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A Burling graph is an induced subgraph of some graph in Burling's construction of triangle-free high-chromatic graphs. We provide a polynomial-time algorithm which decides whether a given graph is a Burling graph and if it is, constructs its intersection model by rectangular frames. That model enables a polynomial-time algorithm for the maximum independent set problem in Burling graphs. As a consequence, we establish Burling graphs as the first known hereditary class of graphs that admits such an algorithm while not being $\chi$-bounded.

In this paper, we introduce the InLUT3D point cloud dataset, a comprehensive resource designed to advance the field of scene understanding in indoor environments. The dataset covers diverse spaces within the W7 faculty buildings of Lodz University of Technology, characterised by high-resolution laser-based point clouds and manual labelling. Alongside the dataset, we propose metrics and benchmarking guidelines essential for ensuring trustworthy and reproducible results in algorithm evaluation. We anticipate that the introduction of the InLUT3D dataset and its associated benchmarks will catalyse future advancements in 3D scene understanding, facilitating methodological rigour and inspiring new approaches in the field.

The dual-phase liquid argon time projection chamber is presently one of the leading technologies to search for dark matter particles with masses below 10 GeV/c$^2$. This was demonstrated by the DarkSide-50 experiment with approximately 50 kg of low-radioactivity liquid argon as target material. The next generation experiment DarkSide-20k, currently under construction, will use 1,000 times more argon and is expected to start operation in 2027. Based on the DarkSide-50 experience, here we assess the DarkSide-20k sensitivity to models predicting light dark matter particles, including Weakly Interacting Massive Particles (WIMPs) and sub-GeV/c$^2$ particles interacting with electrons in argon atoms. With one year of data, a sensitivity improvement to dark matter interaction cross-sections by at least one order of magnitude with respect to DarkSide-50 is expected for all these models. A sensitivity to WIMP--nucleon interaction cross-sections below $1\times10^{-42}$ cm$^2$ is achievable for WIMP masses above 800 MeV/c$^2$. With 10 years exposure, the neutrino fog can be reached for WIMP masses around 5 GeV/c$^2$., Comment: submitted to Nature Communications

We present the comprehensive analysis of the high-amplitude $\delta$ Sct star V2367 Cygni. Firstly, we perform the frequency analysis for the whole available set of the {\it Kepler} and {\it TESS} photometry. Most of the frequency peaks are harmonics or combinations of the three known independent frequencies with the highest amplitudes, i.e., $\nu_1=5.66106$\,d$^{-1}$, $\nu_2=7.14898$\,d$^{-1}$ and $\nu_3=7.77557$\,d$^{-1}$. The total number of independent frequencies is 26 and 25 from the {\it Kepler} and {\it TESS} light curve, respectively. Then, using the $UBVRI$ time-series photometry, we unambiguously identify the dominant frequency $\nu_1$ as the radial mode, whereas in the case of frequencies $\nu_2$ and $\nu_3$ the most probable mode degrees are $\ell=0$ or $\ell=2$. However, only the frequency $\nu_2$ can be associated with a radial mode, and only if higher order effects of rotation are taken into account. Including the rotational mode coupling, we constructed complex seismic models of V2367\,Cyg, which fit $\nu_1$ and $\nu_2$ as radial modes, and reproduce the amplitude of bolometric flux variations (the parameter $f$) for the dominant mode. The empirical values of $f$ are derived from the $UBVRI$ amplitudes and phases. We rely on the Bayesian analysis based on Monte Carlo simulations to derive constraints on evolutionary stage, mass, rotation, overshooting from the convective core and efficiency of convective transport in the envelope. Our seismic analysis clearly indicates that V2367\,Cyg is in a post-MS phase of evolution. This is the first extensive seismic modelling that takes into account the effect of rotational coupling between pulsation modes., Comment: Accepted for the publication in MNRAS

The knowledge of scintillation quenching of $\alpha$-particles plays a paramount role in understanding $\alpha$-induced backgrounds and improving the sensitivity of liquid argon-based direct detection of dark matter experiments. We performed a relative measurement of scintillation quenching in the MeV energy region using radioactive isotopes ($^{222}$Rn, $^{218}$Po and $^{214}$Po isotopes) present in trace amounts in the DEAP-3600 detector and quantified the uncertainty of extrapolating the quenching factor to the low-energy region., Comment: Submitted to Eur. Phys. J. C

When $\mathcal{T}$ is a tree decomposition of a graph $G$, we write $\mu(\mathcal{T})$ for the maximum size of an induced matching in $G$ all of whose edges intersect one bag of $\mathcal{T}$. The induced matching treewidth of a graph $G$ is the minimum value of $\mu(\mathcal{T})$ over all tree decompositions $\mathcal{T}$ of~$G$. Classes of graphs with bounded induced matching treewidth admit polynomial-time algorithms for a number of problems, including INDEPENDENT SET, $k$-COLORING, ODD CYCLE TRANSVERSAL, and FEEDBACK VERTEX SET. In this paper, we focus on structural properties of such classes. First, we show that graphs with bounded induced matching treewidth that exclude a fixed biclique as an induced subgraph have bounded tree-independence number, which is another well-studied parameter defined in terms of tree decompositions. This sufficient condition about excluding a biclique is also necessary, as bicliques have unbounded tree-independence number. Second, we show that graphs with bounded induced matching treewidth that exclude a fixed clique have bounded chromatic number. That is, classes of graphs with bounded induced matching treewidth are $\chi$-bounded. Our results confirm two conjectures from a recent manuscript of Lima et al. [arXiv 2024].

Experiments aimed at direct searches for WIMP dark matter require highly effective reduction of backgrounds and control of any residual radioactive contamination. In particular, neutrons interacting with atomic nuclei represent an important class of backgrounds due to the expected similarity of a WIMP-nucleon interaction, so that such experiments often feature a dedicated neutron detector surrounding the active target volume. In the context of the development of DarkSide-20k detector at INFN Gran Sasso National Laboratory (LNGS), several R&D projects were conceived and developed for the creation of a new hybrid material rich in both hydrogen and gadolinium nuclei to be employed as an essential element of the neutron detector. Thanks to its very high cross-section for neutron capture, gadolinium is one of the most widely used elements in neutron detectors, while the hydrogen-rich material is instrumental in efficiently moderating the neutrons. In this paper results from one of the R&Ds are presented. In this effort the new hybrid material was obtained as a poly(methyl methacrylate) (PMMA) matrix, loaded with gadolinium oxide in the form of nanoparticles. We describe its realization, including all phases of design, purification, construction, characterization, and determination of mechanical properties of the new material.

B cell receptors (BCRs) play a crucial role in recognizing and fighting foreign antigens. High-throughput sequencing enables in-depth sampling of the BCRs repertoire after immunization. However, only a minor fraction of BCRs actively participate in any given infection. To what extent can we accurately identify antigen-specific sequences directly from BCRs repertoires? We present a computational method grounded on sequence similarity, aimed at identifying statistically significant responsive BCRs. This method leverages well-known characteristics of affinity maturation and expected diversity. We validate its effectiveness using longitudinally sampled human immune repertoire data following influenza vaccination and Sars-CoV-2 infections. We show that different lineages converge to the same responding CDR3, demonstrating convergent selection within an individual. The outcomes of this method hold promise for application in vaccine development, personalized medicine, and antibody-derived therapeutics.

We investigate the accelerator stage of a Plasma-Modulated Plasma Accelerator (P-MoPA) [Phys. Rev. Lett. 127, 184801 (2021)] using both the paraxial wave equation and particle-in-cell (PIC) simulations. We show that adjusting the laser and plasma parameters of the modulator stage of a P-MoPA allows the temporal profile of pulses within the pulse train to be controlled, which in turn allows the wake amplitude in the accelerator stage to be as much as 72% larger than that generated by a plasma beat-wave accelerator with the same total drive laser energy. Our analysis shows that Rosenbluth-Liu detuning is unimportant in a P-MoPA if the number of pulses in the train is less than $\sim$ 30, and that this detuning is also partially counteracted by increased red-shifting, and hence increased pulse spacing, towards the back of the train. An analysis of transverse mode oscillations of the driving pulse train is found to be in good agreement with 2D PIC simulations. PIC simulations demonstrating energy gains of $\sim$ 1.5 GeV ($\sim$ 2.5 GeV) for drive pulse energies of 2.4 J (5.0 J) are presented. Our results suggest that P-MoPAs driven by few-joule, picosecond pulses, such as those provided by high-repetition-rate thin-disk lasers, could accelerate electron bunches to multi-GeV energies at pulse repetition rates in the kilohertz range., Comment: 12 pages, 5 figures

The hyperbolicity of a graph, informally, measures how close a graph is (metrically) to a tree. Hence, it is intuitively similar to treewidth, but the measures are formally incomparable. Motivated by the broad study of algorithms and separators on planar graphs and their relation to treewidth, we initiate the study of planar graphs of bounded hyperbolicity. Our main technical contribution is a novel balanced separator theorem for planar $\delta$-hyperbolic graphs that is substantially stronger than the classic planar separator theorem. For any fixed $\delta \geq 0$, we can find balanced separator that induces either a single geodesic (shortest) path or a single geodesic cycle in the graph. An important advantage of our separator is that the union of our separator (vertex set $Z$) with any subset of the connected components of $G - Z$ induces again a planar $\delta$-hyperbolic graph, which would not be guaranteed with an arbitrary separator. Our construction runs in near-linear time and guarantees that size of separator is $\mathrm{poly}(\delta) \cdot \log n$. As an application of our separator theorem and its strong properties, we obtain two novel approximation schemes on planar $\delta$-hyperbolic graphs. We prove that Maximum Independent Set and the Traveling Salesperson problem have a near-linear time FPTAS for any constant $\delta$, running in $n\, \mathrm{polylog}(n) \cdot 2^{\mathcal{O}(\delta^2)} \cdot \varepsilon^{-\mathcal{O}(\delta)}$ time. We also show that our approximation scheme for Maximum Independent Set has essentially the best possible running time under the Exponential Time Hypothesis (ETH). This immediately follows from our third contribution: we prove that Maximum Independent Set has no $n^{o(\delta)}$-time algorithm on planar $\delta$-hyperbolic graphs, unless ETH fails.

We demonstrate resonant excitation of a plasma wave by a train of short laser pulses guided in a pre-formed plasma channel, for parameters relevant to a plasma-modulated plasma accelerator (P-MoPA). We show experimentally that a train of $N \approx 10$ short pulses, of total energy $\sim 1$ J, can be guided through $110$ mm long plasma channels with on-axis densities in the range $10^{17} - 10^{18}$ cm$^{-3}$. The spectrum of the transmitted train is found to be strongly red-shifted when the plasma period is tuned to the intra-train pulse spacing. Numerical simulations are found to be in excellent agreement with the measurements and indicate that the resonantly excited plasma waves have an amplitude in the range $3$ - $10$ GV m$^{-1}$, corresponding to an accelerator stage energy gain of order $1$ GeV., Comment: 13 pages, 14 figures (including Supplemental Material)

We construct complex seismic models of two high-amplitude delta Sct stars, AE UMa and RV Ari, each pulsating in two radial modes: fundamental and first overtone. The models reproduce, besides the frequencies of two radial modes, also the amplitude of bolometric flux variations (the parameter f) for the dominant mode. Applying the Monte Carlo-based Bayesian analysis, we derive strong constraints, on the parameters of the model as well as on the free parameters of the theory. A vast majority of seismic models of the two stars are just at the beginning of hydrogen-shell burning and a small fraction is at the very end of an overall contraction. The stars have a similar age of about 1.6 Gyr for the hydrogen-shell burning phase. Both stars have unusual low overshooting from the convective core; about 0.02 and 0.004 of the pressure scale height for AE UMa and RV Ari, respectively. This result presumably indicates that overshooting should vary with time and scale with a decreasing convective core. The efficiency of convection in the envelope of both stars is rather low and described by the mixing length parameter alphaMLT of about 0.3-0.6. The third frequency of RV Ari, confirmed by us in the TESS photometry, can only be associated with mixed nonradial modes l=1, g4-g8 or l=2, g10-g12. We include the dipole mode into our Bayesian modelling and demonstrate its huge asteroseismic potential., Comment: 13 pages, 8 figures, 8 pages of the appendix, published in MNRAS

We prove that every poset with bounded cliquewidth and with sufficiently large dimension contains the standard example of dimension $k$ as a subposet. This applies in particular to posets whose cover graphs have bounded treewidth, as the cliquewidth of a poset is bounded in terms of the treewidth of the cover graph. For the latter posets, we prove a stronger statement: every such poset with sufficiently large dimension contains the Kelly example of dimension $k$ as a subposet. Using this result, we obtain a full characterization of the minor-closed graph classes $\mathcal{C}$ such that posets with cover graphs in $\mathcal{C}$ have bounded dimension: they are exactly the classes excluding the cover graph of some Kelly example. Finally, we consider a variant of poset dimension called Boolean dimension, and we prove that posets with bounded cliquewidth have bounded Boolean dimension. The proofs rely on Colcombet's deterministic version of Simon's factorization theorem, which is a fundamental tool in formal language and automata theory, and which we believe deserves a wider recognition in structural and algorithmic graph theory.

The direct search for dark matter in the form of weakly interacting massive particles (WIMP) is performed by detecting nuclear recoils (NR) produced in a target material from the WIMP elastic scattering. A promising experimental strategy for direct dark matter search employs argon dual-phase time projection chambers (TPC). One of the advantages of the TPC is the capability to detect both the scintillation and charge signals produced by NRs. Furthermore, the existence of a drift electric field in the TPC breaks the rotational symmetry: the angle between the drift field and the momentum of the recoiling nucleus can potentially affect the charge recombination probability in liquid argon and then the relative balance between the two signal channels. This fact could make the detector sensitive to the directionality of the WIMP-induced signal, enabling unmistakable annual and daily modulation signatures for future searches aiming for discovery. The Recoil Directionality (ReD) experiment was designed to probe for such directional sensitivity. The TPC of ReD was irradiated with neutrons at the INFN Laboratori Nazionali del Sud, and data were taken with 72 keV NRs of known recoil directions. The direction-dependent liquid argon charge recombination model by Cataudella et al. was adopted and a likelihood statistical analysis was performed, which gave no indications of significant dependence of the detector response to the recoil direction. The aspect ratio R of the initial ionization cloud is estimated to be 1.037 +/- 0.027 and the upper limit is R < 1.072 with 90% confidence level, Comment: 20 pages, 10 figures, submitted to Eur. Phys. J. C

We describe a simple scheme, truncated-channel injection, to inject electrons directly into the wakefield driven by a drive pulse guided by an all-optical plasma channel. We use this approach to generate dark-current-free 1.2 GeV, 4.5 % relative energy spread electron bunches with 120 TW laser pulses guided in a 110-mm-long hydrodynamic optical-field-ionized (HOFI) plasma channel. Our experiments and particle-in-cell simulations show that high-quality electron bunches were only obtained when the drive pulse was closely aligned with the channel axis, and was focused close to the density down-ramp formed at the channel entrance. Start-to-end simulations of the channel formation, and electron injection and acceleration show that increasing the channel length to 410 mm would yield 3.65 GeV bunches, with a slice energy spread $\sim 5 \times 10^{-4}$.

The adaptive immune response relies on T cells that combine phenotypic specialization with diversity of T cell receptors (TCRs) to recognize a wide range of pathogens. TCRs are acquired and selected during T cell maturation in the thymus. Characterizing TCR repertoires across individuals and T cell maturation stages is important for better understanding adaptive immune responses and for developing new diagnostics and therapies. Analyzing a dataset of human TCR repertoires from thymocyte subsets, we find that the variability between individuals generated during the TCR V(D)J recombination is maintained through all stages of T cell maturation and differentiation. The inter-individual variability of repertoires of the same cell type is of comparable magnitude to the variability across cell types within the same individual. To zoom in on smaller scales than whole repertoires, we defined a distance measuring the relative overlap of locally similar sequences in repertoires. We find that the whole repertoire models correctly predict local similarity networks, suggesting a lack of forbidden T cell receptor sequences. The local measure correlates well with distances calculated using whole repertoire traits and carries information about cell types.

In many applications in biology, engineering and economics, identifying similarities and differences between distributions of data from complex processes requires comparing finite categorical samples of discrete counts. Statistical divergences quantify the difference between two distributions. However, their estimation is very difficult and empirical methods often fail, especially when the samples are small. We develop a Bayesian estimator of the Kullback-Leibler divergence between two probability distributions that makes use of a mixture of Dirichlet priors on the distributions being compared. We study the properties of the estimator on two examples: probabilities drawn from Dirichlet distributions, and random strings of letters drawn from Markov chains. We extend the approach to the squared Hellinger divergence. Both estimators outperform other estimation techniques, with better results for data with a large number of categories and for higher values of divergences.

This paper presents the challenge report for the 2021 Kidney and Kidney Tumor Segmentation Challenge (KiTS21) held in conjunction with the 2021 international conference on Medical Image Computing and Computer Assisted Interventions (MICCAI). KiTS21 is a sequel to its first edition in 2019, and it features a variety of innovations in how the challenge was designed, in addition to a larger dataset. A novel annotation method was used to collect three separate annotations for each region of interest, and these annotations were performed in a fully transparent setting using a web-based annotation tool. Further, the KiTS21 test set was collected from an outside institution, challenging participants to develop methods that generalize well to new populations. Nonetheless, the top-performing teams achieved a significant improvement over the state of the art set in 2019, and this performance is shown to inch ever closer to human-level performance. An in-depth meta-analysis is presented describing which methods were used and how they faired on the leaderboard, as well as the characteristics of which cases generally saw good performance, and which did not. Overall KiTS21 facilitated a significant advancement in the state of the art in kidney tumor segmentation, and provides useful insights that are applicable to the field of semantic segmentation as a whole., Comment: 34 pages, 12 figures

We present the first measurements of the temporal decay rate of one-dimensional, linear Langmuir waves excited by an ultra-short laser pulse. Langmuir waves with relative amplitudes of approximately $6\%$ were driven by $1.7$ J, $50$ fs laser pulses in hydrogen and deuterium plasmas of density $n_{e0} = 8.4 \times 10^{17}$ cm$^{-3}$. The wakefield lifetimes were measured to be $\tau^\mathrm{H_2}_\mathrm{wf} = (9\pm2)$ ps and $\tau^\mathrm{D_2}_\mathrm{wf} = (16\pm8)$ ps respectively for hydrogen and deuterium. The experimental results were found to be in good agreement with 2D particle-in-cell simulations. In addition to being of fundamental interest, these results are particularly relevant to the development of laser wakefield accelerators (LWFAs) and wakefield acceleration schemes using multiple pulses, such as multi-pulse laser wakefield accelerators (MP-LWFAs).

Pathogens drive changes in host immune systems that in turn exert pressure for pathogens to evolve. Quantifying and understanding this constant coevolutionary process has clear practical global health implications. Yet its relatively easier accessibility compared to macroevolution makes it a fascinating system to learn about the basic laws of evolution. Focusing on immune-viral evolution, we present an overview of theoretical and experimental approaches that have recently started coming together to build the foundations for a quantitative and predictive co-evolutionary theory.

In recent years, hydrodynamic optical-field-ionized (HOFI) channels have emerged as a promising technique to create laser waveguides suitable for guiding tightly-focused laser pulses in a plasma, as needed for laser-plasma accelerators. While experimental advances in HOFI channels continue to be made, the underlying mechanisms and the roles of the main parameters remain largely unexplored. In this work, we propose a start-to-end simulation pipeline of the HOFI channel formation and the resulting guiding properties, and use it to explore the underlying physics and the tunability of HOFI channels. This approach is benchmarked against experimental measurements. HOFI channels are shown to feature excellent guiding properties over a wide range of parameters, making them a promising and tunable waveguide option for laser-plasma accelerators., Comment: 8 pages (+5 appendix), 7 figures, submitted to PRResearch

Antigenic variation is the main immune escape mechanism for RNA viruses like influenza or SARS-CoV-2. While high mutation rates promote antigenic escape, they also induce large mutational loads and reduced fitness. It remains unclear how this cost-benefit trade-off selects the mutation rate of viruses. Using a traveling wave model for the co-evolution of viruses and host immune systems in a finite population, we investigate how immunity affects the evolution of the mutation rate and other non-antigenic traits, such as virulence. We first show that the nature of the wave depends on how cross-reactive immune systems are, reconciling previous approaches. The immune-virus system behaves like a Fisher wave at low cross-reactivities, and like a fitness wave at high cross-reactivities. These regimes predict different outcomes for the evolution of non-antigenic traits. At low cross-reactivities, the evolutionarily stable strategy is to maximize the speed of the wave, implying a higher mutation rate and increased virulence. At large cross-reactivities, where our estimates place H3N2 influenza, the stable strategy is to increase the basic reproductive number, keeping the mutation rate to a minimum and virulence low.