Microbial synthetic biology

In this talk, I will introduce two topics related with microbial engineering; a novel synthetic biology tool for efficient protein synthesis and a novel microbial platform for biorefinery. Firstly, we developed a synthetic Protein Quality Control (ProQC) system to improve the yield of the synthesis of full-length proteins in E. coli. Tightly coupled transcription and translation system in prokaryotes can cause the production of non-functional polypeptides which are translated from early-terminated or degraded transcripts. We used toehold switches to decouple transcription and translation processes. By placing corresponding trigger sequences at 3’-end of mRNA, intact full-length mRNAs could only be translated. When fluorescence tags were attached at both N- and C-terminal ends, we found that equivalent fluorescent intensities from both ends were observed in our system. This result shows that decoupling of transcription and translation processes can be applicable to elevate the quality of gene expression, especially longer proteins. Secondly, we isolated a novel fast-growing bacterium which shows efficient alginate utilization and whose growth rates and sugar uptake rates with most biomassderivable sugars are substantially higher than those of E. coli. We systematically characterized its genome as well as transcriptome to elucidate its metabolism and gene expression architecture. Based on this, we were able to develop genetic toolboxes for its engineering and successfully demonstrated rapid production of a broad spectrum of chemicals (ethanol, 2,3-butanediol, and lycopene) from alginate and mannitol mixtures with high productivities and yields. Collectively, this strain is a powerful platform for conversion of brown macroalgae sugars; moreover, its usage will dramatically accelerate production of value-added biochemicals

Periodic shedding of vortex dipoles from a moving penetrable obstacle in a Bose-Einstein condensate

We investigate vortex shedding from a moving penetrable obstacle in a highly oblate Bose-Einstein condensate. The penetrable obstacle is formed by a repulsive Gaussian laser beam that has the potential barrier height lower than the chemical potential of the condensate. The moving obstacle periodically generates vortex dipoles and the vortex shedding frequency $f_v$ linearly increases with the obstacle velocity $v$ as $f_v=a(v-v_c)$, where $v_c$ is a critical velocity. Based on periodic shedding behavior, we demonstrate deterministic generation of a single vortex dipole by applying a short linear sweep of a laser beam. This method will allow further controlled vortex experiments such as dipole-dipole collisions.Comment: 6 pages, 7 figure

Collisional Dynamics of Half-Quantum Vortices in a Spinor Bose-Einstein Condensate

We present an experimental study on the interaction and dynamics of half-quantum vortices (HQVs) in an antiferromagnetic spinor Bose-Einstein condensate. By exploiting the orbit motion of a vortex dipole in a trapped condensate, we perform a collision experiment of two HQV pairs, and observe that the scattering motions of the HQVs is consistent with the short-range vortex interaction that arises from nonsingular magnetized vortex cores. We also investigate the relaxation dynamics of turbulent condensates containing many HQVs, and demonstrate that spin wave excitations are generated by the collisional motions of the HQVs. The short-range vortex interaction and the HQV-magnon coupling represent two characteristics of the HQV dynamics in the spinor superfluid.Comment: 7 pages, 6 figure

Self-Supervised Curriculum Generation for Autonomous Reinforcement Learning without Task-Specific Knowledge

A significant bottleneck in applying current reinforcement learning algorithms to real-world scenarios is the need to reset the environment between every episode. This reset process demands substantial human intervention, making it difficult for the agent to learn continuously and autonomously. Several recent works have introduced autonomous reinforcement learning (ARL) algorithms that generate curricula for jointly training reset and forward policies. While their curricula can reduce the number of required manual resets by taking into account the agent's learning progress, they rely on task-specific knowledge, such as predefined initial states or reset reward functions. In this paper, we propose a novel ARL algorithm that can generate a curriculum adaptive to the agent's learning progress without task-specific knowledge. Our curriculum empowers the agent to autonomously reset to diverse and informative initial states. To achieve this, we introduce a success discriminator that estimates the success probability from each initial state when the agent follows the forward policy. The success discriminator is trained with relabeled transitions in a self-supervised manner. Our experimental results demonstrate that our ARL algorithm can generate an adaptive curriculum and enable the agent to efficiently bootstrap to solve sparse-reward maze navigation tasks, outperforming baselines with significantly fewer manual resets.Comment: 8 pages, 5 figure

Critical Velocity for Vortex Shedding in a Bose-Einstein Condensate

We present measurements of the critical velocity for vortex shedding in a highly oblate Bose-Einstein condensate with a moving repulsive Gaussian laser beam. As a function of the barrier height $V_0$, the critical velocity $v_c$ shows a dip structure having a minimum at $V_0 \approx \mu$, where $\mu$ is the chemical potential of the condensate. At fixed $V_0\approx 7\mu$, we observe that the ratio of $v_c$ to the speed of sound $c_s$ monotonically increases for decreasing $\sigma/\xi$, where $\sigma$ is the beam width and $\xi$ is the condensate healing length. The measured upper bound for $v_c/c_s$ is about 0.4, which is in good agreement with theoretical predictions for a two-dimensional superflow past a circular cylinder. We explain our results with the density reduction effect of the soft boundary of the Gaussian obstacle, based on the local Landau criterion for superfluidity.Comment: 5 pages, 4 figure

Relaxation of superfluid turbulence in highly oblate Bose-Einstein condensates

We investigate thermal relaxation of superfluid turbulence in a highly oblate Bose-Einstein condensate. We generate turbulent flow in the condensate by sweeping the center region of the condensate with a repulsive optical potential. The turbulent condensate shows a spatially disordered distribution of quantized vortices and the vortex number of the condensate exhibits nonexponential decay behavior which we attribute to the vortex pair annihilation. The vortex-antivortex collisions in the condensate are identified with crescent-shaped, coalesced vortex cores. We observe that the nonexponential decay of the vortex number is quantitatively well described by a rate equation consisting of one-body and two-body decay terms. In our measurement, we find that the local two-body decay rate is closely proportional to $T^2/\mu$, where $T$ is the temperature and $\mu$ is the chemical potential.Comment: 7 pages, 9 figure

Observation of a Geometric Hall Effect in a Spinor Bose-Einstein Condensate with a Skyrmion Spin Texture

For a spin-carrying particle moving in a spatially varying magnetic field, effective electromagnetic forces can arise due to the geometric phase associated with adiabatic spin rotation of the particle. We report the observation of a geometric Hall effect in a spinor Bose-Einstein condensate with a skyrmion spin texture. Under translational oscillations of the spin texture, the condensate resonantly develops a circular motion in a harmonic trap, demonstrating the existence of an effective Lorentz force. When the condensate circulates, quantized vortices are nucleated in the boundary region of the condensate and the vortex number increases over 100 without significant heating. We attribute the vortex nucleation to the shearing effect of the effective Lorentz force from the inhomogeneous effective magnetic field.Comment: 9 pages, 11 figure

Adaptive Noise Reduction Algorithm to Improve R Peak Detection in ECG Measured by Capacitive ECG Sensors

Electrocardiograms (ECGs) can be conveniently obtained using capacitive ECG sensors. However, motion noise in measured ECGs can degrade R peak detection. To reduce noise, properties of reference signal and ECG measured by the sensors are analyzed and a new method of active noise cancellation (ANC) is proposed in this study. In the proposed algorithm, the original ECG signal at QRS interval is regarded as impulsive noise because the adaptive filter updates its weight as if impulsive noise is added. As the proposed algorithm does not affect impulsive noise, the original signal is not reduced during ANC. Therefore, the proposed algorithm can conserve the power of the original signal within the QRS interval and reduce only the power of noise at other intervals. The proposed algorithm was verified through comparisons with recent research using data from both indoor and outdoor experiments. The proposed algorithm will benefit a noise reduction of noisy biomedical signal measured from sensors.11Ysciescopu

Tau functions as Widom constants

We define a tau function for a generic Riemann-Hilbert problem posed on a union of non-intersecting smooth closed curves with jump matrices analytic in their neighborhood. The tau function depends on parameters of the jumps and is expressed as the Fredholm determinant of an integral operator with block integrable kernel constructed in terms of elementary parametrices. Its logarithmic derivatives with respect to parameters are given by contour integrals involving these parametrices and the solution of the Riemann-Hilbert problem. In the case of one circle, the tau function coincides with Widom's determinant arising in the asymptotics of block Toeplitz matrices. Our construction gives the Jimbo-Miwa-Ueno tau function for Riemann-Hilbert problems of isomonodromic origin (Painlev\'e VI, V, III, Garnier system, etc) and the Sato-Segal-Wilson tau function for integrable hierarchies such as Gelfand-Dickey and Drinfeld-Sokolov.Comment: 26 pages, 6 figure

National Trends in Medical Costs and Prognosis of Acute Ischemic Stroke Patients in Endovascular Thrombectomy Era: Analysis Using Medical Claim Data in Korea

Purpose The purpose of this study was to evaluate trends in medical costs and prognosis in acute ischemic stroke (AIS) patients in Korea from 2008 to 2017 using medical claims data. Materials and Methods All data for the past decade was collected from a big data hub provided by the Health Insurance Review & Assessment Service. Using several Korean Standard Classification of Disease codes, we estimated the number of patients, the costs of medical insurance, and prognosis according to the treatment with or without endovascular thrombectomy (EVT) among in-patients with AIS. Results Since 2014, when EVT was covered by insurance, the number of patients who underwent EVT for AIS has increased significantly. Also, in the past decade, the medical costs following inpatient care for AIS with EVT have increased gradually, and the overall medical costs for the first year post-stroke have also increased. The prognosis of AIS patients with EVT was different according to the time of treatment. Annual trends for both mortality and cerebral hemorrhage after treatment of AIS with EVT have gradually decreased. Conclusion In this study, we found that both inpatient medical costs and 1-year cumulative medical costs have gradually increased, and the prognosis has gradually improved in patients receiving EVT treatment among AIS patients