Fermi surface and light quasi particles in hourglass nodal chain metalß-ReO2.

Quantum oscillations (QOs) in magnetic torque and electrical resistivity were measured to investigate the electronic structure ofß-ReO2, a candidate hourglass nodal chain (NC) metal (Dirac loop chain metal). All the de Haas-van Alphen oscillation branches measured at 30 mK in magnetic fields of up to 17.5 T were consistent with first-principles calculations predicting four Fermi surfaces (FSs). The small-electron FS of the four FSs exhibited a very small cyclotron mass, 0.059 times that of the free electrons, which is likely related to the linear dispersion of the energy band. The consistency between the QO results and band calculations indicates the presence of the hourglass NC predicted forß-ReO2in the vicinity of the Fermi energy.

Pond Assay for the Sensory Systems of Caenorhabditis elegans: A Novel Anesthesia-Free Method Enabling Detection of Responses to Extremely Low Chemical Concentrations.

Chemotaxis in the nematode Caenorhabditis elegans has basically been examined using conventional assay methods. Although these can be problematic, for example, in their use of anesthesia, the method has never been improved. We propose a pond assay for the sensory systems (PASS) of C. elegans as a novel population-based method of behavioral analysis. The test solution is injected into a recess(es) formed on agar and the response of C. elegans to its odor and/or taste is examined. Once C. elegans individuals fall into recesses (ponds) filled with liquid, they cannot return to a solid medium. In this way, the animals are trapped with certainty without the use of anesthesia. The anesthesia used to keep animals in the attractant area in conventional chemotaxis assays is no longer required, allowing pure evaluation of the attractant or repellent response to specific substances. Furthermore, the assay itself can be greatly streamlined because the preparation can be completed simply by providing a recess(es) and filling the liquid. The present paper reports the detailed method and effectiveness of the novel PASS.

A novel framework based on a data-driven approach for modelling the behaviour of organisms in chemical plume tracing.

We propose a data-driven approach for modelling an organism's behaviour instead of conventional model-based strategies in chemical plume tracing (CPT). CPT models based on this approach show promise in faithfully reproducing organisms' CPT behaviour. To construct the data-driven CPT model, a training dataset of the odour stimuli input toward the organism is needed, along with an output of the organism's CPT behaviour. To this end, we constructed a measurement system comprising an array of alcohol sensors for the measurement of the input and a camera for tracking the output in a real scenario. Then, we determined a transfer function describing the input-output relationship as a stochastic process by applying Gaussian process regression, and established the data-driven CPT model based on measurements of the organism's CPT behaviour. Through CPT experiments in simulations and a real environment, we evaluated the performance of the data-driven CPT model and compared its success rate with those obtained from conventional model-based strategies. As a result, the proposed data-driven CPT model demonstrated a better success rate than those obtained from conventional model-based strategies. Moreover, we considered that the data-driven CPT model could reflect the aspect of an organism's adaptability that modulated its behaviour with respect to the surrounding environment. However, these useful results came from the CPT experiments conducted in simple settings of simulations and a real environment. If making the condition of the CPT experiments more complex, we confirmed that the data-driven CPT model would be less effective for locating an odour source. In this way, this paper not only poses major contributions toward the development of a novel framework based on a data-driven approach for modelling an organism's CPT behaviour, but also displays a research limitation of a data-driven approach at this stage.

Evidences of inner Se ordering in topological insulator PbBi2Te4-PbBi2Se4-PbSb2Se4 solid solutions.

In topological insulators (TIs), carriers originating from non-stoichiometric defects hamper bulk insulation. In (Bi,Sb)2(Te,Se)3 TIs (BSTS TIs), however, Se atoms strongly prefer specific atomic sites in the crystal structure (Se ordering), and this ordering structure suppresses the formation of point defects and contributes to bulk insulation. It has accelerated the understanding of TIs' surface electron properties and device application. In this study, we select Pb(Bi,Sb)2(Te,Se)4 (Pb-BSTS) TIs, which are reported to have larger bandgap compared to counterpart compound BSTS TIs. The Se ordering geometry was investigated by combining state-of-the-art scanning transmission electron microscopy and powder X-ray diffractometry. We demonstrated the existence of inner Se ordering in PbBi2(Te,Se)4 and also in Pb-BSTS TIs. Quantitative analysis of Se ordering and a qualitative view of atomic non-stoichiometry such as point defects are also presented. Pb-BSTS TIs' Se ordering structure and their large gap nature has the great potential to achieve more bulk insulation than conventional BSTS TIs.

Micro- and Nanopillar Chips for Continuous Separation of Extracellular Vesicles.

Micro- and nanopillar chips are widely used to separate and enrich biomolecules, such as DNA, RNA, protein, and cells, as an analytical technique and to provide a confined nanospace for polymer science analyses. Herein, we demonstrated a continuous accurate and precise separation technique for extracellular vesicles (EVs), nanometer-sized vesicles (typically 50-200 nm) currently recognized as novel biomarkers present in biofluids, based on the principle of electroosmotic flow-driven deterministic lateral displacement in micro- and nanopillar array chips. Notably, the easy-to-operate flow control afforded by electroosmotic flow allowed nanoparticles 50-500 nm in size, including EVs, to be precisely separated and enriched in a continuous manner. By observation of the flow behavior of nanoparticles, we found that electroosmotic flow velocity in the nanopillar arrays did not solely depend on counterion mobility on the surface of nanopillar chips, but rather showed a parabolic flow profile. This hydrodynamic pressure-free and easy-to-use separation and enrichment technique, which requires only electrode insertion into the reservoirs and electric field application, may thus serve as a promising technique for future precise and accurate EV analysis, reflecting both size and composition for research and potential clinical diagnostic applications.

Development of ultra-thin chips for immobilization of Caenorhabditis elegans in microfluidic channels during irradiation and selection of buffer solution to prevent dehydration.

BACKGROUND: Targeted microbeam irradiation of Caenorhabditis elegans allows the effective knockdown of specific regions, thus helping to identify their roles in processes such as locomotion. We previously employed on-chip immobilization of individuals without anesthesia; however, this method was limited by the thickness of the chip, which prevented the detection of ions passing through the animal, and by dehydration of the animals after prolonged immobilization. NEW METHOD: We developed ultra-thin, ion-penetrable, polydimethylsiloxane microfluidic chips, referred to as Worm Sheets, with and without wettability (hydrophilicity/hydrophobicity), and identified suitable buffer conditions for maintaining moisture in the microfluidic channels. RESULTS: Using a collimating microbeam system, we demonstrated that carbon ions (with a range of ∼1 mm) could pass through the chip, thus allowing the ions to be detected and the applied radiation dose to therefore by measured accurately. We also examined the locomotion of C. elegans following on-chip immobilization in different buffers. Locomotion was decreased in certain buffers on unwettable chips as a result of dehydration due to evaporation, but not on wettable chips. However, locomotion was unaffected on either chip in the presence of a gelatin-based wash buffer. COMPARISON WITH EXISTING METHOD(S): We developed 300-µm-ultra-thin, wettable, ion-penetrable chips for immobilizing C. elegans and provided initial guidance regarding suitable buffer solutions to maintain moisture in microfluidic channels. CONCLUSIONS: This improved, wettable chip, together with the identification of suitable buffer conditions, will become a powerful tool for prolonged immobilizing C. elegans, and is widely applicable not only to microbeam irradiation but also to neurobiological assays.

Cell Deposition Microchip with Micropipette Control over Liquid Interface Motion.

Positioning single cells on a solid surface is a crucial technique for understanding the cellular functions and cell-cell interactions in cell culture assays. We developed a microfluidic chip for depositing single cells in microwells using a simple micropipette operation. Cells were delivered to microwells by the meniscus motion of liquid interface. The residue deposits of cells were redistributed with air injection, and the isolated single cells were stored in microwells. Different microwell sizes and depths were studied to evaluate the trapping possibility of cells. Medium replacement and cell viability staining with the isolated single cells were achieved in microwells. The chip will serve as a tool for single-cell patterning in an easy-to-use manner.

Region-specific irradiation system with heavy-ion microbeam for active individuals of Caenorhabditis elegans.

Radiation may affect essential functions and behaviors such as locomotion, feeding, learning and memory. Although whole-body irradiation has been shown to reduce motility in the nematode Caenorhabditis elegans, the detailed mechanism responsible for this effect remains unknown. Targeted irradiation of the nerve ring responsible for sensory integration and information processing would allow us to determine whether the reduction of motility following whole-body irradiation reflects effects on the central nervous system or on the muscle cells themselves. We therefore addressed this issue using a collimating microbeam system. However, radiation targeting requires the animal to be immobilized, and previous studies have anesthetized animals to prevent their movement, thus making it impossible to assess their locomotion immediately after irradiation. We developed a method in which the animal was enclosed in a straight, microfluidic channel in a polydimethylsiloxane chip to inhibit free motion during irradiation, thus allowing locomotion to be observed immediately after irradiation. The head region (including the central nervous system), mid region around the intestine and uterus, and tail region were targeted independently. Each region was irradiated with 12 000 carbon ions (12C; 18.3 MeV/u; linear energy transfer = 106.4 keV/µm), corresponding to 500 Gy at a φ20 µm region. Motility was significantly decreased by whole-body irradiation, but not by irradiation of any of the individual regions, including the central nervous system. This suggests that radiation inhibits locomotion by a whole-body mechanism, potentially involving motoneurons and/or body-wall muscle cells, rather than affecting motor control via the central nervous system and the stimulation response.

Cell cycle tracking for irradiated and unirradiated bystander cells in a single colony with exposure to a soft X-ray microbeam.

PURPOSE: To establish a new experimental technique to explore the photoelectric and subsequent Auger effects on the cell cycles of soft X-ray microbeam-irradiated cells and unirradiated bystander cells in a single colony. MATERIALS AND METHODS: Several cells located in the center of a microcolony of HeLa-Fucci cells consisting of 20-80 cells were irradiated with soft X-ray (5.35 keV) microbeam using synchrotron radiation as a light source. All cells in the colony were tracked for 72 h by time-lapse microscopy imaging. Cell cycle progression, division, and death of each cell in the movies obtained were analyzed by pedigree assay. The number of cell divisions in the microcolony was also determined. RESULTS: The fates of these cells were clarified by tracking both irradiated and unirradiated bystander cells. Irradiated cells showed significant cell cycle retardation, explosive cell death, or cell fusion after a few divisions. These serious effects were also observed in 15 and 26% of the bystander cells for 10 and 20 Gy irradiation, respectively, and frequently appeared in at least two daughter or granddaughter cells from a single-parent cell. CONCLUSIONS: We successfully tracked the fates of microbeam-irradiated cells and unirradiated bystander cells with live cell recordings, which have revealed the dynamics of soft X-ray irradiated and unirradiated bystander cells for the first time. Notably, cell deaths or cell cycle arrests frequently arose in closely related cells. These details would not have been revealed by a conventional immunostaining imaging method. Our approach promises to reveal the dynamic cellular effects of soft X-ray microbeam irradiation and subsequent Auger processes from various endpoints in future studies.

Evaluation of DNA damage induced by Auger electrons from 137Cs.

PURPOSE: To understand the biological effect of external and internal exposure from 137Cs, DNA damage spectrum induced by directly emitted electrons (γ-rays, internal conversion electrons, Auger electrons) from 137Cs was compared with that induced by 137Cs γ-rays. METHODS: Monte Carlo track simulation method was used to calculate the microscopic energy deposition pattern in liquid water. Simulation was performed for the two simple target systems in microscale. Radiation sources were placed inside for one system and outside for another system. To simulate the energy deposition by directly emitted electrons from 137Cs placed inside the system, the multiple ejections of electrons after internal conversion were considered. In the target systems, induction process of DNA damage was modeled and simulated for both direct energy deposition and the water radical reaction on the DNA. The yield and spatial distribution of simple and complex DNA damage including strand breaks and base lesions were calculated for irradiation by electrons and γ-rays from 137Cs. RESULTS: The simulation showed that the significant difference in DNA damage spectrum was not caused by directly ejected electrons and γ-rays from 137Cs. CONCLUSIONS: The result supports the existing perception that the biological effects by internal and external exposure by 137Cs are equivalent.

Cellular automaton-based model for radiation-induced bystander effects.

BACKGROUND: The radiation-induced bystander effect is a biological response observed in non-irradiated cells surrounding an irradiated cell. The bystander effect is known to be induced by two intercellular signaling pathways, the medium-mediated pathway (MDP) and the gap junctional pathway (GJP). To investigate the relative contribution of each signaling pathway, we have developed a mathematical model of the cellular response through these two pathways, with a particular focus on cell-cycle modification. METHODS: The model is based on a cellular automaton and consists of four components: (1) irradiation, (2) generation and diffusion of intercellular signals, (3) induction of DNA double-strand breaks (DSBs), and (4) cell-cycle modification or cell death. The intercellular signals are generated in and released from irradiated cells. The signals through the MDP and the GJP are modeled independently based on diffusion equations. The irradiation and both signals raise the number of DSBs, which determines transitions of cellular states, such as cell-cycle arrest or cell death. RESULTS: Our model reproduced fairly well previously reported experimental data on the number of DSBs and cell survival curves. We examined how radiation dose and intercellular signaling dynamically affect the cell cycle. The analysis of model dynamics for the bystander cells revealed that the number of arrested cells did not increase linearly with dose. Arrested cells were more efficiently accumulated by the GJP than by the MDP. CONCLUSIONS: We present here a mathematical model that integrates various bystander responses, such as MDP and GJP signaling, DSB induction, cell-cycle arrest, and cell death. Because it simulates spatial and temporal conditions of irradiation and cellular characteristics, our model will be a powerful tool to predict dynamical radiobiological responses of a cellular population in which irradiated and non-irradiated cells co-exist.

A mathematical model of radiation-induced responses in a cellular population including cell-to-cell communications.

Cell-to-cell communication is an important factor for understanding the mechanisms of radiation-induced responses such as bystander effects. In this study, a new mathematical model of intercellular signalling between individual cells in a cellular population is proposed. The authors considered two types of transmission of signals: via culture medium and via gap junction. They focus on the effects that radiation and intercellular signalling have on cell-cycle modification. The cell cycle is represented as a virtual clock that includes several checkpoint pathways within a cyclic process. They also develop a grid model and set up diffusion equations to model the propagation of signals to and from spatially located cells. The authors have also considered the role that DNA damage plays in the cycle of cells which can progress through the cell cycle or stop at the G1, S, G2 or M-phase checkpoints. Results of testing show that the proposed model can simulate intercellular signalling and cell-cycle progression in individual cells during and after irradiation.

Theoretical and evolutionary parameter tuning of neural oscillators with a double-chain structure for generating rhythmic signals.

A neural oscillator with a double-chain structure is one of the central pattern generator models used to simulate and understand rhythmic movements in living organisms. However, it is difficult to reproduce desired rhythmic signals by tuning an enormous number of parameters of neural oscillators. In this study, we propose an automatic tuning method consisting of two parts. The first involves tuning rules for both the time constants and the amplitude of the oscillatory outputs based on theoretical analyses of the relationship between parameters and outputs of the neural oscillators. The second involves an evolutionary tuning method with a two-step genetic algorithm (GA), consisting of a global GA and a local GA, for tuning parameters such as neural connection weights that have no exact tuning rule. Using numerical experiments, we confirmed that the proposed tuning method could successfully tune all parameters and generate sinusoidal waves. The tuning performance of the proposed method was less affected by factors such as the number of excitatory oscillators or the desired outputs. Furthermore, the proposed method was applied to the parameter-tuning problem of some types of artificial and biological wave reproduction and yielded optimal parameter values that generated complex rhythmic signals in Caenorhabditis elegans without trial and error.