Unsupervised learning for cross-domain medical image synthesis using deformation invariant cycle consistency networks

Recently, the cycle-consistent generative adversarial networks (CycleGAN) has been widely used for synthesis of multi-domain medical images. The domain-specific nonlinear deformations captured by CycleGAN make the synthesized images difficult to be used for some applications, for example, generating pseudo-CT for PET-MR attenuation correction. This paper presents a deformation-invariant CycleGAN (DicycleGAN) method using deformable convolutional layers and new cycle-consistency losses. Its robustness dealing with data that suffer from domain-specific nonlinear deformations has been evaluated through comparison experiments performed on a multi-sequence brain MR dataset and a multi-modality abdominal dataset. Our method has displayed its ability to generate synthesized data that is aligned with the source while maintaining a proper quality of signal compared to CycleGAN-generated data. The proposed model also obtained comparable performance with CycleGAN when data from the source and target domains are alignable through simple affine transformations

Automated cell tracking using StarDist and TrackMate [version 1; peer review: awaiting peer review]

The ability of cells to migrate is a fundamental physiological process involved in embryonic development, tissue homeostasis, immune surveillance, and wound healing. Therefore, the mechanisms governing cellular locomotion have been under intense scrutiny over the last 50 years. One of the main tools of this scrutiny is live-cell quantitative imaging, where researchers image cells over time to study their migration and quantitatively analyze their dynamics by tracking them using the recorded images. Despite the availability of computational tools, manual tracking remains widely used among researchers due to the difficulty setting up robust automated cell tracking and large-scale analysis. Here we provide a detailed analysis pipeline illustrating how the deep learning network StarDist can be combined with the popular tracking software TrackMate to perform 2D automated cell tracking and provide fully quantitative readouts. Our proposed protocol is compatible with both fluorescent and widefield images. It only requires freely available and open-source software (ZeroCostDL4Mic and Fiji), and does not require any coding knowledge from the users, making it a versatile and powerful tool for the field. We demonstrate this pipeline's usability by automatically tracking cancer cells and T cells using fluorescent and brightfield images. Importantly, we provide, as supplementary information, a detailed step-by-step protocol to allow researchers to implement it with their images

Possible glass-like random singlet magnetic state in 1T-TaS2

Two-dimensional layered transition-metal-dichalcogenide compound 1T-TaS2 shows the rare coexistence of charge density wave (CDW) and electron correlation driven Mott transition. In addition, atomic-cluster spins on the triangular lattice of the CDW state of 1T-TaS2 give rise to the possibility of the exotic spin-singlet state in which quantum fluctuations of spins are strong enough to prevent any long range magnetic ordering down to absolute zero ( 0 K). We present here the evidences of a glass-like random singlet magnetic state in 1T-TaS2 at low temperatures through a study of temperature and time dependence of magnetization. Comparing the experimental results with a representative canonical spin-glass system Au(1.8%Mn), we show that this glass-like state is distinctly different from the well established canonical spin-glass state.Comment: 11 pages, 6 figure

Large, high quality single-crystals of the new Topological Kondo Insulator, SmB6

SmB6 has recently been predicted to be a Topological Kondo Insulator, the first strongly correlated heavy fermion material to exhibit topological surface states. High quality crystals are necessary to investigate the topological properties of this material. Single crystal growth of the rare earth hexaboride, SmB6, has been carried out by the floating zone technique using a high power xenon arc lamp image furnace. Large, high quality single-crystals are obtained by this technique. The crystals produced by the floating zone technique are free of contamination from flux materials and have been characterised by resistivity and magnetisation measurements. These crystals are ideally suited for the investigation of both the surface and bulk properties of SmB6

Topological semimetal in a fermionic optical lattice

Optical lattices play a versatile role in advancing our understanding of correlated quantum matter. The recent implementation of orbital degrees of freedom in chequerboard and hexagonal optical lattices opens up a new thrust towards discovering novel quantum states of matter, which have no prior analogs in solid state electronic materials. Here, we demonstrate that an exotic topological semimetal emerges as a parity-protected gapless state in the orbital bands of a two-dimensional fermionic optical lattice. The new quantum state is characterized by a parabolic band-degeneracy point with Berry flux $2\pi$, in sharp contrast to the $\pi$ flux of Dirac points as in graphene. We prove that the appearance of this topological liquid is universal for all lattices with D$_4$ point group symmetry as long as orbitals with opposite parities hybridize strongly with each other and the band degeneracy is protected by odd parity. Turning on inter-particle repulsive interactions, the system undergoes a phase transition to a topological insulator whose experimental signature includes chiral gapless domain-wall modes, reminiscent of quantum Hall edge states.Comment: 6 pages, 3 figures and Supplementary Informatio

Strain-induced partially flat band, helical snake states, and interface superconductivity in topological crystalline insulators

Topological crystalline insulators in IV-VI compounds host novel topological surface states consisting of multi-valley massless Dirac fermions at low energy. Here we show that strain generically acts as an effective gauge field on these Dirac fermions and creates pseudo-Landau orbitals without breaking time-reversal symmetry. We predict the realization of this phenomenon in IV-VI semiconductor heterostructures, due to a naturally occurring misfit dislocation array at the interface that produces a periodically varying strain field. Remarkably, the zero-energy Landau orbitals form a flat band in the vicinity of the Dirac point, and coexist with a network of snake states at higher energy. We propose that the high density of states of this flat band gives rise to interface superconductivity observed in IV-VI semiconductor multilayers at unusually high temperatures, with non-BCS behavior. Our work demonstrates a new route to altering macroscopic electronic properties to achieve a partially flat band, and paves the way for realizing novel correlated states of matter.Comment: Accepted by Nature Physic

Low Frequency Scattering by a Planar Crack

The detection of cracks with the aid of ultrasonics is an important nondestructive evaluation technique. The corresponding theoretical problem of the scattering of elastic waves by cracks has attracted considerable attention. Scattering of time harmonic plane wave by an isolated two dimensional Griffith, or an penny-shaped crack in an unbounded elastic medium has been studied extensively. However, studies of the scattering problem by a three dimensional crack other than circular shape have been rather limited. Few studies of scattering from an elliptical crack in an elastic body of infinite extent can be found in the literature. Datta[1] studied the problem using the method of matched asymptotic expansion. Gubernatis et al. [2] and Budiansky and O’Connell [3] have used the elastostatic approximation to determine the scattered field. The backscattered field from an elliptical crack has been obtained by Kino [4] in the low frequency limit by a formula derived from elastodynamic reciprocity theorem. An integro-differential equation technique was employed by Roy [5]–[6] to study the same problem.</p

Trophic Garnishes: Cat–Rat Interactions in an Urban Environment

BACKGROUND:Community interactions can produce complex dynamics with counterintuitive responses. Synanthropic community members are of increasing practical interest for their effects on biodiversity and public health. Most studies incorporating introduced species have been performed on islands where they may pose a risk to the native fauna. Few have examined their interactions in urban environments where they represent the majority of species. We characterized house cat (Felis catus) predation on wild Norway rats (Rattus norvegicus), and its population effects in an urban area as a model system. Three aspects of predation likely to influence population dynamics were examined; the stratum of the prey population killed by predators, the intensity of the predation, and the size of the predator population. METHODOLOGY/PRINCIPAL FINDINGS:Predation pressure was estimated from the sizes of the rat and cat populations, and the characteristics of rats killed in 20 alleys. Short and long term responses of rat population to perturbations were examined by removal trapping. Perturbations removed an average of 56% of the rats/alley but had no negative long-term impact on the size of the rat population (49.6+/-12.5 rats/alley and 123.8+/-42.2 rats/alley over two years). The sizes of the cat population during two years (3.5 animals/alley and 2.7 animals/alley) also were unaffected by rat population perturbations. Predation by cats occurred in 9/20 alleys. Predated rats were predominantly juveniles and significantly smaller (144.6 g+/-17.8 g) than the trapped rats (385.0 g+/-135.6 g). Cats rarely preyed on the larger, older portion of the rat population. CONCLUSIONS/SIGNIFICANCE:The rat population appears resilient to perturbation from even substantial population reduction using targeted removal. In this area there is a relatively low population density of cats and they only occasionally prey on the rat population. This occasional predation primarily removes the juvenile proportion of the rat population. The top predator in this urban ecosystem appears to have little impact on the size of the prey population, and similarly, reduction in rat populations doesn't impact the size of the cat population. However, the selected targeting of small rats may locally influence the size structure of the population which may have consequences for patterns of pathogen transmission

Portfolio selection problems in practice: a comparison between linear and quadratic optimization models

Several portfolio selection models take into account practical limitations on the number of assets to include and on their weights in the portfolio. We present here a study of the Limited Asset Markowitz (LAM), of the Limited Asset Mean Absolute Deviation (LAMAD) and of the Limited Asset Conditional Value-at-Risk (LACVaR) models, where the assets are limited with the introduction of quantity and cardinality constraints. We propose a completely new approach for solving the LAM model, based on reformulation as a Standard Quadratic Program and on some recent theoretical results. With this approach we obtain optimal solutions both for some well-known financial data sets used by several other authors, and for some unsolved large size portfolio problems. We also test our method on five new data sets involving real-world capital market indices from major stock markets. Our computational experience shows that, rather unexpectedly, it is easier to solve the quadratic LAM model with our algorithm, than to solve the linear LACVaR and LAMAD models with CPLEX, one of the best commercial codes for mixed integer linear programming (MILP) problems. Finally, on the new data sets we have also compared, using out-of-sample analysis, the performance of the portfolios obtained by the Limited Asset models with the performance provided by the unconstrained models and with that of the official capital market indices