Enhancer RNA Transcriptome-Wide Association Study Reveals a Distinctive Class of Pan-Cancer Susceptibility eRNAs.

Many cancer risk variants are located within enhancer regions and lack sufficient molecular interpretation. Here, we constructed the first comprehensive atlas of enhancer RNA (eRNA)-mediated genetic effects from 28 033 RNA sequencing samples across 11 606 individuals, identifying 21 073 eRNA quantitative trait loci (eRNA-QTLs) significantly associated with eRNA expression. Mechanistically, eRNA-QTLs frequently altered binding motifs of transcription factors.

Impact of rare non-coding variants on human diseases through alternative polyadenylation outliers.

Although rare non-coding variants (RVs) play crucial roles in complex traits and diseases, understanding their mechanisms and identifying disease-associated RVs continue to be major challenges. Here we constructed a comprehensive atlas of alternative polyadenylation (APA) outliers (aOutliers), including 1334 3' UTR and 200 intronic aOutliers, from 15,201 samples across 49 human tissues. These aOutliers exhibit unique characteristics from transcription or splicing outliers, with a pronounced RV enrichment.

Design, Fabrication and Characterization of Disk Resonator Gyroscope with Vibration and Shock Resistance.

This paper presents a comprehensive optimization of an outer frame anchor disk resonator gyroscope (DRG) with enhanced resistance to vibration and shock, achieved by increasing the resonant frequency of the tub and translation modes. Furthermore, the wineglass mode retains a high quality factor, enhancing sensitivity and reducing the angle random walk (ARW). The performance of the proposed DRG is analyzed using dynamic equations, and its structural parameters are optimized through finite element analysis (FEA).

Bridging piezoelectric and electrostatic effects: a novel piezo-MEMS pitch/roll gyroscope with sub 10°/h bias instability.

This paper proposes a novel piezo-MEMS pitch/roll gyroscope that co-integrates piezoelectric and electrostatic effects, for the first time achieves electrostatic mode-matching operation for piezoelectric gyroscopes. Movement of operated out-of-plane (OOP) mode (n = 3) and in-plane (IP) mode (n = 2) are orthogonal, ensuring that the OOP amplitude is not significantly limited by parallel plates set at nodes of IP mode. Therefore, a large OOP driving amplitude actuated by piezoelectric and frequency tuning in the IP sense mode trimmed by electrostatic can be achieved together with a low risk of pull-in, hence releases the trade-off between the tuning range and the linear actuation range.

A nuclear RNA degradation code for eukaryotic transcriptome surveillance.

The RNA exosome plays critical roles in eukaryotic RNA degradation, but it remains unclear how the exosome specifically recognizes its targets. The PAXT connection is an adaptor that recruits the exosome to polyadenylated RNAs in the nucleus, especially transcripts polyadenylated at intronic poly(A) sites. Here we show that PAXT-mediated RNA degradation is induced by the combination of a 5' splice site and a poly(A) junction, but not by either sequence alone.

Intermolecular Assembly of Dual Hydrogen Bonding Regio-Isomers Generates High-Performance AIE Probes.

Regio-isomers are utilized to design innovative AIE luminogens (AIEgens) by regulating molecular aggregation behavior. However, relevant examples are limited, and the underlying mechanism is not fully understood. Herein, a regio-isomer strategy is used to develop AIEgens by precisely regulating the intermolecular interactions in the solid state.

Pan-cancer transcriptome analysis reveals widespread regulation through alternative tandem transcription initiation.

Abnormal transcription initiation from alternative first exon has been reported to promote tumorigenesis. However, the prevalence and impact of gene expression regulation mediated by alternative tandem transcription initiation were mostly unknown in cancer. Here, we developed a robust computational method to analyze alternative tandem transcription start site (TSS) usage from standard RNA sequencing data.

Genome-Wide Identification of the Gene Family and Expression Analysis under Drought Stress in L.

TGA transcription factors belong to Group D of the bZIP transcription factors family and play vital roles in the stress response of plants. is an oil crop with rich economic value. However, a systematic analysis of gene family members in has not yet been reported.

MEMS reservoir computing system with stiffness modulation for multi-scene data processing at the edge.

Reservoir computing (RC) is a bio-inspired neural network structure which can be implemented in hardware with ease. It has been applied across various fields such as memristors, and electrochemical reactions, among which the micro-electro-mechanical systems (MEMS) is supposed to be the closest to sensing and computing integration. While previous MEMS RCs have demonstrated their potential as reservoirs, the amplitude modulation mode was found to be inadequate for computing directly upon sensing.

Upscaling net ecosystem CO exchanges in croplands: The application of integrating object-based image analysis and machine learning approaches.

Accurately estimating the net ecosystem exchange of CO (NEE) in cropland ecosystems is essential for understanding the impacts of agricultural practices and climate conditions. However, significant uncertainties persist in the estimation of regional cropland NEE due to landscape heterogeneity and variations in the efficacy of upscaling models. Here, we applied an integrated approach that combined object-based image analysis (OBIA) techniques with advanced machine learning (ML) approaches to upscale regional cropland NEE.

A Modulation Method for Tunnel Magnetoresistance Current Sensors Noise Suppression.

To mitigate the impact of low-frequency noise from the tunnel magnetoresistance (TMR) current sensor and ambient stray magnetic fields on weak current detection accuracy, we propose a high-resolution modulation-demodulation test method. This method modulates and demodulates the measurement signal, shifting low-frequency noise to the high-frequency band for effective filtering, thereby isolating the target signal from the noise. In this study, we developed a Simulink model for the TMR current sensor modulation-demodulation test method.

A distinct class of pan-cancer susceptibility genes revealed by an alternative polyadenylation transcriptome-wide association study.

Alternative polyadenylation plays an important role in cancer initiation and progression; however, current transcriptome-wide association studies mostly ignore alternative polyadenylation when identifying putative cancer susceptibility genes. Here, we perform a pan-cancer 3' untranslated region alternative polyadenylation transcriptome-wide association analysis by integrating 55 well-powered (n > 50,000) genome-wide association studies datasets across 22 major cancer types with alternative polyadenylation quantification from 23,955 RNA sequencing samples across 7,574 individuals. We find that genetic variants associated with alternative polyadenylation are co-localized with 28.

A decouple-decomposition noise analysis model for closed-loop mode-localized tilt sensors.

The development of mode-localized sensors based on amplitude output metrics has attracted increasing attention in recent years due to the potential of such sensors for high sensitivity and resolution. Mode-localization phenomena leverage the interaction between multiple coupled resonant modes to achieve enhanced performance, providing a promising solution to overcome the limitations of traditional sensing technologies. Amplitude noise plays a key role in determining the resolution of mode-localized sensors, as the output metric is derived from the measured AR (amplitude ratio) within the weakly coupled resonator system.

Immune-response 3'UTR alternative polyadenylation quantitative trait loci contribute to variation in human complex traits and diseases.

Genome-wide association studies (GWASs) have identified thousands of non-coding variants that are associated with human complex traits and diseases. The analysis of such GWAS variants in different contexts and physiological states is essential for deciphering the regulatory mechanisms underlying human disease. Alternative polyadenylation (APA) is a key post-transcriptional modification for most human genes that substantially impacts upon cell behavior.

xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs.

Genome-wide association studies (GWAS) have identified thousands of disease-associated non-coding variants, posing urgent needs for functional interpretation. Molecular Quantitative Trait Loci (xQTLs) such as eQTLs serve as an essential intermediate link between these non-coding variants and disease phenotypes and have been widely used to discover disease-risk genes from many population-scale studies. However, mining and analyzing the xQTLs data presents several significant bioinformatics challenges, particularly when it comes to integration with GWAS data.

scQTLbase: an integrated human single-cell eQTL database.

Genome-wide association studies (GWAS) have identified numerous genetic variants associated with diseases and traits. However, the functional interpretation of these variants remains challenging. Expression quantitative trait loci (eQTLs) have been widely used to identify mutations linked to disease, yet they explain only 20-50% of disease-related variants.

Analysis of the Thermally Induced Packaging Effects on the Frequency Drift of Micro-Electromechanical System Resonant Accelerometer.

Due to the working principle of MEMS resonant accelerometers, their thermally induced frequency drift is an inevitable practical issue for their extensive application. This paper is focused on reducing the thermally induced packaging effects on the frequency drift. A leadless ceramic chip carrier package with a stress-buffering layer was proposed for a MEMS resonant accelerometer, and the influences of packaging structure parameters on the frequency drift were investigated through finite element simulations and verified experimentally.

A Scale Factor Calibration Method for MEMS Resonant Accelerometers Based on Virtual Accelerations.

This paper presents a scale factor calibration method based on virtual accelerations generated by electrostatic force. This method uses a series of voltage signals to simulate the inertial forces caused by the acceleration input, rather than frequent and laborious calibrations with high-precision instruments. The error transfer model of this method is systematically analyzed, and the geometrical parameters of this novel micromachined resonant accelerometer (MRA) are optimized.

Enhanced Terahertz Fingerprint Sensing Mechanism Study of Tiny Molecules Based on Tunable Spoof Surface Plasmon Polaritons on Composite Periodic Groove Structures.

Highly sensitive detection of enhanced terahertz (THz) fingerprint absorption spectrum of trace-amount tiny molecules is essential for biosensing. THz surface plasmon resonance (SPR) sensors based on Otto prism-coupled attenuated total reflection (OPC-ATR) configuration have been recognized as a promising technology in biomedical detection applications. However, THz-SPR sensors based on the traditional OPC-ATR configuration have long been associated with low sensitivity, poor tunability, low refractive index resolution, large sample consumption, and lack of fingerprint analysis.

Input-Output-Improved Reservoir Computing Based on Duffing Resonator Processing Dynamic Temperature Compensation for MEMS Resonant Accelerometer.

An MEMS resonant accelerometer is a temperature-sensitive device because temperature change affects the intrinsic resonant frequency of the inner silicon beam. Most classic temperature compensation methods, such as algorithm modeling and structure design, have large errors under rapid temperature changing due to the hysteresis of the temperature response of the accelerometer. To address this issue, we propose a novel reservoir computing (RC) structure based on a nonlinear silicon resonator, which is specifically improved for predicting dynamic information that is referred to as the input-output-improved reservoir computing (IOI-RC) algorithm.

Design and Simulation Study of an Optical Mode-Localized MEMS Accelerometer.

In this paper, we demonstrate a novel photonic integrated accelerometer based on the optical mode localization sensing mechanism, which is designed on an SOI wafer with a device layer thickness of 220 nm. High sensitivity and large measurement range can be achieved by integrating coupled ring resonators with a suspended directional coupler on a proof mass. With the help of FEA simulation and numerical analysis, the proposed optical mode-localized sensor presents a sensitivity of 10/g (modal power ratio/acceleration) and an inertial displacement of from -8 to 10 microns corresponding to a range from -23.

Utilizing the Intrinsic Mode of Weakly Coupled Resonators for Temperature Compensation.

Accelerometers based on outputting amplitude ratios in weakly coupled resonators (WCRs) are attractive because their parametric sensitivity is higher by two or three orders of magnitudes than those based on outputting frequency. However, the impact of temperature on the coupler is a key factor in accelerometer applications. This paper proposed a novel mode-localized WCR accelerometer with a temperature compensation mechanism, with sensitive elements incorporating a double-ended tuning fork (DETF) resonator, clamped-clamped (CC) resonator, and a micro-lever coupler.

Periodic Heterogeneous Surface with Superhydrophilic/Superhydrophobic Stripes Processed by a Picosecond Laser.

Heterogeneous surface with superhydrophilic/superhydrophobic stripes (HS-s/sS) has great practical significance, which can be used in fuel cell water management, condensation heat transfer enhancement, underwater drag reduction. Herein, a fast and simple method for uniform HS-s/sS on several mesh materials, including copper, stainless steel, and nickel, is achieved by using picosecond (ps) laser line-by-line scanning. Note that the scanning period between the lines is kept constant during processing, the HS-s/sS is formed by self-organized, while the similar structure cannot be processed on solid metal surfaces using the same parameters.

ipaQTL-atlas: an atlas of intronic polyadenylation quantitative trait loci across human tissues.

Functional interpretation of disease-associated non-coding variants remains a significant challenge in the post-GWAS era. Our recent study has identified 3'UTR alternative polyadenylation (APA) quantitative trait loci (3'aQTLs) and connects APA events with QTLs as a major driver of human traits and diseases. Besides 3'UTR, APA events can also occur in intron regions, and increasing evidence has connected intronic polyadenylation with disease risk.

Using population-scale transcriptomic and genomic data to map 3' UTR alternative polyadenylation quantitative trait loci.

3' UTR alternative polyadenylation (APA) quantitative trait loci (3'aQTL) can explain approximately 16.1% of trait-associated non-coding variants and is largely distinct from other molecular QTLs. Here, we describe a bioinformatic protocol for identifying 3'aQTLs through standard RNA-seq and matched genomic data.