Signatures of Secondary Collisionless Magnetic Reconnection Driven by Kink Instability of a Flux Rope

The kinetic features of secondary magnetic reconnection in a single flux rope undergoing internal kink instability are studied by means of three-dimensional Particle-in-Cell simulations. Several signatures of secondary magnetic reconnection are identified in the plane perpendicular to the flux rope: a quadrupolar electron and ion density structure and a bipolar Hall magnetic field develop in proximity of the reconnection region. The most intense electric fields form perpendicularly to the local magnetic field, and a reconnection electric field is identified in the plane perpendicular to the flux rope. An electron current develops along the reconnection line in the opposite direction of the electron current supporting the flux rope magnetic field structure. Along the reconnection line, several bipolar structures of the electric field parallel to the magnetic field occur making the magnetic reconnection region turbulent. The reported signatures of secondary magnetic reconnection can help to localize magnetic reconnection events in space, astrophysical and fusion plasmas

Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology.Comment: Minor update

Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology

Comparison of Leishmania killicki (syn. L-tropica) and Leishmania tropica population structure in Maghreb by microsatellite typing

Leishmania (L.) killicki (syn. L. tropica), which causes cutaneous leishmaniasis in Maghreb, was recently described in this region and identified as a subpopulation of L. tropica. The present genetic analysis was conducted to explore the spatio-temporal distribution of L. killicki (syn. L. tropica) and its transmission dynamics. To better understand the evolution of this parasite, its population structure was then compared with that of L. tropica populations from Morocco. In total 198 samples including 85 L. killicki (syn. L. tropica) (from Tunisia, Algeria and Libya) and 113 L. tropica specimens (all from Morocco) were tested. Theses samples were composed of 168 Leishmania strains isolated from human skin lesions, 27 DNA samples from human skin lesion biopsies, two DNA samples from Ctenodactylus gundi bone marrow and one DNA sample from a Phlebotomus sergenti female. The sample was analyzed by using MultiLocus Enzyme Electrophoresis (MLEE) and MultiLocus Microsatellite Typing (MLMT) approaches. Analysis of the MLMT data support the hypothesis that L. killicki (syn. L. tropica) belongs to the L. tropica complex, despite its strong genetic differentiation, and that it emerged from this taxon by a founder effect. Moreover, it revealed a strong structuring in L. killicki (syn. L. tropica) between Tunisia and Algeria and within the different Tunisian regions, suggesting low dispersion of L. killicki (syn. L. tropica) in space and time. Comparison of the L. tropica (exclusively from Morocco) and L. killicki (syn. L. tropica) population structures revealed distinct genetic organizations, reflecting different epidemiological cycles

Filling a blank on the map: 60 years of fisheries in Equatorial Guinea

Despite a scarcity of pertinent information, it has been possible to reconstruct time series of marine fisheries catches for Equatorial Guinea from 1950 to 2010 using per capita fish consumption and population numbers for small-scale fisheries, catch rates and number of vessels for industrial fisheries and discard rates to estimate the discarded bycatch. Small-scale fisheries, industrial large-scale fisheries, domestic and legal and illegal foreign fisheries and their discards are all included. Total catches were estimated at 2.7 million tonnes over the time period considered, of which 653 000 t were caught domestically compared to 187 000 t reported by FAO. This shows that fisheries have more importance for Equatorial Guinea's food security than the official data suggest. In contrast to what is suggested by official figures, fisheries were shown to be strongly impacted by civil and political unrest; notably, they declined overall because of civil and political conflicts, socio-demographic dynamics, and a growing role of the newly discovered oil resources, which directly and indirectly threaten the food security of the people of Equatorial Guinea

Milne quantization for non-Hermitian systems

We generalize the Milne quantization condition to non-Hermitian systems. In the general case the underlying nonlinear Ermakov–Milne–Pinney equation needs to be replaced by a nonlinear integral differential equation. However, when the system is PT-symmetric or/and quasi/pseudo-Hermitian the equations simplify and one may employ the original energy integral to determine its quantization. We illustrate the working of the general framework with the Swanson model and two explicit examples for pairs of supersymmetric Hamiltonians. In one case both partner Hamiltonians are Hermitian and in the other a Hermitian Hamiltonian is paired by a Darboux transformation to a non-Hermitian one

Universal Vectorial and Ultrasensitive Nanomechanical Force Field Sensor

Miniaturization of force probes into nanomechanical oscillators enables ultrasensitive investigations of forces on dimensions smaller than their characteristic length scale. Meanwhile it also unravels the force field vectorial character and how its topology impacts the measurement. Here we expose an ultrasensitive method to image 2D vectorial force fields by optomechanically following the bidimensional Brownian motion of a singly clamped nanowire. This novel approach relies on angular and spectral tomography of its quasi frequency-degenerated transverse mechanical polarizations: immersing the nanoresonator in a vectorial force field does not only shift its eigenfrequencies but also rotate eigenmodes orientation as a nano-compass. This universal method is employed to map a tunable electrostatic force field whose spatial gradients can even take precedence over the intrinsic nanowire properties. Enabling vectorial force fields imaging with demonstrated sensitivities of attonewton variations over the nanoprobe Brownian trajectory will have strong impact on scientific exploration at the nanoscale

Cardiometabolic risk assessments by body mass index z-score or waist-to-height ratio in a multiethnic sample of sixth-graders

Convention defines pediatric adiposity by the body mass index -score (BMIz) referenced to normative growth charts. Waist-to-height ratio (WHtR) does not depend on sex-and-age references. In the HEALTHY Study enrollment sample, we compared BMIz with WHtR for ability to identify adverse cardiometabolic risk. Among 5,482 sixth-grade students from 42 middle schools, we estimated explanatory variations (R2) and standardized beta coefficients of BMIz or WHtR for cardiometabolic risk factors: insulin resistance (HOMA-IR), lipids, blood pressures, and glucose. For each risk outcome variable, we prepared adjusted regression models for four subpopulations stratified by sex and high versus lower fatness. For HOMA-IR, R2 attributed to BMIz or WHtR was 19%–28% among high-fatness and 8%–13% among lower-fatness students. for lipid variables was 4%–9% among high-fatness and 2%–7% among lower-fatness students. In the lower-fatness subpopulations, the standardized coefficients for total cholesterol/HDL cholesterol and triglycerides tended to be weaker for BMIz (0.13–0.20) than for WHtR (0.17–0.28). Among high-fatness students, BMIz and WHtR correlated with blood pressures for Hispanics and whites, but not black boys (systolic) or girls (systolic and diastolic). In 11-12 year olds, assessments by WHtR can provide cardiometabolic risk estimates similar to conventional BMIz without requiring reference to a normative growth chart

In situ visualization of large-scale turbulence simulations in Nek5000 with ParaView Catalyst

In situ visualization on high-performance computing systems allows us to analyze simulation results that would otherwise be impossible, given the size of the simulation data sets and offline post-processing execution time. We develop an in situ adaptor for Paraview Catalyst and Nek5000, a massively parallel Fortran and C code for computational fluid dynamics. We perform a strong scalability test up to 2048 cores on KTH’s Beskow Cray XC40 supercomputer and assess in situ visualization’s impact on the Nek5000 performance. In our study case, a high-fidelity simulation of turbulent flow, we observe that in situ operations significantly limit the strong scalability of the code, reducing the relative parallel efficiency to only ≈ 21 % on 2048 cores (the relative efficiency of Nek5000 without in situ operations is ≈ 99 %). Through profiling with Arm MAP, we identified a bottleneck in the image composition step (that uses the Radix-kr algorithm) where a majority of the time is spent on MPI communication. We also identified an imbalance of in situ processing time between rank 0 and all other ranks. In our case, better scaling and load-balancing in the parallel image composition would considerably improve the performance of Nek5000 with in situ capabilities. In general, the result of this study highlights the technical challenges posed by the integration of high-performance simulation codes and data-analysis libraries and their practical use in complex cases, even when efficient algorithms already exist for a certain application scenario