OIST Institutional Repository
Not a member yet
2744 research outputs found
Sort by
Variational Recurrent Models for Solving Partially Observable Control Tasks
Get PDFIn partially observable (PO) environments, deep reinforcement learning (RL) agents often suffer from unsatisfactory performance, since two problems need to be tackled together: how to extract information from the raw observations to solve the task, and how to improve the policy. In this study, we propose an RL algorithm for solving PO tasks. Our method comprises two parts: a variational recurrent model (VRM) for modeling the environment, and an RL controller that has access to both the environment and the VRM. The proposed algorithm was tested in two types of PO robotic control tasks, those in which either coordinates or velocities were not observable and those that require long-term memorization. Our experiments show that the proposed algorithm achieved better data efficiency and/or learned more optimal policy than other alternative approaches in tasks in which unobserved states cannot be inferred from raw observations in a simple manner.conference pape
Capturing the nonlinear dynamics of animal behavior with Applications to the Nematode C. elegans
Get PDFOkinawa Institute of Science and Technology Graduate UniversityDoctor of PhilosophyFrom microorganisms to humans, animals behave by making complex changes in their shape and posture over time with remarkable flexibility. To deal with the complexity of animal behavior existing analysis methods view it as a discrete time process, which is composed of transitions between a finite number of stereotyped motifs, such as walking or reaching. This viewpoint, however, ignores the fact that most behavior is not stereotyped. There is, therefore, a need for a perspective that captures the continuous complexity of animal behavior and offers detailed insights into general principles underlying its generation and control.
In my Ph.D. thesis, I propose a new approach of analyzing animal behavior, based on the idea that it is fundamentally a continuous time spatiotemporal dynamical system. I develop methods to transform behavioral recordings into a geometrical object called the ""behavioral state space"". As an organism moves, the corresponding behavioral state traces out a continuous trajectory in the state space, such that the geometry and topology of the trajectories encode quantitative and qualitative properties of behavior. Finally, I characterize an organism's behavioral dynamics in terms of the topological invariants estimated from the local Jacobians of the state space trajectories. The invariants capture essential aspects of a dynamical system, such as the number of degrees of freedom, symmetries in the governing equations of motion, and measures of predictability and variability.
I use the tools and concepts developed the above to perform a detailed characterization of continuous dynamics of freely behaving \textit{C. elegans} worms.doctoral thesi
Heterochirality results from reduction of maternal diaph expression in a terrestrial pulmonate snail
Get PDFoai:oist.repo.nii.ac.jp:00001000Background: Spiral cleavage is a feature of non-ecdysozoan protostomes, in which left-right reversal frequently evolved in gastropod molluscs. In pulmonate gastropods, maternal molecules are responsible for chirality patterning, on which the polarities of visceral and coiling asymmetries depend. In the pond snail, Lymnaea stagnalis (the clade Hygrophila), a frame-shift mutation of one of tandem-duplicated, diaphanous-related formin genes (diaph) resulted in incomplete reversal from dextral to sinistral cleavage. Is this mechanism of chirality regulation common to, or shared with other pulmonates? To answer this question, we examined genes involved in chirality patterning in the land snail, Bradybaena similaris which belongs to the clade Stylommatophora.
Results: Both dextral and sinistral siblings develop from progeny of a racemic mutant of B. similaris. Differences in maternal mRNAs between the two strains were searched by transcriptome analyses. We found fifty maternal transcripts that exhibited less expression in early embryos of the mutant strain. The most conspicuous was a homolog of diaph. The diaph gene was duplicated in the stylommatophoran ancestor (diaph-a and diaph-b), as in the case of the ancestor of Lymnaea (Lsdiaph1 and Lsdiaph2). The quantity of maternal diaph-b mRNA was drastically reduced in early embryos of the racemic mutant compared to wild-type, while diaph-a expression was at nearly the same level in both strains. Unlike the case of Lsdiaph2, which is frame-shifted to produce truncated peptides in the mutant of L. stagnalis, however, Bsdiaph-b mRNA in the mutant strain is not frame-shifted and most probably produces normal Diaph-b protein. These results suggest the presence of regulatory mechanisms of gene expression for chirality patterning in pulmonate gastropods, although genomic analyses are required for confirmation.
Conclusions: Heterochirality resulting from the loss of polarity control in spiral cleavage does not require mutation of the diaph gene in B. similaris. The determination of left-right polarity instead depends on the expression of this diaph gene, which is duplicated in stylommatophoran Bradybaena, as well as in hygrophilan Lymnaea. Our results provide an avenue to identifying a regulatory mechanism that controls the direction of spiral cleavage in gastropods.journal articl
Expansion of the fatty acyl reductase gene family shaped pheromone communication in Hymenoptera
Get PDFFatty acyl reductases (FARs) are involved in the biosynthesis of fatty alcohols that serve a range of biological roles. Insects typically harbor numerous FAR gene family members. While some FARs are involved in pheromone biosynthesis, the biological significance of the large number of FARs in insect genomes remains unclear. Using bumble bee (Bombini) FAR expression analysis and functional characterization, hymenopteran FAR gene tree reconstruction, and inspection of transposable elements (TEs) in the genomic environment of FARs, we uncovered a massive expansion of the FAR gene family in Hymenoptera, presumably facilitated by TEs. The expansion occurred in the common ancestor of bumble bees and stingless bees (Meliponini). We found that bumble bee FARs from the expanded FAR-A ortholog group contribute to the species-specific pheromone composition. Our results indicate that expansion and functional diversification of the FAR gene family played a key role in the evolution of pheromone communication in Hymenoptera.journal articl
Unraveling the Impact of Halide Mixing on Perovskite Stability
Get PDFIncreasing the stability of perovskites is essential for their integration in commercial photovoltaic devices. Halide mixing is suggested as a powerful strategy toward stable perovskite materials. However, the stabilizing effect of the halides critically depends on their distribution in the mixed compound, a topic that is currently under intense debate. Here we successfully determine the exact location of the I and Cl anions in the CH3NH3PbBr3–yIy and CH3NH3PbBr3–zClz mixed halide perovskite lattices and correlate it with the enhanced stability we find for the latter. By combining scanning tunneling microscopy and density functional theory, we predict that, for low ratios, iodine and chlorine incorporation have different effects on the electronic properties and stability of the CH3NH3PbBr3 perovskite material. In addition, we determine the optimal Cl incorporation ratio for stability increase without detrimental band gap modification, providing an important direction for the fabrication of stable perovskite devices. The increased material stability induced by chlorine incorporation is verified by performing photoelectron spectroscopy on a half-cell device architecture. Our findings provide an answer to the current debate on halide incorporation and demonstrate their direct influence on device stability.journal articl
Coupling between Rydberg States and Landau Levels of Electrons Trapped on Liquid Helium
Get PDFWe investigate the coupling between Rydberg states of electrons trapped on a liquid helium surface and Landau levels induced by a perpendicular magnetic field. We show that this realizes a prototype quantum system equivalent to an atom in a cavity, where their coupling strength can be tuned by a parallel magnetic field. We determine experimentally the renormalization of the atomic transition energies induced by the coupling to the cavity, which can be seen as an analog of the Lamb shift. When the coupling is sufficiently strong, the transition between the ground and first excited Rydberg states splits into two resonances corresponding to dressed states with vacuum and one photon in the cavity. Our results are in quantitative agreement with the energy shifts predicted by the effective atom in a cavity model where all parameters are known with high accuracy.journal articl
Chaotic few-body vortex dynamics in rotating Bose-Einstein condensates
Get PDFWe investigate a small vortex-lattice system of four corotating vortices in an atomic Bose-Einstein condensate and find that the vortex dynamics display chaotic behavior after a system quench introduced by reversing the direction of circulation of a single vortex through a phase-imprinting process. By tracking the vortex trajectories and Lyapunov exponent, we show the onset of chaotic dynamics is not immediate, but occurs at later times and is accelerated by the close approach and separation of all vortices in a scattering event. The techniques we develop could potentially be applied to create locally induced chaotic dynamics in larger lattice systems as a stepping stone to study the role of chaotic events in turbulent vortex dynamics.journal articl
Emergence of a Thrombospondin Superfamily at the Origin of Metazoans
Get PDFExtracellular matrix (ECM) is considered central to the evolution of metazoan multicellularity; however, the repertoire of ECM proteins in nonbilaterians remains unclear. Thrombospondins (TSPs) are known to be well conserved from cnidarians to vertebrates, yet to date have been considered a unique family, principally studied for matricellular functions in vertebrates. Through searches utilizing the highly conserved C-terminal region of TSPs, we identify undisclosed new families of TSP-related proteins in metazoans, designated mega-TSP, sushi-TSP, and poriferan-TSP, each with a distinctive phylogenetic distribution. These proteins share the TSP C-terminal region domain architecture, as determined by domain composition and analysis of molecular models against known structures. Mega-TSPs, the only form identified in ctenophores, are typically >2,700 aa and are also characterized by N-terminal leucine-rich repeats and central cadherin/immunoglobulin domains. In cnidarians, which have a well-defined ECM, Mega-TSP was expressed throughout embryogenesis in Nematostella vectensis, with dynamic endodermal expression in larvae and primary polyps and widespread ectodermal expression in adult Nematostella vectensis and Hydra magnipapillata polyps. Hydra Mega-TSP was also expressed during regeneration and siRNA-silencing of Mega-TSP in Hydra caused specific blockade of head regeneration. Molecular phylogenetic analyses based on the conserved TSP C-terminal region identified each of the TSP-related groups to form clades distinct from the canonical TSPs. We discuss models for the evolution of the newly defined TSP superfamily by gene duplications, radiation, and gene losses from a debut in the last metazoan common ancestor. Together, the data provide new insight into the evolution of ECM and tissue organization in metazoans.journal articl
A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis
Get PDFBackground:Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis.
Findings:To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired-end and mate-pair libraries) and PacBio sequencing. RNA sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ∼17–kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was ∼656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although ∼70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, ∼99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules.
Conclusions:Our present sequencing and assembly of the P. naikaiensis nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.journal articl
On-Surface Synthesis of a Nonplanar Porous Nanographene
Get PDFOn-surface synthesis provides an effective approach toward the formation of graphene nanostructures that are difficult to achieve via traditional solution chemistry. Here, we report on the design and synthesis of a nonplanar porous nanographene with 78 sp(2) carbon atoms, namely C78. Through a highly selective oxidative cyclodehydrogenation of 2,3,6,7,10,11-hexa(naphthalen-1-yl)triphenylene (2), propeller nanographene precursor 1 was synthesized in solution. Interestingly, although 1 could not be cyclized further in solution, porous nanographene C78 was successfully achieved from 1 by on-surface assisted cyclodehydrogenation on Au(111). The structure and electronic properties of C78 have been investigated by means of scanning tunneling microscopy, noncontact atomic force microscopy, and scanning tunneling spectroscopy, complemented by computational investigations. Our results provide perspectives for the on-surface synthesis of porous graphene nanostructures, offering a promising strategy for the engineering of graphene materials with tailor-made properties.journal articl