Reproducing FSL's fMRI data analysis via Nipype:Relevance, challenges, and solutions

The "replication crisis" in neuroscientific research has led to calls for improving reproducibility. In traditional neuroscience analyses, irreproducibility may occur as a result of issues across various stages of the methodological process. For example, different operating systems, different software packages, and even different versions of the same package can lead to variable results. Nipype, an open-source Python project, integrates different neuroimaging software packages uniformly to improve the reproducibility of neuroimaging analyses. Nipype has the advantage over traditional software packages (e.g., FSL, ANFI, SPM, etc.) by (1) providing comprehensive software development frameworks and usage information, (2) improving computational efficiency, (3) facilitating reproducibility through sufficient details, and (4) easing the steep learning curve. Despite the rich tutorials it has provided, the Nipype community lacks a standard three-level GLM tutorial for FSL. Using the classical Flanker task dataset, we first precisely reproduce a three-level GLM analysis with FSL via Nipype. Next, we point out some undocumented discrepancies between Nipype and FSL functions that led to substantial differences in results. Finally, we provide revised Nipype code in re-executable notebooks that assure result invariability between FSL and Nipype. Our analyses, notebooks, and operating software specifications (e.g., docker build files) are available on the Open Science Framework platform

Discrete moving breather collisions in a Klein-Gordon chain of oscillators

We study collision processes of moving breathers with the same frequency, traveling with opposite directions within a Klein-Gordon chain of oscillators. Two types of collisions have been analyzed: symmetric and non-symmetric, head-on collisions. For low enough frequency the outcome is strongly dependent of the dynamical states of the two colliding breathers just before the collision. For symmetric collisions, several results can be observed: breather generation, with the formation of a trapped breather and two new moving breathers; breather reflection; generation of two new moving breathers; and breather fusion bringing about a trapped breather. For non-symmetric collisions the possible results are: breather generation, with the formation of three new moving breathers; breather fusion, originating a new moving breather; breather trapping with also breather reflection; generation of two new moving breathers; and two new moving breathers traveling as a ligand state. Breather annihilation has never been observed.Comment: 19 pages, 12 figure

Breather trapping and breather transmission in a DNA model with an interface

We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are oriented in opposite directions. The Hamiltonian of the Peyrard--Bishop model is augmented with a term that includes the dipole--dipole coupling between base pairs. Numerical simulations show the existence of two dynamical regimes. If the translational kinetic energy of a moving breather launched towards the interface is below a critical value, it is trapped in a region around the interface collecting vibrational energy. For an energy larger than the critical value, the breather is transmitted and continues travelling along the double strand with lower velocity. Reflection phenomena never occur. The same study has been carried out when a single dipole is oriented in opposite direction to the other ones. When moving breathers collide with the single inverted dipole, the same effects appear. These results emphasize the importance of this simple type of local inhomogeneity as it creates a mechanism for the trapping of energy. Finally, the simulations show that, under favorable conditions, several launched moving breathers can be trapped successively at the interface region producing an accumulation of vibrational energy. Moreover, an additional colliding moving breather can produce a saturation of energy and a moving breather with all the accumulated energy is transmitted to the chain.Comment: 15 pages, 11 figure

Patients with refractory cytomegalovirus (CMV) infection following allogeneic haematopoietic stem cell transplantation are at high risk for CMV disease and non-relapse mortality

AbstractPre-emptive therapy is an effective approach for cytomegalovirus (CMV) control; however, refractory CMV still occurs in a considerable group of recipients after allogeneic haematopoietic stem cell transplantation (allo-HSCT). Until now, hardly any data have been available about the clinical characteristics and risk factors of refractory CMV, or its potential harmful impact on the clinical outcome following allo-HSCT. We studied transplant factors affecting refractory CMV in the 100 days after allo-HSCT, and the impact of refractory CMV on the risk of CMV disease and non-relapse mortality (NRM). We retrospectively studied 488 consecutive patients with CMV infection after allo-HSCT. Patients with refractory CMV in the 100 days after allo-HSCT had a higher incidence of CMV disease and NRM than those without refractory CMV (11.9% vs. 0.8% and 17.1% vs. 8.3%, respectively). Multivariate analysis showed that refractory CMV infection in the 100 days after allo-HSCT was an independent risk factor for CMV disease (hazard ratio (HR) 10.539, 95% CI 2.467–45.015, p 0.001), and that refractory CMV infection within 60–100 days after allo-HSCT was an independent risk factor for NRM (HR 8.435, 95% CI 1.511–47.099, p 0.015). Clinical factors impacting on the risk of refractory CMV infection included receiving transplants from human leukocyte antigen-mismatched family donors (HR 2.012, 95% CI 1.603–2.546, p <0.001) and acute graft-versus-host disease (HR 1.905, 95% CI 1.352–2.686, p <0.001). We conclude that patients with refractory CMV infection during the early stage after allo-HSCT are at high risk for both CMV disease and NRM

Ieee access special section editorial: Cloud and big data-based next-generation cognitive radio networks

In cognitive radio networks (CRN), secondary users (SUs) are required to detect the presence of the licensed users, known as primary users (PUs), and to find spectrum holes for opportunistic spectrum access without causing harmful interference to PUs. However, due to complicated data processing, non-real-Time information exchange and limited memory, SUs often suffer from imperfect sensing and unreliable spectrum access. Cloud computing can solve this problem by allowing the data to be stored and processed in a shared environment. Furthermore, the information from a massive number of SUs allows for more comprehensive information exchanges to assist the

Relative Equilibria in the Four-Vortex Problem with Two Pairs of Equal Vorticities

We examine in detail the relative equilibria in the four-vortex problem where two pairs of vortices have equal strength, that is, \Gamma_1 = \Gamma_2 = 1 and \Gamma_3 = \Gamma_4 = m where m is a nonzero real parameter. One main result is that for m > 0, the convex configurations all contain a line of symmetry, forming a rhombus or an isosceles trapezoid. The rhombus solutions exist for all m but the isosceles trapezoid case exists only when m is positive. In fact, there exist asymmetric convex configurations when m < 0. In contrast to the Newtonian four-body problem with two equal pairs of masses, where the symmetry of all convex central configurations is unproven, the equations in the vortex case are easier to handle, allowing for a complete classification of all solutions. Precise counts on the number and type of solutions (equivalence classes) for different values of m, as well as a description of some of the bifurcations that occur, are provided. Our techniques involve a combination of analysis and modern and computational algebraic geometry

Stationary strings and branes in the higher-dimensional Kerr-NUT-(A)dS spacetimes

We demonstrate complete integrability of the Nambu-Goto equations for a stationary string in the general Kerr-NUT-(A)dS spacetime describing the higher-dimensional rotating black hole. The stationary string in D dimensions is generated by a 1-parameter family of Killing trajectories and the problem of finding a string configuration reduces to a problem of finding a geodesic line in an effective (D-1)-dimensional space. Resulting integrability of this geodesic problem is connected with the existence of hidden symmetries which are inherited from the black hole background. In a spacetime with p mutually commuting Killing vectors it is possible to introduce a concept of a $\xi$-brane, that is a p-brane with the worldvolume generated by these fields and a 1-dimensional curve. We discuss integrability of such $\xi$-branes in the Kerr-NUT-(A)dS spacetime.Comment: 8 pages, no figure

Competition between spin and charge polarized states in nanographene ribbons with zigzag edges

Effects of the nearest neighbor Coulomb interaction on nanographene ribbons with zigzag edges are investigated using the extended Hubbard model within the unrestricted Hartree-Fock approximation. The nearest Coulomb interaction stabilizes a novel electronic state with the opposite electric charges separated and localized along both edges, resulting in a finite electric dipole moment pointing from one edge to the other. This charge-polarized state competes with the peculiar spin-polarized state caused by the on-site Coulomb interaction and is stabilized by an external electric field.Comment: 4 pages; 4 figures; accepted for publication in Phys. Rev. B; related Web site: http://staff.aist.go.jp/k.harigaya/index_E.htm