Classification of diffraction patterns in single particle imaging experiments performed at X-ray free-electron lasers using a convolutional neural network

Single particle imaging (SPI) is a promising method for native structure determination which has undergone a fast progress with the development of X-ray Free-Electron Lasers. Large amounts of data are collected during SPI experiments, driving the need for automated data analysis. The necessary data analysis pipeline has a number of steps including binary object classification (single versus multiple hits). Classification and object detection are areas where deep neural networks currently outperform other approaches. In this work, we use the fast object detector networks YOLOv2 and YOLOv3. By exploiting transfer learning, a moderate amount of data is sufficient for training of the neural network. We demonstrate here that a convolutional neural network (CNN) can be successfully used to classify data from SPI experiments. We compare the results of classification for the two different networks, with different depth and architecture, by applying them to the same SPI data with different data representation. The best results are obtained for YOLOv2 color images linear scale classification, which shows an accuracy of about 97% with the precision and recall of about 52% and 61%, respectively, which is in comparison to manual data classification.Comment: 23 pages, 6 figures, 3 table

Single photon imaging at ultra-high resolution

Abstract We present a detection system capable of imaging both single photon/positive ion and multiple coincidence photons/positive ions with extremely high spatial resolution. In this detector the photoelectrons excited by the incoming photons are multiplied by microchannel plate(s) (MCP). The process of multiplication is spatially constrained within an MCP pore, which can be as small as 4 μm for commercially available MCPs. An electron cloud originated by a single photoelectron is then encoded by a pixellated custom analog ASIC consisting of 105 K charge sensitive pixels of 50 μm in size arranged on a hexagonal grid. Each pixel registers the charge with an accuracy o

Large-scale brain modes reorganize between infant sleep states and carry prognostic information for preterms

Sleep architecture carries vital information about brain health across the lifespan. In particular, the ability to express distinct vigilance states is a key physiological marker of neurological wellbeing in the newborn infant although systems-level mechanisms remain elusive. Here, we demonstrate that the transition from quiet to active sleep in newborn infants is marked by a substantial reorganization of large-scale cortical activity and functional brain networks. This reorganization is attenuated in preterm infants and predicts visual performance at two years. We find a striking match between these empirical effects and a computational model of large-scale brain states which uncovers fundamental biophysical mechanisms not evident from inspection of the data. Active sleep is defined by reduced energy in a uniform mode of neural activity and increased energy in two more complex anteroposterior modes. Preterm-born infants show a deficit in this sleep-related reorganization of modal energy that carries novel prognostic information.Peer reviewe

Spin-models, dynamics and criticality with atoms in tilted optical superlattices

Funding: Strathclyde: UK EPSRC Programme Grant DesOEQ (EP/P009565/1), the European Union Horizon 2020 collaborative project QuProCS — QuantumProbes for Complex Systems (Grant Agreement No. 641277), and by the EOARD via AFOSR Grant No. FA9550-18-1-0064.We show that atoms in tilted optical superlattices provide a platform for exploring coupled spin chains of forms that are not present in other systems. In particular, using a period-2 superlattice in one dimension, we show that coupled Ising spin chains with XZ and ZZ spin coupling terms can be engineered. We use optimized tensor network techniques to explore the criticality and nonequilibrium dynamics in these models, finding a tricritical Ising point in regimes that are accessible in current experiments. These setups are ideal for studying low-entropy physics, as initial entropy is “frozen-out” in realizing the spin models, and provide an example of the complex critical behavior that can arise from interaction-projected models.Publisher PDFPeer reviewe

Resonant two-site tunnelling dynamics of bosons in a tilted optical superlattice

Funding: Strathclyde: UK EPSRC Program Grant DesOEQ (No.EP/P009565/1), the European Union Horizon 2020 collaborative project Quantum Probes for Complex Systems (Grant Agreement No. 641277), and by the EOARD via AFOSR Grant No. FA9550-18-1-0064.We study the nonequilibrium dynamics of a one-dimensional Bose-Hubbard model in a gradient potential and a superlattice, beginning from a deep Mott insulator regime with an average filling of one particle per site. Studying a quench that is near resonance to tunneling of the particles over two lattice sites, we show how a spin model emerges consisting of two coupled Ising chains that are coupled by interaction terms in a staggered geometry. We compare and contrast the behavior in this case with that in a previously studied case where the resonant tunneling was over a single site. Using optimized tensor network techniques to calculate finite-temperature behavior of the model, as well as finite-size scaling for the ground state, we conclude that the universality class of the phase transition for the coupled chains is that of a tricritical Ising point. We also investigate the out-of-equilibrium dynamics after the quench in the vicinity of the resonance and compare dynamics with recent experiments realized without the superlattice geometry. This model is directly realizable in current experiments and reflects a general way to realize spin models with ultracold atoms in optical lattices.Publisher PDFPeer reviewe

Dynamical density delay maps: simple, new method for visualising the behaviour of complex systems

Background. Physiologic signals, such as cardiac interbeat intervals, exhibit complex fluctuations. However, capturing important dynamical properties, including nonstationarities may not be feasible from conventional time series graphical representations. Methods. We introduce a simple-to-implement visualisation method, termed dynamical density delay mapping (``D3-Map'' technique) that provides an animated representation of a system's dynamics. The method is based on a generalization of conventional two-dimensional (2D) Poincar� plots, which are scatter plots where each data point, x(n), in a time series is plotted against the adjacent one, x(n+1). First, we divide the original time series, x(n) (n=1,..., N), into a sequence of segments (windows). Next, for each segment, a three-dimensional (3D) Poincar� surface plot of x(n), x(n+1), hx(n),x(n+1) is generated, in which the third dimension, h, represents the relative frequency of occurrence of each (x(n),x(n+1)) point. This 3D Poincar\'e surface is then chromatised by mapping the relative frequency h values onto a colour scheme. We also generate a colourised 2D contour plot from each time series segment using the same colourmap scheme as for the 3D Poincar\'e surface. Finally, the original time series graph, the colourised 3D Poincar\'e surface plot, and its projection as a colourised 2D contour map for each segment, are animated to create the full ``D3-Map.'' Results. We first exemplify the D3-Map method using the cardiac interbeat interval time series from a healthy subject during sleeping hours. The animations uncover complex dynamical changes, such as transitions between states, and the relative amount of time the system spends in each state. We also illustrate the utility of the method in detecting hidden temporal patterns in the heart rate dynamics of a patient with atrial fibrillation. The videos, as well as the source code, are made publicly available. Conclusions. Animations based on density delay maps provide a new way of visualising dynamical properties of complex systems not apparent in time series graphs or standard Poincar\'e plot representations. Trainees in a variety of fields may find the animations useful as illustrations of fundamental but challenging concepts, such as nonstationarity and multistability. For investigators, the method may facilitate data exploration

Magnetic Dirac semimetal state of (Mn,Ge)Bi2_2Te4_4

For quantum electronics, the possibility to finely tune the properties of magnetic topological insulators (TIs) is a key issue. We studied solid solutions between two isostructural Z$_2$ TIs, magnetic MnBi$_2$Te$_4$ and nonmagnetic GeBi$_2$Te$_4$, with Z$_2$ invariants of 1;000 and 1;001, respectively. For high-quality, large mixed crystals of Ge$_x$Mn$_{1-x}$Bi$_2$Te$_4$, we observed linear x-dependent magnetic properties, composition-independent pairwise exchange interactions along with an easy magnetization axis. The bulk band gap gradually decreases to zero for $x$ from 0 to 0.4, before reopening for $x>0.6$, evidencing topological phase transitions (TPTs) between topologically nontrivial phases and the semimetal state. The TPTs are driven purely by the variation of orbital contributions. By tracing the x-dependent $6p$ contribution to the states near the fundamental gap, the effective spin-orbit coupling variation is extracted. As $x$ varies, the maximum of this contribution switches from the valence to the conduction band, thereby driving two TPTs. The gapless state observed at $x=0.42$ closely resembles a Dirac semimetal above the Neel temperature and shows a magnetic gap below, which is clearly visible in raw photoemission data. The observed behavior of the Ge$_x$Mn$_{1-x}$Bi$_2$Te$_4$ system thereby demonstrates an ability to precisely control topological and magnetic properties of TIs

Post-bronchoscopy fatal endobronchial hemorrhage in a woman with bronchopulmonary mucormycosis: a case report

<p>Abstract</p> <p>Introduction</p> <p>During infection, Mucorales fungi invade major blood vessels, leading to extensive necrosis, and in cases of extensive pulmonary disease, bleeding into the lungs may occur.</p> <p>Case presentation</p> <p>We report an unexpected event of post-bronchoscopy fatal endobronchial hemorrhage in a 62-year-old HIV-negative Italian woman with well controlled diabetes mellitus who presented with diffuse cavitated pulmonary lesions. Fiberoptic bronchoscopy revealed bilateral obstruction of the segmental bronchi. Fatal massive bleeding occurred after standard biopsy procedures. Histologic examination showed that the hyphae were more deeply colored by hematoxylin-eosin (H&E) than by other stains for fungi. Culture and autopsy confirmed bronchopulmonary mucormycosis.</p> <p>Conclusion</p> <p>Infection by Mucorales fungi should be considered in the diabetes population regardless of the degree of metabolic control. In these patients, particular caution should be taken during bronchoscopic procedures because of the greater friability of the fungal lesions.</p