Robust Attitude and Heading Estimation under Dynamic Motion and Magnetic Disturbance.

Robust and accurate attitude and heading estimation using Micro-Electromechanical System (MEMS) Inertial Measurement Units (IMU) is the most crucial technique that determines the accuracy of various downstream applications, especially pedestrian dead reckoning (PDR), human motion tracking, and Micro Aerial Vehicles (MAVs). However, the accuracy of the Attitude and Heading Reference System (AHRS) is often compromised by the noisy nature of low-cost MEMS-IMUs, dynamic motion-induced large external acceleration, and ubiquitous magnetic disturbance. To address these challenges, we propose a novel data-driven IMU calibration model that employs Temporal Convolutional Networks (TCNs) to model random errors and disturbance terms, providing denoised sensor data. For sensor fusion, we use an open-loop and decoupled version of the Extended Complementary Filter (ECF) to provide accurate and robust attitude estimation. Our proposed method is systematically evaluated using three public datasets, TUM VI, EuRoC MAV, and OxIOD, with different IMU devices, hardware platforms, motion modes, and environmental conditions; and it outperforms the advanced baseline data-driven methods and complementary filter on two metrics, namely absolute attitude error and absolute yaw error, by more than 23.4% and 23.9%. The generalization experiment results demonstrate the robustness of our model on different devices and using patterns.

Effects of the spatial patterns of urban parks on public satisfaction: evidence from Shanghai, China.

Context: Urban parks need to meet the growing demand for activities vital to residents' well-being and urban development. A holistic understanding of public satisfaction with urban parks is a prerequisite for improving management. Objective: The spatial patterns and composition of urban parks vary greatly, and the objective of this study is to comprehensively investigate public satisfaction with urban parks and the impact of their structure. Methods: With the metropolis of Shanghai, China, as an example, we employed 111,814 social media data sets for 50 urban park sites to quantify public satisfaction via the long short-term memory model. We analyzed the internal, boundary and external dimensions of spatial patterns and described the internal landscape patterns from the perspectives of size, heterogeneity, aggregation, shape, diversity and landscape elements. Moreover, we used all-subset regression and hierarchical partitioning to quantify the relationship and mechanism of action between spatial patterns and public satisfaction. Results: The results indicate that the mean value of public satisfaction with urban parks was 0.716 (ranging from 0 to 1), which is generally positive or neutral. Satisfaction was influenced by the internal, boundary, and external spatial patterns of urban parks. The independent contribution rates of external transportation facility density (51.49%) and internal edge density (48.51%) to satisfaction. Conclusions: We highlight the roles of spatial patterns, especially the degree of external transportation convenience and the edge density of urban parks at the landscape level. The findings provide guidance and recommendations for the planning and design of public satisfaction-oriented urban parks. Supplementary Information: The online version contains supplementary material available at 10.1007/s10980-023-01615-z.

Applying T-classifier, binary classifiers, upon high-throughput TCR sequencing output to identify cytomegalovirus exposure history.

With the continuous development of information technology and the running speed of computers, the development of informatization has led to the generation of increasingly more medical data. Solving unmet needs such as employing the constantly developing artificial intelligence technology to medical data and providing support for the medical industry is a hot research topic. Cytomegalovirus (CMV) is a kind of virus that exists widely in nature with strict species specificity, and the infection rate among Chinese adults is more than 95%. Therefore, the detection of CMV is of great importance since the vast majority of infected patients are in a state of invisible infection after the infection, except for a few patients with clinical symptoms. In this study, we present a new method to detect CMV infection status by analyzing high-throughput sequencing results of T cell receptor beta chains (TCRß). Based on the high-throughput sequencing data of 640 subjects from cohort 1, Fisher's exact test was performed to evaluate the relationship between TCRß sequences and CMV status. Furthermore, the number of subjects with these correlated sequences to different degrees in cohort 1 and cohort 2 were measured to build binary classifier models to identify whether the subject was CMV positive or negative. We select four binary classification algorithms: logistic regression (LR), support vector machine (SVM), random forest (RF), and linear discriminant analysis (LDA) for side-by-side comparison. According to the performance of different algorithms corresponding to different thresholds, four optimal binary classification algorithm models are obtained. The logistic regression algorithm performs best when Fisher's exact test threshold is 10-5, and the sensitivity and specificity are 87.5% and 96.88%, respectively. The RF algorithm performs better at the threshold of 10-5, with a sensitivity of 87.5% and a specificity of 90.63%. The SVM algorithm also achieves high accuracy at the threshold value of 10-5, with a sensitivity of 85.42% and specificity of 96.88%. The LDA algorithm achieves high accuracy with 95.83% sensitivity and 90.63% specificity when the threshold value is 10-4. This is probably because the two-dimensional distribution of CMV data samples is linearly separable, and linear division models such as LDA are more effective, while the division effect of nonlinear separable algorithms such as random forest is relatively inaccurate. This new finding may be a potential diagnostic method for CMV and may even be applicable to other viruses, such as the infectious history detection of the new coronavirus.

Divergence in the Regulation of the Salt Tolerant Response Between Arabidopsis thaliana and Its Halophytic Relative Eutrema salsugineum by mRNA Alternative Polyadenylation.

Salt tolerance is an important mechanism by which plants can adapt to a saline environment. To understand the process of salt tolerance, we performed global analyses of mRNA alternative polyadenylation (APA), an important regulatory mechanism during eukaryotic gene expression, in Arabidopsis thaliana and its halophytic relative Eutrema salsugineum with regard to their responses to salt stress. Analyses showed that while APA occurs commonly in both Arabidopsis and Eutrema, Eutrema possesses fewer APA genes than Arabidopsis (47% vs. 54%). However, the proportion of APA genes was significantly increased in Arabidopsis under salt stress but not in Eutrema. This indicated that Arabidopsis is more sensitive to salt stress and that Eutrema exhibits an innate response to such conditions. Both species utilized distal poly(A) sites under salt stress; however, only eight genes were found to overlap when their 3' untranslated region (UTR) lengthen genes were compared, thus revealing their distinct responses to salt stress. In Arabidopsis, genes that use distal poly(A) sites were enriched in response to salt stress. However, in Eutrema, the use of poly(A) sites was less affected and fewer genes were enriched. The transcripts with upregulated poly(A) sites in Arabidopsis showed enriched pathways in plant hormone signal transduction, starch and sucrose metabolism, and fatty acid elongation; in Eutrema, biosynthetic pathways (stilbenoid, diarylheptanoid, and gingerol) and metabolic pathways (arginine and proline) showed enrichment. APA was associated with 42% and 29% of the differentially expressed genes (DE genes) in Arabidopsis and Eutrema experiencing salt stress, respectively. Salt specific poly(A) sites and salt-inducible APA events were identified in both species; notably, some salt tolerance-related genes and transcription factor genes exhibited differential APA patterns, such as CIPK21 and LEA4-5. Our results suggest that adapted species exhibit more orderly response at the RNA maturation step under salt stress, while more salt-specific poly(A) sites were activated in Arabidopsis to cope with salinity conditions. Collectively, our findings not only highlight the importance of APA in the regulation of gene expression in response to salt stress, but also provide a new perspective on how salt-sensitive and salt-tolerant species perform differently under stress conditions through transcriptome diversity.

Integration of Multimodal Data from Disparate Sources for Identifying Disease Subtypes.

Studies over the past decade have generated a wealth of molecular data that can be leveraged to better understand cancer risk, progression, and outcomes. However, understanding the progression risk and differentiating long- and short-term survivors cannot be achieved by analyzing data from a single modality due to the heterogeneity of disease. Using a scientifically developed and tested deep-learning approach that leverages aggregate information collected from multiple repositories with multiple modalities (e.g., mRNA, DNA Methylation, miRNA) could lead to a more accurate and robust prediction of disease progression. Here, we propose an autoencoder based multimodal data fusion system, in which a fusion encoder flexibly integrates collective information available through multiple studies with partially coupled data. Our results on a fully controlled simulation-based study have shown that inferring the missing data through the proposed data fusion pipeline allows a predictor that is superior to other baseline predictors with missing modalities. Results have further shown that short- and long-term survivors of glioblastoma multiforme, acute myeloid leukemia, and pancreatic adenocarcinoma can be successfully differentiated with an AUC of 0.94, 0.75, and 0.96, respectively.

Discovery of primary prostate cancer biomarkers using cross cancer learning.

Prostate cancer (PCa), the second leading cause of cancer death in American men, is a relatively slow-growing malignancy with multiple early treatment options. Yet, a significant number of low-risk PCa patients are over-diagnosed and over-treated with significant and long-term quality of life effects. Further, there is ever increasing evidence of metastasis and higher mortality when hormone-sensitive or castration-resistant PCa tumors are treated indistinctively. Hence, the critical need is to discover clinically-relevant and actionable PCa biomarkers by better understanding the biology of PCa. In this paper, we have discovered novel biomarkers of PCa tumors through cross-cancer learning by leveraging the pathological and molecular similarities in the DNA repair pathways of ovarian, prostate, and breast cancer tumors. Cross-cancer disease learning enriches the study population and identifies genetic/phenotypic commonalities that are important across diseases with pathological and molecular similarities. Our results show that ADIRF, SLC2A5, C3orf86, HSPA1B are among the most significant PCa biomarkers, while MTRNR2L1, EEPD1, TEPP and VN1R2 are jointly important biomarkers across prostate, breast and ovarian cancers. Our validation results have further shown that the discovered biomarkers can predict the disease state better than any randomly selected subset of differentially expressed prostate cancer genes.

Identification of Specific N6-Methyladenosine RNA Demethylase FTO Inhibitors by Single-Quantum-Dot-Based FRET Nanosensors.

The fat mass and obesity-associated enzyme (FTO) can catalyze the demethylation of N6-methyladenosine (m6A) residues in mRNA, regulates the cellular level of m6A modification, and plays a critical role in human obesity and cancers. Herein, we develop a single-quantum-dot (QD)-based fluorescence resonance energy transfer (FRET) sensor for the identification of specific FTO demethylase inhibitors. The FTO-mediated demethylation of m6A can induce the cleavage of demethylated DNA to generate the biotinylated DNA fragments, which may function as capture probes to assemble the Cy5-labeled reporter probes onto the QD surface, enabling the occurrence of FRET between the QD and Cy5. The presence of inhibitors can inhibit the FTO demethylation and consequently abolish FRET between the QD and Cy5. The inhibition effect of inhibitors upon FTO demethylation can be simply evaluated by monitoring the decrease of Cy5 counts. We use this nanosensor to screen several small-molecule inhibitors and identify diacerein as a highly selective inhibitor of FTO. Diacerein can inhibit the demethylation activity of endogenous FTO in HeLa cells. Interestingly, diacerein is neither a structural mimic of 2-oxoglutarate (2-OG) nor a chelator of metal ions, and it can selectively inhibit FTO demethylation by competitively binding the m6A-containing substrate.

Correction: Development of a bidirectional isothermal amplification strategy for the sensitive detection of transcription factors in cancer cells.

Correction for 'Development of a bidirectional isothermal amplification strategy for the sensitive detection of transcription factors in cancer cells' by Yan Zhang et al., Chem. Commun., 2020, 56, 8952-8955, DOI: 10.1039/D0CC03134H.

Development of a bidirectional isothermal amplification strategy for the sensitive detection of transcription factors in cancer cells.

We developed a new strategy to sensitively detect transcription factors (TFs) based on the integration of a bidirectional isothermal exponential amplification reaction (EXPAR) with endonuclease IV (endo IV)-assisted cycle digestion of signal probes. This assay exhibits ultrahigh sensitivity with a detection limit of 1.29 × 10-14 M, and it can measure endogenous NF-κB p50 in HeLa cell extracts. Moreover, this strategy can be applied to screen TF inhibitors and detect other TFs by simply changing the TF-binding sequence.

OsCpn60ß1 is Essential for Chloroplast Development in Rice (Oryza sativa L.).

The chaperonin 60 (Cpn60) protein is of great importance to plants due to its involvement in modulating the folding of numerous chloroplast protein polypeptides. In chloroplasts, Cpn60 is differentiated into two subunit types-Cpn60α and Cpn60ß and the rice genome encodes three α and three ß plastid chaperonin subunits. However, the functions of Cpn60 family members in rice were poorly understood. In order to investigate the molecular mechanism of OsCpn60ß1, we attempted to disrupt the OsCpn60ß1 gene by CRISPR/Cas9-mediated targeted mutagenesis in this study. We succeeded in the production of homozygous OsCpn60ß1 knockout rice plants. The OsCpn60ß1 mutant displayed a striking albino leaf phenotype and was seedling lethal. Electron microscopy observation demonstrated that chloroplasts were severely disrupted in the OsCpn60ß1 mutant. In addition, OsCpn60ß1 was located in the chloroplast and OsCpn60ß1 is constitutively expressed in various tissues particularly in the green tissues. The label-free qualitative proteomics showed that photosynthesis-related pathways and ribosomal pathways were significantly inhibited in OsCpn60ß1 mutants. These results indicate that OsCpn60ß1 is essential for chloroplast development in rice.

Pseudomonas fluorescens promote photosynthesis, carbon fixation and cadmium phytoremediation of hyperaccumulator Sedum alfredii.

Plant growth-promoting bacteria (PGPB) can promote photosynthesis and biomass production of hyperaccumulators, achieving enhanced phytoremediation efficiency of cadmium (Cd). A better understanding of the mechanisms controlling photosynthesis of hyperaccumulating plants by PGPB is necessary for developing strategies that promote the practical phytoextraction of Cd-polluted soils. In this study, chlorophyll fluorescence, gas exchange, and transcriptome sequencing were conducted to evaluate the physiological and transcriptional changes on photosynthesis and carbon fixation in hyperaccumulator Sedum alfredii after inoculation with PGPB Pseudomonas fluorescens. The results showed that bacterial inoculation significantly enhanced maximum quantum yield of PS II (Fv/Fm), effective quantum yield of PS II (ΦPSII), photochemical quenching (qP) and chlorophyll concentration, while reduced non-photochemical quenching (NPQ) of S. alfredii. Further, inoculation resulted in an increased net photosynthetic rates (Pn), intercellular CO2 concentration (Ci), transpiration rate (Tr) and stomatal conductance (Gs) of the studied plant. At the transcriptional level, 70 photosynthetic genes and 42 C4-pathway carbon fixation related genes were significantly up-regulated in response to inoculation, which could be the reason for enhanced photosynthesis and dry biomass. To sum up, this P. fluorescens strain can simultaneously promote growth and Cd uptake of S. alfredii, which can be a promising bacterial agent applied to Cd phytoremediation practices.

Transcriptome-wide analysis of the difference of alternative splicing in susceptible and resistant silkworm strains after BmNPV infection.

Novel alternative splicing events were identified from BmNPV-susceptible and -resistant silkworm strains after BmNPV infection using high-throughput RNA-sequencing strategy. In total, 12.82 Gb clean RNA-seq data were generated for the two midgut samples from BmNPV-susceptible and -resistant silkworm strains, and 14.78 Gb clean data for the two fat body samples. The number of alternative splicing events and isoforms in the BmNPV-susceptible silkworm strain was more than that in the BmNPV-resistant silkworm strain. Furthermore, alternative splicing genes uniquely present in BmNPV-resistant silkworm strain were involved in functions about ribosome, whereas, alternative splicing genes uniquely present in BmNPV-susceptible silkworm strain were implicated in functions like DNA helicase activity and signal transduction. Additionally, 33 expressed SR or SR-like proteins were identified, and three genes encoding SR or SR-like proteins (tetratricopeptide repeat protein 14 homolog, ubiquitin carboxyl-terminal hydrolase 32 and zinc finger CCCH domain-containing protein 18) have a higher number of different alternative splicing events between two silkworm strains. The present study suggested BmNPV treatment may have a smaller effect on the mRNA transcription in BmNPV-resistant silkworms than that in BmNPV-susceptible silkworms, and functions of alternative splicing genes are different between the two silkworm strains.

Highly Efficient Nanoscale Analysis of Plant Stomata and Cell Surface Using Polyaddition Silicone Rubber.

Stomata control gas exchange and water transpiration and are one of the most important physiological apparatuses in higher plants. The regulation of stomatal aperture is closely coordinated with photosynthesis, nutrient uptake, plant growth, development, and so on. With advances in scanning electron microscopy (SEM), high-resolution images of plant stomata and cell surfaces can be obtained from detached plant tissues. However, this method does not allow for rapid analysis of the dynamic variation of plant stomata and cell surfaces in situ under nondestructive conditions. In this study, we demonstrated a novel plant surface impression technique (PSIT, Silagum-Light as correction impression material based on A-silicones for all two-phase impression techniques) that allows for precise analysis of plant stomata aperture and cell surfaces. Using this method, we successfully monitored the dynamic variation of stomata and observed the nanoscale microstructure of soybean leaf trichomes and dragonfly wings. Additionally, compared with the analytical precision and the time used for preparing the observation samples between PSIT and traditional SEM, the results suggested that the analytical precision of PSIT was the same to traditional SEM, but the PSIT was more easy to operate. Thus, our results indicated that PSIT can be widely applied to the plant science field.

Hypermethylation of miR-338-3p and Impact of its Suppression on Cell Metastasis Through N-Cadherin Accumulation at the Cell -Cell Junction and Degradation of MMP in Gastric Cancer.

BACKGROUND/AIMS: MicroRNAs (miRNAs) have been well studied in human carcinogenesis and cancer progression. Our previous study showed the down-regulation of miR-338-3p expression in human gastric cancer (GC). However, the reasons of this dysregulation remain largely unclear. METHODS: Bisulfite sequence analysis was performed to explore the methylation status of the promoter region of miR-338-3p. Cell wound-healing and transwell assays were performed to examine the capacity of cell migration and cell interaction. A dual-luciferase reporter was used to validate the bioinformatics-predicted target gene of miR-338-3p. Western blotting, RNA interference, and immunofluorescence (IF) were used to evaluate the expression of MMPs and the location of N-cadherin to determine the mechanism underlying miR-338-3p-induced anti-tumor effects. RESULTS: miR-338-3p was epigenetically silenced, and this loss of expression was significantly correlated with the Borrmann Stage in GC. Restoring miR-338-3p expression in BGC-823 cells inhibited cell migration and invasion. Moreover, Ras-related protein (Rab-14) and Hedgehog acyltransferase (Hhat) were identified as direct targets of miR-338-3p. Both enforced expression of miR-338-3p and small interfering RNA induced Rab14-mediated accumulation of N-cadherin in the cell -cell junctions or Hhat-associated matrix metalloproteinase (MMP) degradation, which may underline the metastasis defects caused by loss of miR-338-3p in GC. CONCLUSION: These data indicate that miR-338-3p functions as a tumor suppressor in GC, and that the hypermethylation status of its CpG island might be a novel potential strategy for treating GC.

Coating Titania Nanoparticles with Epoxy-Containing Catechol Polymers via Cu(0)-Living Radical Polymerization as Intelligent Enzyme Carriers.

Immobilization of enzyme could offer the biocatalyst with increased stability and important recoverability, which plays a vital role in the enzyme's industrial applications. In this study, we present a new strategy to build an intelligent enzyme carrier by coating titania nanoparticles with thermoresponsive epoxy-functionalized polymers. Zero-valent copper-mediated living radical polymerization (Cu(0)-LRP) was utilized herein to copolymerize N-isopropylacrylamide (NIPAM) and glycidyl acrylate (GA) directly from an unprotected dopamine-functionalized initiator to obtain an epoxy-containing polymer with terminal anchor for the "grafting to" or "one-pot" modification of titania nanoparticles. A rhodamine B-labeled laccase has been subsequently used as a model enzyme for successful immobilization to yield an intelligent titania/laccase hybrid bifunctional catalyst. The immobilized laccase has shown excellent thermal stability under ambient or even relatively high temperature above the lower critical solution temperature (LCST) at which temperature the hybrid particles could be facilely recovered for reuse. The enzyme activity could be maintained during the repeated use after recovery and enzymatic degradation of bisphenol A was proven to be efficient. The photocatalytic ability of titania was also investigated by fast degradation of rhodamine B under the excitation of simulated sunlight. Therefore, this study has provided a facile strategy for the immobilization of metal oxide catalysts with enzymes, which constructs a novel bifunctional catalyst that will be promising for the "one-pot" degradation of different organic pollutants.

Rab14 Act as Oncogene and Induce Proliferation of Gastric Cancer Cells via AKT Signaling Pathway.

Rab14 is a member of RAS oncogene family, and its dysfunction has been reported to be involved in various types of human cancer. However, its expression and function were still unclear in gastric cancer. The aim of this study was to investigate the function and mechanism of Rab14 in gastric cancer cell lines. Quantitative real-time PCR (qRT-PCR) was performed in 17 gastric adenocarcinoma tissues and 4 cell lines to detect the expression of Rab14. 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyl-tetrazolium bromide (MTT), colony formation and flow cytometry assays were employed to determine the proliferative ability, cell cycle transition and apoptosis in vitro in BGC-823 or SGC-7901 cells. Western blot was performed to investigate the pathways and mechanism of Rab14 regulation. In this study, we show that Rab14 presents a significant up-regulated expression among the paired tissue samples and cell lines in gastric cancer. When we overexpressed Rab14 in SGC-7901 cells or silenced Rab14 in BGC-823 cells, we found that Rab14 could modify cell growth, cell cycle or apoptosis, which accompanied with an obvious regulation of CCND1, CDK2 and BAX involving in AKT signaling pathway. In conclusion, this study provides a new evidence on that Rab14 functions as a novel tumor oncogene and could be a potential therapeutic target in gastric cancer.

Archaea: the first domain of diversified life.

The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.