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 28.57% of cancer loci and contribute a significant portion of cancer heritability. We further identify 642 significant cancer susceptibility genes predicted to modulate cancer risk via alternative polyadenylation, 62.46% of which have been overlooked by traditional expression- and splicing- studies. As proof of principle validation, we show that alternative alleles facilitate 3' untranslated region lengthening of CRLS1 gene leading to increased protein abundance and promoted proliferation of breast cancer cells. Together, our study highlights the significant role of alternative polyadenylation in discovering new cancer susceptibility genes and provides a strong foundational framework for enhancing our understanding of the etiology underlying human cancers.

[The cases of tracing the source of patients infected with Omicron variant of SARS-CoV-2 based on wastewater-based epidemiology in Shenzhen]

Wastewater-based epidemiology (WBE) is an emerging discipline, which has been applied to drug abuse tracking and infectious disease pathogen surveillance. During the COVID-19 epidemic, WBE has been applied to monitor the epidemic trend and SARS-CoV-2 variants etc. In order to detect hidden COVID-19 cases and prevent transmission in the community, wastewater surveillance system for monitoring SARS-CoV-2 RNA was developed in Shenzhen. The sewage sampling sites were set up in key places such as the port areas, urban villages and residential communities of Futian, Nanshan, Luohu and Yantian districts. From July 26 to November 30, 2022, a total of 369 sewage sampling sites were set up, covering 1.93 million people. Continuous sampling was carried out for 3 hours in the peak period of water use every day. Sewage virus enrichment and SARS-CoV-2 nucleic acid detection were carried out by polyethylene glycol precipitation method and RT-qPCR, and a positive water sample disposal process was molded. This article aims to introduce the case of source tracing of COVID-19 infected patients based on urban sewage in Shenzhen. The sewage monitoring of Honghu water treatment plant in Luohu District played an early warning role, and the source of infection was traced. In the disposal of positive water samples in Futian South Road, Futian District, the important experience of monitoring point layout was obtained. In the sewage monitoring of Nanshan village, Nanshan District, the existence of occult infection was revealed. Sharing the experience of tracing the source of COVID-19 patients to avoid the spread of COVID-19 in the community based on wastewater surveillance of SARS-CoV-2 RNA in Shenzhen, and summarizing the advantages and application prospects of sewage surveillance can provide new ideas for monitoring emerging or re-emerging pathogens that are known to exhibit gastrointestinal excretion in the future.

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. Single-cell eQTLs (sc-eQTLs) studies provide an immense opportunity to identify new disease risk genes with expanded eQTL scales and transcriptional regulation at a much finer resolution. However, there is no comprehensive database dedicated to single-cell eQTLs that users can use to search, analyse and visualize them. Therefore, we developed the scQTLbase (http://bioinfo.szbl.ac.cn/scQTLbase), the first integrated human sc-eQTLs portal, featuring 304 datasets spanning 57 cell types and 95 cell states. It contains ∼16 million SNPs significantly associated with cell-type/state gene expression and ∼0.69 million disease-associated sc-eQTLs from 3 333 traits/diseases. In addition, scQTLbase offers sc-eQTL search, gene expression visualization in UMAP plots, a genome browser, and colocalization visualization based on the GWAS dataset of interest. scQTLbase provides a one-stop portal for sc-eQTLs that will significantly advance the discovery of disease susceptibility genes.

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. Here, we mapped 9,493 3'-untranslated region APA quantitative trait loci in 18 human immune baseline cell types and 8 stimulation conditions (immune 3'aQTLs). Through the comparison between baseline and stimulation data, we observed the high responsiveness of 3'aQTLs to immune stimulation (response 3'aQTLs). Co-localization and mendelian randomization analyses of immune 3'aQTLs identified 678 genes where 3'aQTL are associated with variation in complex traits, 27.3% of which were derived from response 3'aQTLs. Overall, these analyses reveal the role of immune 3'aQTLs in the determination of complex traits, providing new insights into the regulatory mechanisms underlying disease etiologies.

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. Here, we developed xQTLbiolinks as the first comprehensive and scalable tool for bulk and single-cell xQTLs data retrieval, quality control and pre-processing from public repositories and our integrated resource. In addition, xQTLbiolinks provided a robust colocalization module through integration with GWAS summary statistics. The result generated by xQTLbiolinks can be flexibly visualized or stored in standard R objects that can easily be integrated with other R packages and custom pipelines. We applied xQTLbiolinks to cancer GWAS summary statistics as case studies and demonstrated its robust utility and reproducibility. xQTLbiolinks will profoundly accelerate the interpretation of disease-associated variants, thus promoting a better understanding of disease etiologies. xQTLbiolinks is available at https://github.com/lilab-bioinfo/xQTLbiolinks.

[Analysis on the secondary attack rates of SARS-CoV-2 Omicron variant and the associated factors]

Objective: To evaluate the secondary attack rates of the SARS-CoV-2 Omicron variant and the associated factors. Methods: A total of 328 primary cases and 40 146 close contacts of the SARS-CoV-2 Omicron variant routinely detected in local areas of Jiangsu Province from February to April 2022 were selected in this study, and those with positive nucleic acid test results during 7 days of centralized isolation medical observation were defined as secondary cases. The demographic information and clinical characteristics were collected, and the secondary attack rate (SAR) and the associated factors were analyzed by using a multivariate logistic regression model. Results: A total of 1 285 secondary cases of close contacts were reported from 328 primary cases, with a SAR of 3.2% (95%CI: 3.0%-3.4%). Among the 328 primary cases, males accounted for 61.9% (203 cases), with the median age (Q1, Q3) of 38.5 (27, 51) years old. Among the 1 285 secondary cases, males accounted for 59.1% (759 cases), with the median age (Q1, Q3) of 34 (17, 52) years old. The multivariate logistic regression model showed that the higher SAR was observed in the primary male cases (OR=1.632, 95%CI: 1.418-1.877), younger than 20 years old (OR=1.766, 95%CI: 1.506-2.072),≥60 years old (OR=1.869, 95%CI: 1.476-2.365), infected with the BA.2 strain branch (OR=2.906, 95%CI: 2.388-3.537), the confirmed common cases (OR=2.572, 95%CI: 2.036-3.249), and confirmed mild cases (OR=1.717, 95%CI: 1.486-1.985). Meanwhile, the higher SAR was observed in the close contacts younger than 20 years old (OR=2.604, 95%CI: 2.250-3.015),≥60 years old (OR=1.287, 95%CI: 1.052-1.573) and exposure for co-residence (OR=27.854, 95%CI: 23.470-33.057). Conclusion: The sex and age of the primary case of the Omicron variant, the branch of the infected strain, case severity of the primary case, as well as the age and contact mode of close contacts are the associated factors of SAR.

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. Because of the thermal mismatch between dissimilar materials, the thermo-mechanical stress within the resonant beam leads to a change in the effective stiffness and causes the frequency drift to decrease linearly with increasing temperature. Furthermore, our investigations reveal that increasing the stress-buffering layer thickness and reducing the solder layer thickness can significantly minimize the thermo-mechanical stress within the resonant beam. As the neutral plane approaches the horizontal symmetry plane of the resonant beam when optimizing the packaging structure, the effects of the compressive and tensile stresses on the effective stiffness of the resonant beam will cancel each other out, which can dramatically reduce the frequency drift. These findings provide guidelines for packaging design through which to improve the temperature stability of MEMS resonant accelerometers.

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. The experimental results demonstrate that, referring to the traditional earth's gravitational field tumble calibration method, the error of the scale factor calibration is 0.46% within ±1 g by using our method. Moreover, the scale factor is compensated by virtual accelerations. After compensation, the maximum temperature drift of the scale factor decreases from 2.46 Hz/g to 1.02 Hz/g, with a temperature range from 40 °C to 80 °C.

[Prediction of 1p/19q codeletion status in diffuse lower-grade glioma using multimodal MRI radiomics]

OBJECTIVE

To develop a noninvasive method for prediction of 1p/19q codeletion in diffuse lower-grade glioma (DLGG) based on multimodal magnetic resonance imaging (MRI) radiomics.

METHODS

We collected MRI data from 104 patients with pathologically confirmed DLGG between October, 2015 and September, 2022. A total of 535 radiomics features were extracted from T₂WI, T₁WI, FLAIR, CE-T₁WI and DWI, including 70 morphological features, 90 first order features, and 375 texture features. We constructed logistic regression (LR), logistic regression least absolute shrinkage and selection operator (LRlasso), support vector machine (SVM) and Linear Discriminant Analysis (LDA) radiomics models and compared their predictive performance after 10-fold cross validation. The MRI images were reviewed by two radiologists independently for predicting the 1p/19q status. Receiver operating characteristic curves were used to evaluate classification performance of the radiomics models and the radiologists.

RESULTS

The 4 radiomics models (LR, LRlasso, SVM and LDA) achieved similar area under the curve (AUC) in the validation dataset (0.833, 0.819, 0.824 and 0.819, respectively; P>0.1), and their predictive performance was all superior to that of resident physicians of radiology (AUC=0.645, P=0.011, 0.022, 0.016, 0.030, respectively) and similar to that of attending physicians of radiology (AUC=0.838, P>0.05).

CONCLUSION

Multiparametric MRI radiomics models show good performance for noninvasive prediction of 1p/19q codeletion status in patients with in diffuse lower-grade glioma.

[Preliminary experience of gasless transoral vestibular robotic thyroidectomy]

Objective: To explore the feasibility and safety of the gasless transoral vestibular robotic thyroidectomy using skin suspension. Methods: The clinical data of 20 patients underwent gasless transoral vestibular robotic thyroidectomy in the Department of Otorhinolaryngology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University from February 2022 to May 2022 were retrospectively analyzed. Among them, 18 were females and 2 were males, aged (38.7±8.0) years old. The intraoperative blood loss, operation time, postoperative hospital stay, postoperative drainage volume, postoperative pain visual analogue scale (VAS) score, postoperative swallowing function swallowing impairment score-6 (SIS-6), postoperative aesthetic VAS score, postoperative voice handicap index-10 (VHI-10) voice quality, postoperative pathology and complications were recorded. SPSS 25.0 was used for statistical analysis of the data. Results: The operations were successfully completed without conversion to open surgery in all patients. Pathological examination showed papillary thyroid carcinoma in 18 cases, retrosternal nodular goiter in 1 case, and cystic change in goiter in 1 case. The operative time for thyroid cancer was 161.50 (152.75, 182.50) min [M (P₂₅, P₇₅), the same below] and the average operative time for benign thyroid diseases was 166.50 minutes. The intraoperative blood loss 25.00 (21.25, 30.00) ml. In 18 cases of thyroid cancer, the mean diameter of the tumors was (7.22±2.02) mm, and lymph nodes (6.56±2.14) were dissected in the central region, with a lymph node metastasis rate of 61.11%. The postoperative pain VAS score was 3.00 (2.25, 4.00) points at 24 hours, the mean postoperative drainage volume was (118.35±24.32) ml, the postoperative hospital stay was 3.00 (3.00, 3.75) days, the postoperative SIS-6 score was (4.90±1.58) points at 3 months, and the postoperative VHI-10 score was 7.50 (2.00, 11.00) points at 3 months. Seven patients had mild mandibular numbness, 10 patients had mild cervical numbness, and 3 patients had temporary hypothyroidism three months after surgery and 1 patient had skin flap burn, but recovered one month after surgery. All patients were satisfied with the postoperative aesthetic effects, and the postoperative aesthetic VAS score was 10.00 (10.00, 10.00). Conclusion: Gasless transoral vestibular robotic thyroidectomy using skin suspension is a safe and feasible option with good postoperative aesthetic effect, which can provide a new treatment option for some selected patients with thyroid tumors.

[Epidemiological characteristics of a 2019-nCoV outbreak caused by Omicron variant BF.7 in Shenzhen]

Objective: To explore the epidemiological characteristic of a COVID-19 outbreak caused by 2019-nCoV Omicron variant BF.7 and other provinces imported in Shenzhen and analyze transmission chains and characteristics. Methods: Field epidemiological survey was conducted to identify the transmission chain, analyze the generation relationship among the cases. The 2019-nCoV nucleic acid positive samples were used for gene sequencing. Results: From 8 to 23 October, 2022, a total of 196 cases of COVID-19 were reported in Shenzhen, all the cases had epidemiological links. In the cases, 100 were men and 96 were women, with a median of age, M (Q₁, Q₃) was 33(25, 46) years. The outbreak was caused by traverlers initial cases infected with 2019-nCoV who returned to Shenzhen after traveling outside of Guangdong Province.There were four transmission chains, including the transmission in place of residence and neighbourhood, affecting 8 persons, transmission in social activity in the evening on 7 October, affecting 65 persons, transmission in work place on 8 October, affecting 48 persons, and transmission in a building near the work place, affecting 74 persons. The median of the incubation period of the infection, M (Q₁, Q₃) was 1.44 (1.11, 2.17) days. The incubation period of indoor exposure less than that of the outdoor exposure, M (Q₁, Q₃) was 1.38 (1.06, 1.84) and 1.95 (1.22, 2.99) days, respcetively (Wald χ²=10.27, P=0.001). With the increase of case generation, the number and probability of gene mutation increased. In the same transmission chain, the proportion of having 1-3 mutation sites was high in the cases in the first generation. Conclusions: The transmission chains were clear in this epidemic. The incubation period of Omicron variant BF.7 infection was shorter, the transmission speed was faster, and the gene mutation rate was higher. It is necessary to conduct prompt response and strict disease control when epidemic occurs.

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. Here, we propose an enhanced tunable high-sensitivity and trace-amount THz-SPR biosensor based on a composite periodic groove structure (CPGS). The elaborate geometric design of the spoof surface plasmon polaritons (SSPPs) metasurface increases the number of electromagnetic hot spots on the surface of the CPGS, improves the near-field enhancement effect of SSPPs, and enhances the interaction between THz wave and the sample. The results show that the sensitivity (S), figure of merit (FOM) and Q-factor (Q) can be increased to 6.55 THz/RIU, 4234.06 1/RIU and 629.28, respectively, when the refractive index range of the sample to measure is between 1 and 1.05 with the resolution 1.54×10-5 RIU. Moreover, by making use of the high structural tunability of CPGS, the best sensitivity (SPR frequency shift) can be obtained when the resonant frequency of the metamaterial approaches the biological molecule oscillation. These advantages make CPGS a strong candidate for the high-sensitivity detection of trace-amount biochemical samples.

Radiomics signature based on CECT for non-invasive prediction of response to anti-PD-1 therapy in patients with hepatocellular carcinoma

PURPOSE

This study aimed to develop a radiomics signature (RS) based on contrast-enhanced computed tomography (CECT) and evaluate its potential predictive value in hepatocellular carcinoma (HCC) patients receiving anti-PD-1 therapy.

METHOD

CECT scans of 76 HCC patients who received anti-PD-1 therapy were obtained in this study (training group = 53 and validation group = 23). The least absolute shrinkage and selection operator (LASSO) regression was applied to select radiomics features of primary and metastatic lesions and establish a RS to predict lesion-level response. Then, a nomogram combined the mean RS (MRS) and clinical variables with patient-level response as the end point.

RESULTS

In the lesion-level analysis, the area under the curves (AUCs) of RS in the training and validation groups were 0.751 (95% CI, 0.668-0.835) and 0.734 (95% CI, 0.604-0.864), respectively. In the patient-level analysis, the AUCs of the nomogram in the training and validation groups were 0.897 (95% CI, 0.798-0.996) and 0.889 (95% CI, 0.748-1.000), respectively. The nomogram stratified patients into low- and high-risk groups, which showed a significant difference in progression-free survival (PFS) (p<0.05).

CONCLUSIONS

The RS is a noninvasive biomarker for predicting anti-PD-1 therapy response in patients with HCC. The nomogram may be of clinical use for identifying high-risk patients and formulating individualised treatments.

Stent pretreatment for internal carotid artery exposed to necrotic lesions in nasopharyngeal carcinoma

BACKGROUND

Post radiation nasopharyngeal necrosis (PRNN) invading the internal carotid artery (ICA) contributes to the death of 69.2-72.7% of PRNN patients. ICA occlusion is an effective treatment to avoid fatal bleeding, while some patients are intolerant. We present a novel method that allows for these patients without interrupting blood flow through the ICA.

METHODOLOGY

This study enrolled patients with PRNN-invaded ICA who were not suitable for ICA occlusion from April 2020 to November 2022. ICA stent pretreatment was performed in the 36 patients and followed the endoscopic nasopharyngectomy (ENPG) or conservative treatment for PRNN. We report the survival outcome and incidence of complications after stent implantation and compare the survival outcomes of ENPG and conservative treatment for PRNN followed by stent implantation.

RESULTS

ICA stent pretreatment was performed in the 36 enrolled patients, among which 14 underwent ENPG, and 22 received conservative treatment. 27.8% patients died after a median follow-up of 15 months. The Kaplan-Meier estimates of overall survival were higher in the ENPG group than in the conservative treatment group. Karnofsky performance status (KPS) was significantly higher in the ENPG group than in the non-ENPG group.

CONCLUSIONS

The innovative application of ICA stents is a promising treatment to improve outcomes in patients with PRNN invading the ICA who are unsuitable for ICA embolization, especially when followed by endoscopic surgery. However, methods to avoid postoperative cerebral ischemia and nasopharyngeal hemorrhage still require further study.

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. It combines the polynomial fitting with the RC on the input data mapping ensuring that the system always resides in the rich nonlinear state. Meanwhile, the output layer is also optimized by vector concatenation operation for higher memory capacity. Therefore, the new system has better performance in dynamic temperature compensation. In addition, the method is real-time, with easy hardware implementation that can be integrated with MEMS sensors. The experiment's result showed a 93% improvement in IOI-RC compared to raw data in a temperature range of -20-60 °C. The study confirmed the feasibility of RC in realizing dynamic temperature compensation precisely, which provides a potential real-time online temperature compensation method and a sensor system with edge computing.

Dietary Total Antioxidant Capacity and Cognitive Function in Older Adults in the United States: The NHANES 2011-2014

OBJECTIVES

Oxidative stress level takes part in the development of cognitive decline. However, the association between total antioxidant capacity (TAC) from diet and cognitive function is controversial. The aim of this study was to investigate the relationship between TAC and the cognitive function of older adults in the U.S.

DESIGN

A cross-sectional study.

SETTING

National Health and Nutrition Examination Surveys database.

PARTICIPANTS

2712 older adults aged over 60 years.

MEASUREMENTS

TAC was calculated from 8 antioxidative vitamins based on the reference values for vitamin C equivalent antioxidant capacity obtained from individuals' 24 h dietary recall. Four memory-related assessments were employed [Immediate Recall test (IRT), Delayed Recall test (DRT), Animal Fluency test (AFT), and Digit Symbol Substitution test (DSST)].

RESULTS

Among the 2712 participants, the median age was 68 years, and 50.4% were women. Participants in the group with higher TAC levels had relatively higher IRT, AFT and DSST scores (P=0.025, P=0.008, P<0.001, respectively). In adjusted weighted linear regression, log-transformed TAC was positively associated with AFT (β=1.10, 95%CI: 0.51, 1.70) and DSST (β=2.81, 95%CI: 1.16, 4.45). Compared with the first quartile, the participants in the second (Q2 vs. Q1, OR=0.66, 95%CI: 0.43,1.02) and fourth quartile (Q4 vs. Q1, OR=0.47, 95%CI:0.28, 0.78) of log-transformed TAC showed a decreased risk of impaired cognitive function (ICF) after adjusting for confounders. The dose-response analysis indicated a gradual descent in the risk of ICF as TAC increases. Diabetes mellitus (DM) mediated part of the effect of TAC on ICF. The relationship between TAC and ICF was more pronounced in subjects with DM (Q4 vs Q1, OR=0.36, 95%CI:0.17, 0.74).

CONCLUSION

Our findings support that higher dietary antioxidant potential was related to a decreased risk of cognitive dysfunction, particularly in the subjects with DM who may have oxidative injury. DM was one of the factors mediating the effect of TAC on ICF.

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 -23.5 to 29.4 g. The free spectral range is 4.05 nm around 1.55 microns. The acceleration resolution limited by thermomechanical noise is 4.874 μg. The comprehensive performance of this design is competitive with existing MEMS mode localized accelerometers. It demonstrates the potential of the optical mode-localized inertial sensors as candidates for state-of-the-art sensors in the future.

Advances in the application of named reactions in polymer synthesis

With the development of polymer science, more and more named reactions have been applied to synthesizing polymers. Introducing new reactions into polymer synthesis is undoubtedly an excellent expansion for monomer and polymer libraries. In this review, the named reactions employed in polymer-chain synthesis were divided into seven types: electrophilic reactions, nucleophilic reactions, transition metal-mediated cross-coupling reactions, free radical reactions, pericyclic reactions, multi-component reactions and rearrangement reactions. The discussion was mainly focused on the progress in the utilization of these named reactions in polymer synthesis, which could be a valuable reference for researchers in the polymer field.

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. The processing parameters, including scanning speed, defocus amount (DA), scanning period, and single pulse energy are systematically investigated to optimize HS-s/sS fabrication. It is found that the period of processed stripe on the mesh material is ∼1 mm, which is much larger than the scanning period. Interestingly, the as-prepared mesh surface show superhydrophobicity in the convex striped surface and superhydrophilicity in concave striped parts. The scanning electron microscopy results show that the structures on convex stripe are mainly composed of disordered hill-like structures, while the structures on the concave stripe mainly consist of periodic nanostripe structures. Moreover, the proportion of oxygen on the convex stripe is obviously higher than that on the concave stripe. The underlying mechanism of the HS-s/sS formation can be attributed to the interference between surface phonon polaritons (SPP) and the incident picosecond laser, as well as surface shock wave caused by the picosecond laser. We believe that such functional surfaces will be promising candidates for controlling liquid motion and fluid diversion processes.

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. The DETF out-of-phase mode is utilized, which is only sensitive to temperature, to measure the temperature change of WCRs and complete the temperature compensation using the compensation algorithm. This proposed method has no time delay in measuring the temperature of sensitive elements and no temperature difference caused by the uneven temperature field. The parametric sensitivity in amplitude ratio (AR) to acceleration drifting with temperature was theoretically analyzed, and the novel device was designed and fabricated by a silicon-on-glass process. Both simulation and experiment results demonstrated that the coupling stiffness drifted with temperature, which resulted in the drifts of its sensitivity to acceleration and zero-bias stability. Using the intrinsic mode of WCRs, in terms of the DETF out-of-phase mode, as an in situ thermometer and carrying out the temperature compensation algorithm, the drift of zero bias could be suppressed from 102 mg to 4.5 mg (g is the gravity acceleration), and the drift of the parameter sensitivity in AR was suppressed from 0.74 AR/g to 0.02 AR/g with the temperature range from 330 K to 370 K and acceleration range from 0 g to 0.2 g.

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. This protocol allows users to analyze dynamic APA events, identify common genetic variants associated with differential 3′ UTR usage, and predict the potential causal variants that affect APA.

For complete details on the use and execution of this protocol, please refer to Li et al. (2021).

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Identification and quantification of APA events across multiple RNA-seq samples

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3aQTL-pipe facilitates identification of APA-associated genetic variants

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Identification of potential causal SNPs for dynamics APA events by fine mapping

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Development of a wide-range soft sensor for predicting wastewater BOD5 using an eXtreme gradient boosting (XGBoost) machine

In wastewater monitoring, detecting extremely high pollutant concentrations is necessary to properly calibrate the treatment process. However, existing hardware sensors have a limited linear range which may fail to measure extremely high levels of pollutants; and likewise, the conventional "soft" model sensors are not suitable for the highly-skewed data distributions either. This study developed a new soft sensor by using eXtreme Gradient Boosting (XGBoost) machine learning to 'measure' the wastewater organics (in terms of 5-day biochemical oxygen demand (BOD5)). The soft sensor was tested on influent and effluent BOD5 of two different wastewater treatment plants to validate the results. The model results showed that XGBoost can detect these extreme values better than conventional soft sensors. This new soft sensor can function using a sparse input matrix via XGBoost's sparsity awareness algorithm - which can address the limitation of the conventional soft sensor with the fallibility of supporting hardware sensors even.

DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning

Alternative polyadenylation (APA) is a crucial step in post-transcriptional regulation. Previous bioinformatic studies have mainly focused on the recognition of polyadenylation sites (PASs) in a given genomic sequence, which is a binary classification problem. Recently, computational methods for predicting the usage level of alternative PASs in the same gene have been proposed. However, all of them cast the problem as a non-quantitative pairwise comparison task and do not take the competition among multiple PASs into account. To address this, here we propose a deep learning architecture, Deep Regulatory Code and Tools for Alternative Polyadenylation (DeeReCT-APA), to quantitatively predict the usage of all alternative PASs of a given gene. To accommodate different genes with potentially different numbers of PASs, DeeReCT-APA treats the problem as a regression task with a variable-length target. Based on a convolutional neural network-long short-term memory (CNN-LSTM) architecture, DeeReCT-APA extracts sequence features with CNN layers, uses bidirectional LSTM to explicitly model the interactions among competing PASs, and outputs percentage scores representing the usage levels of all PASs of a gene. In addition to the fact that only our method can quantitatively predict the usage of all the PASs within a gene, we show that our method consistently outperforms other existing methods on three different tasks for which they are trained: pairwise comparison task, highest usage prediction task, and ranking task. Finally, we demonstrate that our method can be used to predict the effect of genetic variations on APA patterns and sheds light on future mechanistic understanding in APA regulation. Our code and data are available at https://github.com/lzx325/DeeReCT-APA-repo.

Modeling and Parameter Sensitivity Improvement in ΔE-Effect Magnetic Sensor Based on Mode Localization Effect

A mode-localized ΔE-effect magnetic sensor model is established theoretically and numerically. Based on the designed weakly coupled resonators with multi-layer film structure, it is investigated how the ΔE-effect of the magnetostrictive film under the external magnetic field causes the stiffness perturbation of the coupled resonators to induce the mode localization effect. Using the amplitude ratio (AR) as the output in the mode-localized ΔE-effect magnetic sensor can improve the relative sensitivity by three orders of magnitude compared with the traditional frequency output, which has been verified by simulations based on the finite element method (FEM). In addition, the effects of material properties and geometric dimensions on sensor performance parameters, such as sensitivity, linear range, and static operating point are also analyzed and studied in detail, providing the theoretical basis for the design and optimization of the mode-localized ΔE-effect magnetic sensor in different application scenarios. By reasonably optimizing the key parameters of the weekly coupled resonators, a mode-localized ΔE-effect magnetic sensor with the sensitivity of 18 AR/mT and a linear range of 0.8 mT can be achieved.

A Novel Self-Temperature Compensation Method for Mode-Localized Accelerometers

Mode-localized sensing paradigms applied to accelerometers have recently become popular research subjects. However, the output of mode-localized accelerometers is influenced by environment temperature due to the difference in the thermal properties of the coupling resonators and the temperature dependence of coupling stiffness. To improve the performance of mode-localized accelerometers against temperature, we proposed an in situ self-temperature compensation method by utilizing the resonant frequency besides of amplitude ratios, which can be implied online. Experimental results showed that there were nearly 79-times and 87-times improvement in zeros bias and scale factor, respectively.

Enhancing the Recognition Task Performance of MEMS Resonator-Based Reservoir Computing System via Nonlinearity Tuning

Reservoir computing (RC) is a potential neuromorphic paradigm for physically realizing artificial intelligence systems in the Internet of Things society, owing to its well-known low training cost and compatibility with nonlinear devices. Micro-electro-mechanical system (MEMS) resonators exhibiting rich nonlinear dynamics and fading behaviors are promising candidates for high-performance hardware RC. Previously, we presented a non-delay-based RC using one single micromechanical resonator with hybrid nonlinear dynamics. Here, we innovatively introduce a nonlinear tuning strategy to analyze the computing properties (the processing speed and recognition accuracy) of the presented RC. Meanwhile, we numerically and experimentally analyze the influence of the hybrid nonlinear dynamics using the image classification task. Specifically, we study the transient nonlinear saturation phenomenon by fitting quality factors under different vacuums, as well as searching the optimal operating point (the edge of chaos) by the static bifurcation analysis and dynamic vibration numerical models of the Duffing nonlinearity. Our results in the optimal operation conditions experimentally achieved a high classification accuracy of (93 ± 1)% and several times faster than previous work on the handwritten digits recognition benchmark, profit from the perfect high signal-to-noise ratios (quality factor) and the nonlinearity of the dynamical variables.

An Endpoint Detection System for Ion Beam Etching Using Optical Emission Spectroscopy

An ion beam etching system with etching endpoint detection (EPD) capability based on optical emission spectroscopy (OES) was conceived, built, and tested. An expansion chamber was added on the right side of the etching chamber to fix the optical detector for in-situ detecting. In this system, the optical detector was mounted on a seven-shaped bracket, which was fixed by two straight guides, thus the position of the optical detector could be adjusted arbitrarily to collect the emission spectrum generated by the sample during the etching process. The signal was transmitted by optical fiber to the computer for processing, and the etching endpoint could be detected after analyzing the data. Firstly, we used simple substances (Al, Cr, Si, and Mg) to analyze the feasibility of the system and determine the best position of the optical detector. In addition, we also tested the detection limit of the system. Finally, a complex multilayer film sample with different materials was tested, and the results showed that the system could clearly detect the characteristic emission lines of different layers and had a good real-time performance and excellent endpoint detection capabilities.

Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law

This study globally investigates the allelic splicing pattern in multiple tissues of an F1 hybrid mouse and reveals the underlying driving forces shaping such tissue-dependent splicing divergence.

Alternative splicing is ubiquitous, but the mechanisms underlying its pattern of evolutionary divergence across mammalian tissues are still underexplored. Here, we investigated the cis-regulatory divergences and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid between two mouse species. Large splicing changes between tissues are highly conserved and likely reflect functional tissue-dependent regulation. In particular, micro-exons frequently exhibit this pattern with high inclusion levels in the brain. Cis-divergence of splicing appears to be largely non-adaptive. Although divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform apparently tolerate more mutations, explaining why their exon sequences are highly conserved but their intronic splicing site flanking regions are not. Moreover, we demonstrate that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attribute such buffering effect to trans-regulatory splicing efficiency.

Novel nondelay-based reservoir computing with a single micromechanical nonlinear resonator for high-efficiency information processing

Reservoir computing is a potential neuromorphic paradigm for promoting future disruptive applications in the era of the Internet of Things, owing to its well-known low training cost and compatibility with hardware. It has been successfully implemented by injecting an input signal into a spatially extended reservoir of nonlinear nodes or a temporally extended reservoir of a delayed feedback system to perform temporal information processing. Here we propose a novel nondelay-based reservoir computer using only a single micromechanical resonator with hybrid nonlinear dynamics that removes the usually required delayed feedback loop. The hybrid nonlinear dynamics of the resonator comprise a transient nonlinear response, and a Duffing nonlinear response is first used for reservoir computing. Due to the richness of this nonlinearity, the usually required delayed feedback loop can be omitted. To further simplify and improve the efficiency of reservoir computing, a self-masking process is utilized in our novel reservoir computer. Specifically, we numerically and experimentally demonstrate its excellent performance, and our system achieves a high recognition accuracy of 93% on a handwritten digit recognition benchmark and a normalized mean square error of 0.051 in a nonlinear autoregressive moving average task, which reveals its memory capacity. Furthermore, it also achieves 97.17 ± 1% accuracy on an actual human motion gesture classification task constructed from a six-axis IMU sensor. These remarkable results verify the feasibility of our system and open up a new pathway for the hardware implementation of reservoir computing.

Systematic Analysis of Monoallelic Gene Expression and Chromatin Accessibility Across Multiple Tissues in Hybrid Mice

In diploid eukaryotic organisms, both alleles of each autosomal gene are usually assumed to be simultaneously expressed at similar levels. However, some genes can be expressed preferentially or strictly from a single allele, a process known as monoallelic expression. Classic monoallelic expression of X-chromosome-linked genes, olfactory receptor genes and developmentally imprinted genes is the result of epigenetic modifications. Genetic-origin-dependent monoallelic expression, however, is caused by cis-regulatory differences between the alleles. There is a paucity of systematic study to investigate these phenomena across multiple tissues, and the mechanisms underlying such monoallelic expression are not yet fully understood. Here we provide a detailed portrait of monoallelic gene expression across multiple tissues/cell lines in a hybrid mouse cross between the Mus musculus strain C57BL/6J and the Mus spretus strain SPRET/EiJ. We observed pervasive tissue-dependent allele-specific gene expression: in total, 1,839 genes exhibited monoallelic expression in at least one tissue, and 410 genes in at least two tissues. Among these 88 are monoallelic genes with different active alleles between tissues, probably representing genetic-origin-dependent monoallelic expression. We also identified six autosomal monoallelic genes with the active allele being identical in all eight tissues, which are likely novel candidates of imprinted genes. To depict the underlying regulatory mechanisms at the chromatin layer, we performed ATAC-seq in two different cell lines derived from the F1 mouse. Consistent with the global expression pattern, cell-type dependent monoallelic peaks were found, and a higher proportion of C57BL/6J-active peaks were observed in both cell types, implying possible species-specific regulation. Finally, only a small part of monoallelic gene expression could be explained by allelic differences in chromatin organization in promoter regions, suggesting that other distal elements may play important roles in shaping the patterns of allelic gene expression across tissues.