Advances in the multimodal analysis of the 3D chromatin structure and gene regulation

Recent studies have demonstrated that the three-dimensional conformation of the chromatin plays a crucial role in gene regulation, with aberrations potentially leading to various diseases. Advanced methodologies have revealed a link between the chromatin conformation and biological function. This review divides these methodologies into sequencing-based and imaging-based methodologies, tracing their development over time. We particularly highlight innovative techniques that facilitate the simultaneous mapping of RNAs, histone modifications, and proteins within the context of the 3D architecture of chromatin. This multimodal integration substantially improves our ability to establish a robust connection between the spatial arrangement of molecular components in the nucleus and their functional roles. Achieving a comprehensive understanding of gene regulation requires capturing diverse data modalities within individual cells, enabling the direct inference of functional relationships between these components. In this context, imaging-based technologies have emerged as an especially promising approach for gathering spatial information across multiple components in the same cell.

Switchable tribology of ferroelectrics

Switchable tribological properties of ferroelectrics offer an alternative route to visualize and control ferroelectric domains. Here, we observe the switchable friction and wear behavior of ferroelectrics using a nanoscale scanning probe-down domains have lower friction coefficients and show slower wear rates than up domains and can be used as smart masks. This asymmetry is enabled by flexoelectrically coupled polarization in the up and down domains under a sufficiently high contact force. Moreover, we determine that this polarization-sensitive tribological asymmetry is widely applicable across various ferroelectrics with different chemical compositions and crystalline symmetry. Finally, using this switchable tribology and multi-pass patterning with a domain-based dynamic smart mask, we demonstrate three-dimensional nanostructuring exploiting the asymmetric wear rates of up and down domains, which can, furthermore, be scaled up to technologically relevant (mm-cm) size. These findings demonstrate that ferroelectrics are electrically tunable tribological materials at the nanoscale for versatile applications.

Probabilistic computing with NbOx metal-insulator transition-based self-oscillatory pbit

Energy-based computing is a promising approach for addressing the rising demand for solving NP-hard problems across diverse domains, including logistics, artificial intelligence, cryptography, and optimization. Probabilistic computing utilizing pbits, which can be manufactured using the semiconductor process and seamlessly integrated with conventional processing units, stands out as an efficient candidate to meet these demands. Here, we propose a novel pbit unit using an NbOx volatile memristor-based oscillator capable of generating probabilistic bits in a self-clocking manner. The noise-induced metal-insulator transition causes the probabilistic behavior, which can be effectively modeled using a multi-noise-induced stochastic process around the metal-insulator transition temperature. We demonstrate a memristive Boltzmann machine based on our proposed pbit and validate its feasibility by solving NP-hard problems. Furthermore, we propose a streamlined operation methodology that considers the autocorrelation of individual bits, enabling energy-efficient and high-performance probabilistic computing.

Where should siRNAs go: applicable organs for siRNA drugs

RNA interference mediated by small interfering RNAs (siRNAs) has been exploited for the development of therapeutics. siRNAs can be a powerful therapeutic tool because the working mechanisms of siRNAs are straightforward. siRNAs determine targets based on their sequence and specifically regulate the gene expression of the target gene. However, efficient delivery of siRNAs to the target organ has long been an issue that needs to be solved. Tremendous efforts regarding siRNA delivery have led to significant progress in siRNA drug development, and from 2018 to 2022, a total of five siRNA drugs were approved for the treatment of patients. Although all FDA-approved siRNA drugs target the hepatocytes of the liver, siRNA-based drugs targeting different organs are in clinical trials. In this review, we introduce siRNA drugs in the market and siRNA drug candidates in clinical trials that target cells in multiple organs. The liver, eye, and skin are the preferred organs targeted by siRNAs. Three or more siRNA drug candidates are in phase 2 or 3 clinical trials to suppress gene expression in these preferred organs. On the other hand, the lungs, kidneys, and brain are challenging organs with relatively few clinical trials. We discuss the characteristics of each organ related to the advantages and disadvantages of siRNA drug targeting and strategies to overcome the barriers in delivering siRNAs based on organ-specific siRNA drugs that have progressed to clinical trials.

Anisotropic leaky-like perturbation with subwavelength gratings enables zero crosstalk

Electromagnetic coupling via an evanescent field or radiative wave is a primary characteristic of light, allowing optical signal/power transfer in a photonic circuit but limiting integration density. A leaky mode, which combines both evanescent field and radiative wave, causes stronger coupling and is thus considered not ideal for dense integration. Here we show that a leaky oscillation with anisotropic perturbation rather can achieve completely zero crosstalk realized by subwavelength grating (SWG) metamaterials. The oscillating fields in the SWGs enable coupling coefficients in each direction to counteract each other, resulting in completely zero crosstalk. We experimentally demonstrate such an extraordinarily low coupling between closely spaced identical leaky SWG waveguides, suppressing the crosstalk by ≈40 dB compared to conventional strip waveguides, corresponding to ≈100 times longer coupling length. This leaky-SWG suppresses the crosstalk of transverse-magnetic (TM) mode, which is challenging due to its low confinement, and marks a novel approach in electromagnetic coupling applicable to other spectral regimes and generic devices.

Critical transition and reversion of tumorigenesis

Cancer is caused by the accumulation of genetic alterations and therefore has been historically considered to be irreversible. Intriguingly, several studies have reported that cancer cells can be reversed to be normal cells under certain circumstances. Despite these experimental observations, conceptual and theoretical frameworks that explain these phenomena and enable their exploration in a systematic way are lacking. In this review, we provide an overview of cancer reversion studies and describe recent advancements in systems biological approaches based on attractor landscape analysis. We suggest that the critical transition in tumorigenesis is an important clue for achieving cancer reversion. During tumorigenesis, a critical transition may occur at a tipping point, where cells undergo abrupt changes and reach a new equilibrium state that is determined by complex intracellular regulatory events. We introduce a conceptual framework based on attractor landscapes through which we can investigate the critical transition in tumorigenesis and induce its reversion by combining intracellular molecular perturbation and extracellular signaling controls. Finally, we present a cancer reversion therapy approach that may be a paradigm-changing alternative to current cancer cell-killing therapies.

Soft subdermal implant capable of wireless battery charging and programmable controls for applications in optogenetics

Optogenetics is a powerful technique that allows target-specific spatiotemporal manipulation of neuronal activity for dissection of neural circuits and therapeutic interventions. Recent advances in wireless optogenetics technologies have enabled investigation of brain circuits in more natural conditions by releasing animals from tethered optical fibers. However, current wireless implants, which are largely based on battery-powered or battery-free designs, still limit the full potential of in vivo optogenetics in freely moving animals by requiring intermittent battery replacement or a special, bulky wireless power transfer system for continuous device operation, respectively. To address these limitations, here we present a wirelessly rechargeable, fully implantable, soft optoelectronic system that can be remotely and selectively controlled using a smartphone. Combining advantageous features of both battery-powered and battery-free designs, this device system enables seamless full implantation into animals, reliable ubiquitous operation, and intervention-free wireless charging, all of which are desired for chronic in vivo optogenetics. Successful demonstration of the unique capabilities of this device in freely behaving rats forecasts its broad and practical utilities in various neuroscience research and clinical applications.

Application of Wearable Inertial Sensors and A New Test Battery for Distinguishing Retrospective Fallers from Non-fallers among Community-dwelling Older People

Considering the challenge of population ageing and the substantial health problem among the elderly population from falls, the purpose of this study was to verify whether it is possible to distinguish accurately between older fallers and non-fallers, based on data from wearable inertial sensors collected during a specially designed test battery. A comprehensive but practical test battery using 5 wearable inertial sensors for multifactorial fall risk assessment was designed. This was followed by an experimental study on 196 community-dwelling Korean older women, categorized as fallers (N1 = 82) and non-fallers (N2 = 114) based on prior history of falls. Six machine learning models (logistic regression, naïve bayes, decision tree, random forest, boosted tree and support vector machine) were proposed for faller classification. Results indicated that compared with non-fallers, fallers performed significantly worse on the test battery. In addition, the application of sensor data and support vector machine for faller classification achieved an overall accuracy of 89.4% with 92.7% sensitivity and 84.9% specificity. These findings suggest that wearable inertial sensor based systems show promise for elderly fall risk assessment, which could be implemented in clinical practice to identify "at-risk" individuals reliably to promote proactive fall prevention.