Abstract
The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics ...Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.
VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. Now in its 11th year, VectorBase ...currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing Galaxy to support user-based workflows. VectorBase also actively supports our community through hands-on workshops and online tutorials. All information and data are freely available from our website at https://www.vectorbase.org/.
Abstract
The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) is a Bioinformatics Resource Center funded by the National Institutes of Health with ...additional funding from the Wellcome Trust. VEuPathDB supports >600 organisms that comprise invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Since 2004, VEuPathDB has analyzed omics data from the public domain using contemporary bioinformatic workflows, including orthology predictions via OrthoMCL, and integrated the analysis results with analysis tools, visualizations, and advanced search capabilities. The unique data mining platform coupled with >3000 pre-analyzed data sets facilitates the exploration of pertinent omics data in support of hypothesis driven research. Comparisons are easily made across data sets, data types and organisms. A Galaxy workspace offers the opportunity for the analysis of private large-scale datasets and for porting to VEuPathDB for comparisons with integrated data. The MapVEu tool provides a platform for exploration of spatially resolved data such as vector surveillance and insecticide resistance monitoring. To address the growing body of omics data and advances in laboratory techniques, VEuPathDB has added several new data types, searches and features, improved the Galaxy workspace environment, redesigned the MapVEu interface and updated the infrastructure to accommodate these changes.
Graphical Abstract
Graphical Abstract
With the rise in new soft robotic applications, the control requirements increase. Therefore, precise control methods for soft robots are required. However, the dynamic control of soft robots, which ...is required for fast movements, is still an open topic and will be discussed here. In this contribution, one kinematic and two dynamic control methods for soft robots are examined. Thereby, an LQI controller with gain scheduling, which is new to soft robotic applications, and an MPC controller are presented. The controllers are compared in a simulation regarding their accuracy and robustness. Additionally, the required implementation effort and computational effort is examined. For this purpose, the trajectory tracking control of a simple soft robot is studied for different trajectories. The soft robot is beam-shaped and tendon-actuated. It is modeled using the piecewise constant curvature model, which is one of the most popular modeling techniques in soft robotics. In this paper, it is shown that all three controllers are able to follow the examined trajectories. However, the dynamic controllers show much higher accuracy and robustness than the kinematic controller. Nevertheless, it should be noted that the implementation and computational effort for the dynamic controllers is significantly higher. Therefore, kinematic controllers should be used if movements are slow and small oscillations can be accepted, while dynamic controllers should be used for faster movements with higher accuracy or robustness requirements.
A prospective, randomized, double-blind study of 437 patients undergoing arthroscopic diagnostic and operative procedures found that no deep infections occurred in any patient and only one ...superficial infection occurred in a patient who did not receive prophylactic antibiotics. One patient had a mild allergic reaction to the antibiotic that resolved after treatment with Benadryl. These results suggest that the routine use of prophylactic antibiotics is not indicated for patients undergoing arthroscopic surgery and that the slight risk of infection is outweighed by the cost of the antibiotics and the slight risk of allergic reaction.
Entanglement, the non-local correlations present in multipartite quantum systems, is a curious feature of quantum mechanics and the fuel of quantum technology. It is therefore a major priority to ...develop energy-conserving and simple methods for generating high-fidelity entangled states. In the case of light, entanglement can be realized by interactions with matter, although the required nonlinear interaction is typically weak, thereby limiting its applicability. Here, we show how a single two-level emitter deterministically coupled to light in a nanophotonic waveguide is used to realize genuine photonic quantum entanglement for excitation at the single photon level. By virtue of the efficient optical coupling, two-photon interactions are strongly mediated by the emitter realizing a giant nonlinearity that leads to entanglement. We experimentally generate and verify energy-time entanglement by violating a Bell inequality (Clauder-Horne-Shimony-Holt Bell parameter of \(S=2.67(16)>2\)) in an interferometric measurement of the two-photon scattering response. As an attractive feature of this approach, the two-level emitter acts as a passive scatterer initially prepared in the ground state, i.e., no advanced spin control is required. This experiment is a fundamental advancement that may pave a new route for ultra-low energy-consuming synthesis of photonic entangled states for quantum simulators or metrology.
Decoherence of a quantum system arising from its interaction with an environment is a key concept for understanding the transition between the quantum and classical world as well as performance ...limitations in quantum technology applications. The effects of large, weakly coupled environments are often described as a classical, fluctuating field whose dynamics is unaffected by the qubit, whereas a fully quantum description still implies some back-action from the qubit on the environment. Here we show direct experimental evidence for such a back-action for an electron-spin-qubit in a GaAs quantum dot coupled to a mesoscopic environment of order \(10^6\) nuclear spins. By means of a correlation measurement technique, we detect the back-action of a single qubit-environment interaction whose duration is comparable to the qubit's coherence time, even in such a large system. We repeatedly let the qubit interact with the spin bath and measure its state. Between such cycles, the qubit is reinitialized to different states. The correlations of the measurement outcomes are strongly affected by the intermediate qubit state, which reveals the action of a single electron spin on the nuclear spins.
We present efficient methods to reliably characterize and tune gate-defined semiconductor spin qubits. Our methods are designed to target the tuning procedures of semiconductor double quantum dot in ...GaAs heterostructures, but can easily be adapted to other quantum-dot-like qubit systems. These tuning procedures include the characterization of the inter-dot tunnel coupling, the tunnel coupling to the surrounding leads and the identification of the various fast initialization points for the operation of the qubit. Since semiconductor-based spin qubits are compatible with standard semiconductor process technology and hence promise good prospects of scalability, the challenge of efficiently tuning the dot's parameters will only grow in the near future, once the multi-qubit stage is reached. With the anticipation of being used as the basis for future automated tuning protocols, all measurements presented here are fast-to-execute and easy-to-analyze characterization methods. They result in quantitative measures of the relevant qubit parameters within a couple of seconds, and require almost no human interference.
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