings, we do not observe any of the usual intervening ordered phases. Instead, the system phase separates under strong confinement, or forms a layered re-entrant liquid phase under weaker confinement. It is plausible that this behavior is due to the larger positional freedom in a soft confining potential and to the contribution that the confinement energy makes to the total free energy. The fact that specific structures can be induced or suppressed by simply changing the confinement conditions (e.g. in a dielectrophoretic trap) is important for applications that involve self-assembled structures of colloidal particles.Comment: 5 pages, 5 figure

Re-entrant melting and freezing in a model system of charged colloids

We studied the phase behavior of charged and sterically stabilized colloids using confocal microscopy in a less polar solvent (dielectric constant 5.4). Upon increasing the colloid volume fraction we found a transition from a fluid to a body centered cubic crystal at 0.0415+/-0.0005, followed by re-entrant melting at 0.1165+/-0.0015. A second crystal of different symmetry, random hexagonal close-packed, was formed at a volume fraction around 0.5, similar to that of hard spheres. We attribute the intriguing phase behavior to particle interactions that depend strongly on volume fraction, mainly due to changes in the colloid charge. In this low polarity system the colloids acquire charge through ion adsorption. The low ionic strength leads to fewer ions per colloid at elevated volume fractions and consequently a density-dependent colloid charge.Comment: 25 pages, 5 figures 1 tabl

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.

doi:10.1093/nar/gkn23

Age-Related Changes in Frontal Network Structural and Functional Connectivity in Relation to Bimanual Movement Control

Changes in both brain structure and neurophysiological function regulating homotopic as well as heterotopic interhemispheric interactions (IHIs) are assumed to be responsible for the bimanual performance deficits in older adults. However, how the structural and functional networks regulating bimanual performance decline in older adults, as well as the interplay between brain structure and function remain largely unclear. Using a dual-site transcranial magnetic stimulation paradigm, we examined the age-related changes in the interhemispheric effects from the dorsolateral prefrontal cortex and dorsal premotor cortex onto the contralateral primary motor cortex (M1) during the preparation of a complex bimanual coordination task in human. Structural properties of these interactions were assessed with diffusion-based fiber tractography. Compared with young adults, older adults showed performance declines in the more difficult bimanual conditions, less optimal brain white matter (WM) microstructure, and a decreased ability to regulate the interaction between dorsolateral prefrontal cortex and M1. Importantly, we found that WM microstructure, neurophysiological function, and bimanual performance were interrelated in older adults, whereas only the task-related changes in IHI predicted bimanual performance in young adults. These results reflect unique interactions between structure and function in the aging brain, such that declines in WM microstructural organization likely lead to dysfunctional regulation of IHI, ultimately accounting for bimanual performance deficits

The 2009 framework for undergraduate medical education in the Netherlands

The 2009 Framework defines the joint Dutch national learning outcomes to be attained by medical students after completing their three-year master programme in medicine. The Framework thus helps to guarantee to society at large and to patients in particular that medical graduates who are starting out as practitioners have attained a certain professional level. This level is the aggregate of the physicians’ target profile, physicians’ (sub-) competencies to be achieved and the list of issues relating to illness and health. In addition, the Framework also defines the profile of the bachelor and the learning outcomes of the bachelor programme in medicine

The 2009 framework for undergraduate medical education in the Netherlands

The 2009 Framework defines the joint Dutch national learning outcomes to be attained by medical students after completing their three-year master programme in medicine. The Framework thus helps to guarantee to society at large and to patients in particular that medical graduates who are starting out as practitioners have attained a certain professional level. This level is the aggregate of the physicians’ target profile, physicians’ (sub-) competencies to be achieved and the list of issues relating to illness and health. In addition, the Framework also defines the profile of the bachelor and the learning outcomes of the bachelor programme in medicine

Multi-netclust: an efficient tool for finding connected clusters in multi-parametric networks

Summary: Multi-netclust is a simple tool that allows users to extract connected clusters of data represented by different networks given in the form of matrices. The tool uses user-defined threshold values to combine the matrices, and uses a straightforward, memory-efficient graph algorithm to find clusters that are connected in all or in either of the networks. The tool is written in C/C++ and is available either as a form-based or as a command-line-based program running on Linux platforms. The algorithm is fast, processing a network of > 106 nodes and 108 edges takes only a few minutes on an ordinary computer

Microarray data mining using Bioconductor packages

BACKGROUND: This paper describes the results of a Gene Ontology (GO) term enrichment analysis of chicken microarray data using the Bioconductor packages. By checking the enriched GO terms in three contrasts, MM8-PM8, MM8-MA8, and MM8-MM24, of the provided microarray data during this workshop, this analysis aimed to investigate the host reactions in chickens occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. The results of GO enrichment analysis using GO terms annotated to chicken genes and GO terms annotated to chicken-human orthologous genes were also compared. Furthermore, a locally adaptive statistical procedure (LAP) was performed to test differentially expressed chromosomal regions, rather than individual genes, in the chicken genome after Eimeria challenge. RESULTS: GO enrichment analysis identified significant (raw p-value < 0.05) GO terms for all three contrasts included in the analysis. Some of the GO terms linked to, generally, primary immune responses or secondary immune responses indicating the GO enrichment analysis is a useful approach to analyze microarray data. The comparisons of GO enrichment results using chicken gene information and chicken-human orthologous gene information showed more refined GO terms related to immune responses when using chicken-human orthologous gene information, this suggests that using chicken-human orthologous gene information has higher power to detect significant GO terms with more refined functionality. Furthermore, three chromosome regions were identified to be significantly up-regulated in contrast MM8-PM8 (q-value < 0.01). CONCLUSION: Overall, this paper describes a practical approach to analyze microarray data in farm animals where the genome information is still incomplete. For farm animals, such as chicken, with currently limited gene annotation, borrowing gene annotation information from orthologous genes in well-annotated species, such as human, will help improve the pathway analysis results substantially. Furthermore, LAP analysis approach is a relatively new and very useful way to be applied in microarray analysis

Pioneering Alternative Forms of Collaboration

One key experience of human work, life, and play is people working together on a common goal. Yet this aspect of working together does not have one primary recognizable instantiation of what it means to work together. Words like collaboration and cooperation are often used to describe such instances, but even words like ‘collaboration’ don’t always have a neat formula for working through a collaboration. In this article we examine and reflect on our own collaborative experiences as a research group. We do this through an examination of past experiences, and through a method of writing that developed in our group. We have called this type of writing a ‘swarm,’ and we explore our working together, and swarm writing, as a new type of collaborative instantiation that allows scholars, their research, and their tools and processes to self-organize as complex, open systems