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In understanding and redesigning the function of proteins in modern biochemistry, protein engineers are increasingly focusing on exploring regions in proteins called loops. Analyzing various characteristics of these regions helps the experts design the transfer of the desired function from one protein to another. This process is denoted as loop grafting. We designed a set of interactive visualizations that provide experts with visual support through all the loop grafting pipeline steps. The workflow is divided into several phases, reflecting the steps of the pipeline. Each phase is supported by a specific set of abstracted 2D visual representations of proteins and their loops that are interactively linked with the 3D View of proteins. By sequentially passing through the individual phases, the user shapes the list of loops that are potential candidates for loop grafting. Finally, the actual in-silico insertion of the loop candidates from one protein to the other is performed, and the results are visually presented to the user. In this way, the fully computational rational design of proteins and their loops results in newly designed protein structures that can be further assembled and tested through in-vitro experiments. We showcase the contribution of our visual support design on a real case scenario changing the enantiomer selectivity of the engineered enzyme. Moreover, we provide the readers with the experts' feedback.

This article focuses on the development and evaluation of Small-sized Czech sentence embedding models. Small models are important components for real-time industry applications in resource-constrained environments. Given the limited availability of labeled Czech data, alternative approaches, including pre-training, knowledge distillation, and unsupervised contrastive fine-tuning, are investigated. Comprehensive intrinsic and extrinsic analyses are conducted, showcasing the competitive performance of our models compared to significantly larger counterparts, with approximately 8 times smaller size and 5 times faster speed than conventional Base-sized models. To promote cooperation and reproducibility, both the models and the evaluation pipeline are made publicly accessible. Ultimately, this article presents practical applications of the developed sentence embedding models in Seznam.cz, the Czech search engine. These models have effectively replaced previous counterparts, enhancing the overall search experience for instance, in organic search, featured snippets, and image search. This transition has yielded improved performance., Comment: Accepted at the Thirty-Sixth Annual Conference on Innovative Applications of Artificial Intelligence (IAAI-24). IAAI Innovative Application Award. 9 pages

This paper presents a multi-layer software architecture to perform cooperative missions with a fleet of quadrotors providing support in electrical power line inspection operations. The proposed software framework guarantees the compliance with safety requirements between drones and human workers while ensuring that the mission is carried out successfully. Besides, cognitive capabilities are integrated in the multi-vehicle system in order to reply to unforeseen events and external disturbances. The feasibility and effectiveness of the proposed architecture are demonstrated by means of realistic simulations., Comment: 6 pages, 7 figures, conference

An application of stereo thermal vision to perform preliminary inspection operations of electrical power lines by a particular class of small Unmanned Aerial Vehicles (UAVs), aka Micro Unmanned Aerial Vehicles (MAVs), is presented in this paper. The proposed hardware and software setup allows the detection of overheated power equipment, one of the major causes of power outages. The stereo vision complements the GPS information by finely detecting the potential source of damage while also providing a measure of the harm extension. The reduced sizes and the light weight of the vehicle enable to survey areas otherwise difficult to access with standard UAVs. Gazebo simulations and real flight experiments demonstrate the feasibility and effectiveness of the proposed setup., Comment: 8 pages, 15 figures, conference

Integration of Visual Inertial Odometry (VIO) methods into a modular control system designed for deployment of Unmanned Aerial Vehicles (UAVs) and teams of cooperating UAVs in real-world conditions are presented in this paper. Reliability analysis and fair performance comparison of several methods integrated into a control pipeline for achieving full autonomy in real conditions is provided. Although most VIO algorithms achieve excellent localization precision and negligible drift on artificially created datasets, the aspects of reliability in non-ideal situations, robustness to degraded sensor data, and the effects of external disturbances and feedback control coupling are not well studied. These imperfections, which are inherently present in cases of real-world deployment of UAVs, negatively affect the ability of the most used VIO approaches to output a sensible pose estimation. We identify the conditions that are critical for a reliable flight under VIO localization and propose workarounds and compensations for situations in which such conditions cannot be achieved. The performance of the UAV system with integrated VIO methods is quantitatively analyzed w.r.t. RTK ground truth and the ability to provide reliable pose estimation for the feedback control is demonstrated onboard a UAV that is tracking dynamic trajectories under challenging illumination.

We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus, biochemists rely to a large extent only on quantitative analysis of geometric and physico-chemical properties. However, the usage of abstract methods to study inherently spatial data hinders the exploration and poses a considerable workload. sMolBoxes link quantitative analysis of a user-defined set of properties with interactive 3D visualizations. They enable visual explanations of molecular behaviors, which lead to an efficient discovery of biochemically significant parts of the MD simulation. sMolBoxes follow a node-based model for flexible definition, combination, and immediate evaluation of properties to be investigated. Progressive analytics enable fluid switching between multiple properties, which facilitates hypothesis generation. Each sMolBox provides quick insight to an observed property or function, available in more detail in the bigBox View. The case study illustrates that even with relatively few sMolBoxes, it is possible to express complex analyses tasks, and their use in exploratory analysis is perceived as more efficient than traditional scripting-based methods., Comment: 10 pages, 9 figures, IEEE VIS, TVCG

The rainbow Tur\'an number, a natural extension of the well studied traditional Tur\'an number, was introduced in 2007 by Keevash, Mubayi, Sudakov and Verstra\"ete. The rainbow Tur\'an number of a graph $H$, $ex^{*}(n,H)$, is the largest number of edges for an $n$ vertex graph $G$ which can be properly edge colored with no rainbow $H$ subgraph. We explore the reduction method for finding upper bounds on rainbow Tur\'an numbers, and use this to inform results for the rainbow Tur\'an numbers of double stars, caterpillars, and perfect binary trees. In addition, we define $k$-unique colorings and the related $k$-unique Tur\'an numbers. We provide preliminary results on this new variant on the classic problem.

The question of the existence of pairs and groups among the meteor showers is opened for a long time. The double station video observation of the 2006 Geminid meteor shower, one of the most active annual showers, is used for the search of such events. The atmospheric trajectories of the observed meteors, photometric masses, and both time and spatial distances of meteoroids in the atmosphere were determined using a double station video observation. Time gaps among them were analysed statistically. The Monte Carlo simulation was used for the determination of the probability of random pairings. Higher than expected number of candidates for pairs was found among 2006 Geminids. Evaluation of Poisson distribution shows that a significant fraction of them may be real cases. However, the Monte Carlo simulation did not confirm this result and provided a different view. Analysis of geometrical positions of candidate pairs also did not support the presence of real pairs and groups. Although we cannot exclude that some of them may be physically connected pairs, all the observed cases can be explained as the coincidental appearance of unrelated meteors., Comment: 8 pages, 7 figures, 3 tables, accepted for publication in A&A

Biocompatible nanoscale probes for sensitive detection of paramagnetic species and molecules associated with their (bio)chemical transformations would provide a desirable tool for a better understanding of cellular redox processes. Here, we describe an analytical tool based on quantum sensing techniques. We magnetically coupled negatively charged nitrogen-vacancy (NV) centers in nanodiamonds (NDs) with nitroxide radicals present in a bioinert polymer coating of the NDs. We demonstrated that the T1 spin relaxation time of NV centers is very sensitive to the number of nitroxide radicals, with a resolution down to ~10 spins per ND (detection of approximately $ 10^-23 $ mol in a localized volume). The detection is based on T1 shortening upon the radical attachment and we propose a theoretical model describing this phenomenon. We further show this colloidally stable, water-soluble system can be used dynamically for spatiotemporal readout of a redox chemical process (oxidation of ascorbic acid) occurring near the ND surface in an aqueous environment under ambient conditions., Comment: 26 pages (plus 18 pages of supporting information), 3 figures (plus 8 figures in supporting information)

Organizations struggle to comply with legal requirements as well as customers calls for better data protection. On the implementation level, incorporation of privacy protections in products and services depends on the commitment of the engineers who design them. We interviewed six senior engineers, who work for globally leading IT corporations and research institutions to investigate their motivation and ability to comply with privacy regulations. Our findings point to a lack of perceived responsibility, control, autonomy, and frustrations with interactions with the legal world. While we increasingly call on engineers to go beyond functional requirements and be responsive to human values in our increasingly technological society, we may be facing the dilemma of asking engineers to live up to a challenge they are currently not ready to embrace., Comment: System engineers; information privacy; motivation; attitude; Theory of Planned Behaviour; responsibility

We determine the leading Fock state light front wave functions (LFWFs) of the pion and kaon via light front projections of the covariant Bethe-Salpeter wave function. Using these LFWFs we study the multi-dimensional images of the valence quarks in the pion and kaon that are provided by their generalized parton distribution functions (GPDs) and transverse momentum dependent parton distribution functions (TMDs). Moments of the GPDs are taken to obtain the electromagnetic and gravitational form factors of the pion and kaon, and comparisons to available experimental and lattice data are made. Highlights from this study include predictions that the mean-squared impact parameter for the quarks in the pion and kaon are: $\langle \vec{b}_T^2\rangle_{u}^\pi=0.11$fm$^2$, $\langle \vec{b}_T^2\rangle_{s}^K=0.08$fm$^2$, and $\langle \vec{b}_T^2\rangle_{u}^K=0.13$fm$^2$, and therefore the $s$ quark in the kaon is much closer to the center of transverse momentum than the $u$ quark. From the electromagnetic and gravitational form factors we find that the light-cone energy radii are about 60\% smaller than the light-cone charge radii for each quark sector in the pion and kaon. A quantitative measure of the importance of the leading Fock state is obtained via comparison with a full DSE calculation (containing an infinite tower of Fock states) for the pion form factor.