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The rapid growth of spatially resolved transcriptomics technology provides new perspectives on spatial tissue architecture. Deep learning has been widely applied to derive useful representations for spatial transcriptome analysis. However, effectively integrating spatial multi-modal data remains challenging. Here, we present ConGcR, a contrastive learning-based model for integrating gene expression, spatial location, and tissue morphology for data representation and spatial tissue architecture identification. Graph convolution and ResNet were used as encoders for gene expression with spatial location and histological image inputs, respectively. We further enhanced ConGcR with a graph auto-encoder as ConGaR to better model spatially embedded representations. We validated our models using 16 human brains, four chicken hearts, eight breast tumors, and 30 human lung spatial transcriptomics samples. The results showed that our models generated more effective embeddings for obtaining tissue architectures closer to the ground truth than other methods. Overall, our models not only can improve tissue architecture identification’s accuracy but also may provide valuable insights and effective data representation for other tasks in spatial transcriptome analyses.

Objectives To assess the effect and safety of Zoladex (Goserelin acetate) 10.8 mg in patients with uterine fibroids.Methods Fifty-three patients received Goserelin acetate 10.8 mg once and surgery was conducted at 12 weeks ± 7 days after drug injection. All assessments form baseline to week12/before surgery were carried out: fibroids volume, uterine volume, serum hormone (E2, FSH, LH), hemoglobin concentration, uterine arterial resistance index (UA-RI), fibroid arterial RI (FA-RI) and improvements of symptoms (Uterine Fibroid Symptom and Quality of Life (UFS-QOL) and Health-Related Quality of Life (HRQL) scores). Adverse events (AEs) were recorded to evaluate the safety.Results After 12 weeks of treatment, the volume of uterine fibroids was significantly smaller than before (249.19 ± 297.04 vs. 195.77 ± 418.27 cm3, p

Background Cervical cancer remains a global health challenge. The identification of new immunotherapeutic targets may provide a promising platform for advancing cervical cancer treatment.Objective This study aims to investigate the role of CUB domain-containing protein 1 (CDCP1) in cervical cancer progression and evaluate its potential as a therapeutic target.Methods We performed comprehensive analyses using patient cohorts and preclinical models to examine the association between CDCP1 expression and cervical cancer prognosis. Then in immunodeficient and immunocompetent mouse models, we further investigated the impact of CDCP1 on the tumor immune microenvironment, focusing on its effects on tumor-infiltrating T cells, including cytotoxic T lymphocytes (CTLs) and regulatory T cells (Tregs). Mechanistic studies were performed to elucidate the pathways involved in CDCP1-mediated immune modulation, in particular its interaction with the T cell receptor CD6 and the activation of the JAK-STAT signaling pathway.Results Our results show that CDCP1 overexpression is associated with poor prognosis and T cell infliction in cervical cancer. Specifically, it affects the activity of CTLs and Tregs. Mechanistically, CDCP1 binds to CD6 and inhibits the JAK-STAT pathway of T cells. The study further demonstrates that targeting CDCP1 with the inhibitor 8-prenylnaringenin (8PN) effectively suppresses tumor growth in vivo and enhances antitumor immunity.Conclusions CDCP1 plays a critical role in cervical cancer progression by modulating the tumor immune microenvironment. Targeting CDCP1 offers a promising therapeutic strategy to improve the outcome of patients with cervical cancer.

In a kind of precision industrial equipment, small diameter abreast optical fibers are used for high-speed communication among functional nodes. The arrangement order at both terminals of the abreast optical fibers need to comply with communication protocols. In this paper, we propose an automatic terminal sequence consistency verification method based on computer vision. The Hue Saturation Value (HSV) color space is used for improving the image feature extraction capability. An abreast optical fiber sequence dictionary which converts the protocol logic into an input-output mapping table is provided to follow protocol confidentiality and improve inspecting speed. A light control baffle position adaptive algorithm is designed for improving the accuracy of optical fiber incident light control. The experimental results show that the method can achieve the conductivity inspection of 1 optical fiber every 50 seconds, and the inspection accuracy is over 96.5%, which generally improves the inspection efficiency by 45% compared with manual inspection.

IntroductionAcupuncture and tuina, acknowledged as ancient and highly efficacious therapeutic modalities within the domain of Traditional Chinese Medicine (TCM), have provided pragmatic treatment pathways for numerous patients. To address the problems of ambiguity in the concept of Traditional Chinese Medicine (TCM) acupuncture and tuina treatment protocols, the lack of accurate quantitative assessment of treatment protocols, and the diversity of TCM systems, we have established a map-filling technique for modern literature to achieve personalized medical recommendations.Methods(1) Extensive acupuncture and tuina data were collected, analyzed, and processed to establish a concise TCM domain knowledge base. (2)A template-free Chinese text NER joint training method (TemplateFC) was proposed, which enhances the EntLM model with BiLSTM and CRF layers. Appropriate rules were set for ERE. (3) A comprehensive knowledge graph comprising 10,346 entities and 40,919 relationships was constructed based on modern literature.ResultsA robust TCM KG with a wide range of entities and relationships was created. The template-free joint training approach significantly improved NER accuracy, especially in Chinese text, addressing issues related to entity identification and tokenization differences. The KG provided valuable insights into acupuncture and tuina, facilitating efficient information retrieval and personalized treatment recommendations.DiscussionThe integration of KGs in TCM research is essential for advancing diagnostics and interventions. Challenges in NER and ERE were effectively tackled using hybrid approaches and innovative techniques. The comprehensive TCM KG our built contributes to bridging the gap in TCM knowledge and serves as a valuable resource for specialists and non-specialists alike.

Abstract Radar signal sorting is a vital component of electronic warfare reconnaissance, serving as the basis for identifying the source of radar signals. However, traditional radar signal sorting methods are increasingly inadequate and computationally complex in modern electromagnetic environments. To address this issue, this paper presents a novel machine-learning-based approach for radar signal sorting. Our method utilizes SemHybridNet, a Semantically Enhanced Hybrid CNN-Transformer Network, for the classification of semantic information in two-dimensional radar pulse images obtained by converting the original radar data. SemHybridNet incorporates two innovative modules: one for extracting period structure features, and the other for ensuring effective integration of local and global features. Notably, SemHybridNet adopts an end-to-end structure, eliminating the need for repetitive looping over the original sequence and reducing computational complexity. We evaluate the performance of our method through conducting comprehensive comparative experiments. The results demonstrate our method significantly outperforms the traditional methods, particularly in environments with high missing and noise pulse rates. Moreover, the ablation studies confirm the effectiveness of these two proposed modules in enhancing the performance of SemHybridNet. In conclusion, our method holds promise for enhancing electronic warfare reconnaissance capabilities and opens new avenues for future research in this field.

Abstract Lunar surface chemistry is essential for revealing petrological characteristics to understand the evolution of the Moon. Existing chemistry mapping from Apollo and Luna returned samples could only calibrate chemical features before 3.0 Gyr, missing the critical late period of the Moon. Here we present major oxides chemistry maps by adding distinctive 2.0 Gyr Chang’e-5 lunar soil samples in combination with a deep learning-based inversion model. The inferred chemical contents are more precise than the Lunar Prospector Gamma-Ray Spectrometer (GRS) maps and are closest to returned samples abundances compared to existing literature. The verification of in situ measurement data acquired by Chang'e 3 and Chang'e 4 lunar rover demonstrated that Chang’e-5 samples are indispensable ground truth in mapping lunar surface chemistry. From these maps, young mare basalt units are determined which can be potential sites in future sample return mission to constrain the late lunar magmatic and thermal history.

The changes in cardiomyocyte action potentials are related to variations in intra- and extracellular ion concentrations. Abnormal ion concentrations can lead to irregular action potentials, subsequently affecting wave propagation in myocardial tissue and potentially resulting in the formation of spiral waves. Therefore, timely monitoring of ion concentration changes is essential. This study presents a novel machine learning classification model that predicts ion concentration changes based on action potential variation data. We conducted simulations using a single-cell model, generating a dataset of 850 action potential variations corresponding to different ion concentration changes. The model demonstrated excellent predictive performance, achieving an accuracy of 0.988 on the test set. Additionally, the causes of spontaneous spiral wave generation in the heart are insufficiently studied. This study presents a new mechanism whereby changes in extracellular potassium ion concentration leads to the spontaneous generation of spiral waves. By constructing composite myocardial tissue containing both myocardial and fibroblast cells, we observed that variations in extracellular potassium ion concentration can either trigger or inhibit cardiomyocyte excitation. We developed three tissue structures, and by appropriately adjusting the extracellular potassium ion concentration, we observed the spontaneous generation of single spiral waves, symmetrical spiral wave pairs, and asymmetrical double spiral waves.

Due to the similar characteristics of chaotic systems and cryptography, public key encryption algorithms based on chaotic systems are worth in-depth research and have high value for the future. Chebyshev polynomials have good properties and are often used in the design of public key algorithms. This paper improves the Bose Multi-Chaotic Public Key Cryptographic Algorithm (BMPKC) by applying Chebyshev polynomials. The proposed algorithm (CMPKC-ki) introduces the selective coefficient ki based on the properties of Chebyshev polynomials, allowing the special functions that need to be negotiated in the original system to be freely and randomly chosen as Chebyshev polynomials, and can also be expanded to m levels. The improved cryptographic algorithm also utilizes chaotic hash functions and logistic mapping to generate pseudo-random sequences and overcomes shortcomings of the Bose algorithm by iteratively iterating the selected Chebyshev polynomials based on the number of 0s or 1s in the pseudo-random sequence, thus providing better security. Analysis and software testing results indicate that this algorithm has strong robustness against brute force attacks, achieving a higher attack time for breaking the private key compared to the CEPKC, BMPKC, and CMPKC algorithms. Compared to the CMPKC algorithm, our proposal algorithm achieves better performance in the encryption and decryption phases. Furthermore, we combine this Multi-Chaotic System Key Exchange Protocol with the Advanced Encryption Standard (AES) algorithm, while providing a demonstration, offering more possibilities for practical applications of this system.

Introduction: As the evaluation indices, cancer grading and subtyping have diverse clinical, pathological, and molecular characteristics with prognostic and therapeutic implications. Although researchers have begun to study cancer differentiation and subtype prediction, most of relevant methods are based on traditional machine learning and rely on single omics data. It is necessary to explore a deep learning algorithm that integrates multi-omics data to achieve classification prediction of cancer differentiation and subtypes.Methods: This paper proposes a multi-omics data fusion algorithm based on a multi-view graph neural network (MVGNN) for predicting cancer differentiation and subtype classification. The model framework consists of a graph convolutional network (GCN) module for learning features from different omics data and an attention module for integrating multi-omics data. Three different types of omics data are used. For each type of omics data, feature selection is performed using methods such as the chi-square test and minimum redundancy maximum relevance (mRMR). Weighted patient similarity networks are constructed based on the selected omics features, and GCN is trained using omics features and corresponding similarity networks. Finally, an attention module integrates different types of omics features and performs the final cancer classification prediction.Results: To validate the cancer classification predictive performance of the MVGNN model, we conducted experimental comparisons with traditional machine learning models and currently popular methods based on integrating multi-omics data using 5-fold cross-validation. Additionally, we performed comparative experiments on cancer differentiation and its subtypes based on single omics data, two omics data, and three omics data.Discussion: This paper proposed the MVGNN model and it performed well in cancer classification prediction based on multiple omics data.

In the realm of cardiac research, the control of spiral waves and turbulent states has been a persistent focus for scholars. Among various avenues of investigation, the modulation of ion currents represents a crucial direction. It has been proved that the methods involving combined control of currents are superior to singular approaches. While previous studies have proposed some combination strategies, further reinforcement and supplementation are required, particularly in the context of controlling arrhythmias through the combined regulation of two potassium ion currents. This study employs the Luo–Rudy phase I cardiac model, modulating the maximum conductance of the time-dependent potassium current and the time-independent potassium current, to investigate the effects of this combined modulation on spiral waves and turbulent states. Numerical simulation results indicate that, compared to modulating a single current, combining reductions in the conductance of two potassium ion currents can rapidly control spiral waves and turbulent states in a short duration. This implies that employing blockers for both potassium ion currents concurrently represents a more efficient control strategy. The control outcomes of this study represent a novel and effective combination for antiarrhythmic interventions, offering potential avenues for new antiarrhythmic drug targets.

Summary: Cervical cancer remains a significant health issue in developing countries. However, finding a preclinical model that accurately reproduces tumor characteristics is challenging. Therefore, we established a patient-derived organoids (PDOs) biobank containing 67 cases of heterogeneous cervical cancer that mimic the histopathological and genomic characteristics of parental tumors. The in vitro response of the organoids indicated their ability to capture the radiological heterogeneity of the patients. To model individual responses to adoptive T cell therapy (ACT), we expanded tumor-infiltrating lymphocytes (TILs) ex vivo and co-cultured them with paired organoids. The PDOs-TILs co-culture system demonstrates clear responses that correspond to established immunotherapy efficiency markers like the proportion of CTLs. This study supports the potential of the PDOs platform to guide treatment in prospective interventional trials in cervical cancer.

Adenoid hypertrophy is a pathological condition characterized by the enlargement of the adenoids in children, which may lead to various problems. The conventional manual measurement is time-consuming and subject to subjective errors. Previous automated methods based on landmark detection in X-ray images have shown reliability. However, these methods neglect global features, making it difficult to locate landmarks accurately and thus affecting adenoid-to-nasopharyngeal (AN) ratio estimation when migrating to MRI images. In this paper, we first apply a deep-learning method to automatically assess adenoid hypertrophy in MRI images. We propose an adenoid network (ADNet) to capture local and global features near landmarks to achieve accurate landmark localization. Specifically, ADNet uses an encoder-decoder architecture where we employ a depthwise separable convolution-based encoder to extract local features and then employ an adaptive convolution-based decoder to capture global features. We collected a dataset of 500 cephalometric MRI images to train and evaluate the performance of the proposed model. Our experimental results demonstrate that our network achieves state-of-the-art performance with an average radial error of 4.85 pixels for landmark detection, an average successful detection rate of 96% within 15 pixels, and an error of 0.026 for the calculated AN ratio.

Abstract More and more people are under high pressure in modern society, leading to growing mental disorders, such as antenatal depression for pregnant women. Antenatal depression can affect pregnant woman’s physical and psychological health and child outcomes, and cause postpartum depression. Therefore, it is essential to detect the antenatal depression of pregnant women early. This study aims to predict pregnant women’s antenatal depression and identify factors that may lead to antenatal depression. First, a questionnaire was designed, based on the daily life of pregnant women. The survey was conducted on pregnant women in a hospital, where 5666 pregnant women participated. As the collected data is unbalanced and has high dimensions, we developed a one-class classifier named Stacked Auto Encoder Support Vector Data Description (SAE-SVDD) to distinguish depressed pregnant women from normal ones. To validate the method, SAE-SVDD was firstly applied on three benchmark datasets. The results showed that SAE-SVDD was effective, with its F-scores better than other popular classifiers. For the antenatal depression problem, the F-score of SAE- SVDD was higher than 0.87, demonstrating that the questionnaire is informative and the classification method is successful. Then, by an improved Term Frequency-Inverse Document Frequency (TF-IDF) analysis, the critical factors of antenatal depression were identified as work stress, marital status, husband support, passive smoking, and alcohol consumption. With its generalizability, SAE-SVDD can be applied to analyze other questionnaires.

Due to its very desirable properties, Chebyshev polynomials are often used in the design of public key cryptographic systems. This paper discretizes the Chebyshev mapping, generalizes the properties of Chebyshev polynomials, and proposes an improved public key encryption algorithm based on Chebyshev chaotic mapping and RSA, i.e., CRPKC−Ki. This algorithm introduces alternative multiplication coefficients Ki, the selection of which is determined by the size of TrTdxmod N=TdTrxmod N, and the specific value selection rules are shared secrets among participants, overcoming the shortcomings of previous schemes. In the key generation and encryption/decryption stages, more complex intermediate processes are used to achieve higher algorithm complexity, making the algorithm more robust against ordinary attacks. The algorithm is also compared with other RSA-based algorithms to demonstrate its effectiveness in terms of performance and security.

In the context of escalating global environmental concerns, the importance of preserving water resources and upholding ecological equilibrium has become increasingly apparent. As a result, the monitoring and prediction of water quality have emerged as vital tasks in achieving these objectives. However, ensuring the accuracy and dependability of water quality prediction has proven to be a challenging endeavor. To address this issue, this study proposes a comprehensive weight-based approach that combines entropy weighting with the Pearson correlation coefficient to select crucial features in water quality prediction. This approach effectively considers both feature correlation and information content, avoiding excessive reliance on a single criterion for feature selection. Through the utilization of this comprehensive approach, a comprehensive evaluation of the contribution and importance of the features was achieved, thereby minimizing subjective bias and uncertainty. By striking a balance among various factors, features with stronger correlation and greater information content can be selected, leading to improved accuracy and robustness in the feature-selection process. Furthermore, this study explored several machine learning models for water quality prediction, including Support Vector Machines (SVMs), Multilayer Perceptron (MLP), Random Forest (RF), XGBoost, and Long Short-Term Memory (LSTM). SVM exhibited commendable performance in predicting Dissolved Oxygen (DO), showcasing excellent generalization capabilities and high prediction accuracy. MLP demonstrated its strength in nonlinear modeling and performed well in predicting multiple water quality parameters. Conversely, the RF and XGBoost models exhibited relatively inferior performance in water quality prediction. In contrast, the LSTM model, a recurrent neural network specialized in processing time series data, demonstrated exceptional abilities in water quality prediction. It effectively captured the dynamic patterns present in time series data, offering stable and accurate predictions for various water quality parameters.

Managed pressure drilling (MPD) is the most effective means to ensure drilling safety, and MPD is able to avoid further deterioration of complex working conditions through precise control of the wellhead back pressure. The key to the success of MPD is the well control strategy, which currently relies heavily on manual experience, hindering the automation and intelligence process of well control. In response to this issue, an MPD knowledge graph is constructed in this paper that extracts knowledge from published papers and drilling reports to guide well control. In order to improve the performance of entity extraction in the knowledge graph, a few-shot Chinese entity recognition model CEntLM-KL is extended from the EntLM model, in which the KL entropy is built to improve the accuracy of entity recognition. Through experiments on benchmark datasets, it has been shown that the proposed model has a significant improvement compared to the state-of-the-art methods. On the few-shot drilling datasets, the F-1 score of entity recognition reaches 33%. Finally, the knowledge graph is stored in Neo4J and applied for knowledge inference.

Abstract The Keras deep learning framework is employed to study MRI brain data in a preliminary analysis of brain structure using a convolutional neural network. The results obtained are matched with the content of personality questionnaires. The Big Five personality traits provide easy differentiation for dividing personalities into different groups. Until now, the highest accuracy obtained from the results of personality prediction from the analysis of brain structure is about 70%. Although there is still no effective evidence to prove a clear relationship between brain structure and personality, the obtained results could prove helpful in understanding the basic relationship between brain structure and personality characteristics.

Spatial transcriptomics is an emerging technology widely applied to the analyses of tissue architecture and corresponding biological functions. Substantial computational methods have been developed for analyzing spatial transcriptomics data. These methods generate embeddings from gene expression and spatial locations for spot clustering or tissue architecture segmentation. Although the hyperparameters used to produce an embedding can be tuned for a given training set, a fixed embedding has variable performance from case to case due to data distributions. Therefore, selecting an effective embedding for new data in advance would be useful. For this purpose, we developed an embedding evaluation method named message passing-Moran’s I with maximum filtering (MP-MIM), which combines message passing-based embedding transformation with spatial autocorrelation analysis. We applied a graph convolution to aggregate spatial transcriptomics data and employed global Moran’s I to measure spatial autocorrelation and select the most effective embedding to infer tissue architecture. Sixteen spatial transcriptomics samples generated from the human brain were used to validate our method. The results show that MP-MIM can accurately identify high-quality embeddings that produce a high correlation between the predicted tissue architecture and the ground truth. Overall, our study provides a novel method to select embeddings for new test data and enhance the usability of deep learning tools for spatial transcriptome analyses.

Chaotic time series are widely present in practice, but due to their characteristics—such as internal randomness, nonlinearity, and long-term unpredictability—it is difficult to achieve high-precision intermediate or long-term predictions. Multi-layer perceptron (MLP) networks are an effective tool for chaotic time series modeling. Focusing on chaotic time series modeling, this paper presents a generalized degree of freedom approximation method of MLP. We then obtain its Akachi information criterion, which is designed as the loss function for training, hence developing an overall framework for chaotic time series analysis, including phase space reconstruction, model training, and model selection. To verify the effectiveness of the proposed method, it is applied to two artificial chaotic time series and two real-world chaotic time series. The numerical results show that the proposed optimized method is effective to obtain the best model from a group of candidates. Moreover, the optimized models perform very well in multi-step prediction tasks.

Temporal action localization (TAL) aims to predict action instance categories in videos and identify their start and end times. However, existing Transformer-based backbones focus only on global or local features, resulting in the loss of information. In addition, both global and local self-attention mechanisms tend to average embeddings, thereby reducing the preservation of critical features. To solve these two problems better, we propose two kinds of attention mechanisms, namely multi-headed local self-attention (MLSA) and max-average pooling attention (MA) to extract simultaneously local and global features. In MA, max-pooling is used to select the most critical information from local clip embeddings instead of averaging embeddings, and average-pooling is used to aggregate global features. We use MLSA for modeling local temporal context. In addition, to enhance collaboration between MA and MLSA, we propose the double attention block (DABlock), comprising MA and MLSA. Finally, we propose the final network double attention network (DANet), composed of DABlocks and other advanced blocks. To evaluate DANet’s performance, we conduct extensive experiments for the TAL task. Experimental results demonstrate that DANet outperforms the other state-of-the-art models on all datasets. Finally, ablation studies demonstrate the effectiveness of the proposed MLSA and MA. Compared with structures using backbone with convolution and global Transformer, DABlock consisting of MLSA and MA has a superior performance, achieving an 8% and 0.5% improvement on overall average mAP, respectively.

Hybrid recommendation algorithms perform well in improving the accuracy of recommendation systems. However, in specific applications, they still cannot reach the requirements of the recommendation target due to the gap between the design of the algorithms and data characteristics. In this paper, in order to learn higher-order feature interactions more efficiently and to distinguish the importance of different feature interactions better on the prediction results of recommendation algorithms, we propose a light and FM deep neural network (LFDNN), a hybrid recommendation model including four modules. The LightGBM module applies gradient boosting decision trees for feature processing, which improves LFDNN’s ability to handle dense numerical features; the shallow model introduces the FM model for explicitly modeling the finite-order feature crosses, which strengthens the expressive ability of the model; the deep neural network module uses a fully connected feedforward neural network to allow the model to obtain more high-order feature crosses information and mine more data patterns in the features; finally, the Fusion module allows the shallow model and the deep model to obtain a better fusion effect. The results of comparison, parameter influence and ablation experiments on two real advertisement datasets shows that the LFDNN reaches better performance than the representative recommendation models.

Background: Cervical cancer (CC) is the most common gynecological malignancy. Recently, an increasing number of studies have indicated that osteopontin (OPN) is a promising diagnostic and prognostic biomarker for CC. However, the biological role and detailed mechanism of OPN in CC remain unclear.Methods: The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets and a clinical sample microarray were used in our study. To identify the clinicopathological characteristics of OPN in CC, we compared the expression of OPN between normal and CC tissue samples and analyzed the correlations between OPN expression and multiple clinicopathological features. To identify biological processes involving OPN, OPN-associated genes were screened with Pearson correlation analysis and applied in hallmark gene set enrichment analysis (GSEA). Additionally, leukocyte infiltration was evaluated based on OPN expression. Finally, OPN-related signaling pathways were identified by GSEA.Results: OPN expression was higher in CC samples than in normal tissue samples and positively correlated with age, FIGO stage, tumor size, lymphovascular invasion and an unfavorable prognosis. OPN-associated genes were mainly enriched in the immune response, and increased OPN expression was accompanied by increased M2 macrophage infiltration. Additionally, OPN was correlated with hypoxia, high glycolytic metabolism, apoptosis, angiogenesis, epithelial-mesenchymal transition and multiple signaling pathways (the p53 pathway, the PI3K/Akt pathway, IL6/STAT3 signaling, mTORC1 signaling and KRAS signaling).Conclusion: Our study showed that OPN is involved in immunological activities and multiple tumor processes, identifying it as a potential therapeutic target and useful prognostic factor in CC patients.

Predicting peptide inter-residue contact maps plays an important role in computational biology, which determines the topology of the peptide structure. However, due to the limited number of known homologous structures, there is still much room for inter-residue contact map prediction. Current models are not sufficient for capturing the high accuracy relationship between the residues, especially for those with a long-range distance. In this article, we developed a novel deep neural network framework to refine the rough contact map produced by the existing methods. The rough contact map is used to construct the residue graph that is processed by the graph convolutional neural network (GCN). GCN can better capture the global information and is therefore used to grasp the long-range contact relationship. The residual convolutional neural network is also applied in the framework for learning local information. We conducted the experiments on four different test datasets, and the inter-residue long-range contact map prediction accuracy demonstrates the effectiveness of our proposed method.

Using Chang’E data, the authors here identify more than 109,000 previously unrecognized lunar craters and date almost 19,000 craters based on transfer learning with deep neural networks. A new lunar crater database is derived and distributed to the planetary community.

Abstract Endometriosis is a chronic inflammatory disease. Pain is the most common symptom in endometriosis. Endometriosis-associated pain is caused by inflammation, and is related to aberrant innervation. Although the specific mechanism between endometriosis-associated pain and the interaction of aberrant innervation and inflammation remains unclear, many studies have confirmed certain correlations between them. In addition, we found that some chronic inflammatory autoimmune diseases (AIDs) such as inflammatory bowel disease (IBD) and rheumatoid arthritis (RA) share similar characteristics: the changes in dysregulation of inflammatory factors as well as the function and innervation of the autonomic nervous system (ANS). The mechanisms underlying the interaction between the ANS and inflammation have provided new advances among these disorders. Therefore, the purpose of this review is to compare the changes in inflammation and ANS in endometriosis, IBD, and RA; and to explore the role and possible mechanism of sympathetic and parasympathetic nerves in endometriosis-associated inflammation by referring to IBD and RA studies to provide some reference for further endometriosis research and treatment.

Single-cell sequencing technology can generate RNA-sequencing data at the single cell level, and one important single-cell RNA-sequencing data analysis method is to identify their cell types without supervised information. Clustering is an unsupervised approach that can help find new insights into biology especially for exploring the biological functions of specific cell type. However, it is challenging for traditional clustering methods to obtain high-quality cell type recognition results. In this research, we propose a novel Clustering method based on Matching Clusters Structures (MCSC) for identifying cell types among single-cell RNA-sequencing data. Firstly, MCSC obtains two different groups of clustering results from the same K-means algorithm because its initial centroids are randomly selected. Then, for one group, MCSC uses shared nearest neighbour information to calculate a label transition matrix, which denotes label transition probability between any two initial clusters. Each initial cluster may be reassigned if merging results after label transition satisfy a consensus function that maximizes structural matching degree of two different groups of clustering results. In essence, the MCSC may be interpreted as a label training process. We evaluate the proposed MCSC with five commonly used datasets and compare MCSC with several classical and state-of-the-art algorithms. The experimental results show that MCSC outperform other algorithms.

Accurately identifying protein-ATP (Adenosine-5'-triphosphate) binding sites is significant for protein function annotation and new drug invention. Previous studies often utilize classical machine learning classification algorithms to predict protein-ATP binding sites based on protein primary sequence. However, deep learning as a newly developed technique has shown outstanding performance in various fields. In this work, we introduce the deep convolutional neural network for protein-ATP binding sites prediction based on sequence information. Two classification networks are developed including a residual-inception-based predictor and a multi-inception-based predictor, then the ensemble learning is applied by giving optimized weights to each network architecture to combine them for more superior performance. We examine the performance of our proposed method on two groups of independent testing sets including a classic ATP-binding benchmark dataset and a newly proposed ATP-binding dataset. As a result, our proposed method outperforms other state-of-art sequence-based predictors with the AUC of 0.922 and 0.896 respectively which illustrates the efficacy of deep learning technique in protein-ATP binding sites prediction. The source code and benchmark datasets can be downloaded at https://github.com/tlsjz/ATPbinding.

Urine excretory proteins are among the most commonly used biomarkers in body fluids. Computational identification of urine excretory proteins can provide very useful information for identifying targeted disease biomarkers in urine by linking transcriptome or proteomics data. There are few methods based on conventional machine learning algorithms for predicting urine excretory proteins, and most of these methods strongly depend on the extraction of features from urine excretory proteins. An end-to-end model for urine excretory protein prediction, called DeepUEP, is presented using deep neural networks relying on only amino acid sequence information. The model achieves good performance and outperforms existing methods on training and testing sets. By comparing known urinary protein biomarkers with the results of the model, we find that the model can achieve a true-positive rate of over 80% for urinary protein biomarkers that have been detected in more than one study. We also combine our model with transcriptome and proteomics data from lung cancer patients to predict the potential urinary protein biomarkers of lung cancer. A web server is developed for the prediction of urine excretory proteins, and it can be accessed at the following URL: http://www.csbg-jlu.info/DeepUEP/. We believe that our prediction model and web server are useful for biomedical researchers who are interested in identifying urinary protein biomarkers, especially for candidate proteins in transcriptome or proteomics analyses of diseased tissues.

Speech recognition technology has played an indispensable role in realizing human-computer intelligent interaction. However, most of the current Chinese speech recognition systems are provided online or offline models with low accuracy and poor performance. To improve the performance of offline Chinese speech recognition, we propose a hybrid acoustic model of deep convolutional neural network, long short-term memory, and deep neural network (DCNN-LSTM-DNN, DLD). This model utilizes DCNN to reduce frequency variation and adds a batch normalization (BN) layer after its convolutional layer to ensure the stability of data distribution, and then use LSTM to effectively solve the gradient vanishing problem. Finally, the fully connected structure of DNN is utilized to efficiently map the input features into a separable space, which is helpful for data classification. Therefore, leveraging the strengths of DCNN, LSTM, and DNN by combining them into a unified architecture can effectively improve speech recognition performance. Our model was tested on the open Chinese speech database THCHS-30 released by the Center for Speech and Language Technology (CSLT) of Tsinghua University, and it was concluded that the DLD model with 3 layers of LSTM and 3 layers of DNN had the best performance, reaching 13.49% of words error rate (WER).

An energy supply and demand forecasting system can help decision-makers grasp more comprehensive information, make accurate decisions and even plan a carbon-neutral future when adjusting energy structure, developing alternative energy resources and so on. This paper presents a hierarchical design of an energy supply and demand forecasting system based on web crawler and a grey dynamic model called GM(1,1) which covers all the process of data collection, data analysis and data prediction. It mainly consists of three services, namely Crawler Service (CS), Algorithm Service (AS), Data Service (DS). The architecture of multiple loose coupling services makes the system flexible in more data, and more advanced prediction algorithms for future energy forecasting works. In order to make higher prediction accuracy based on GM(1,1), this paper illustrates some basic enhanced methods and their combinations with adaptable variable weights. An implementation for testing the system was applied, where the model was set up for coal, oil and natural gas separately, and the enhanced GM was better with relative error about 9.18% than original GM on validation data between 2010 and 2020. All results are available for reference on adjusting of energy structure and developing alternative energy resources.

Background: Endometrial cancer (EC) is one of the most common gynecological malignancies in women. Cholesterol metabolism has been confirmed to be closely related to tumor proliferation, invasion and metastasis. However, the correlation between cholesterol homeostasis-related genes and prognosis of EC remains unclear.Methods: EC patients from the Cancer Genome Atlas (TCGA) database were randomly divided into training cohort and test cohort. Transcriptome analysis, univariate survival analysis and LASSO Cox regression analysis were adopted to construct a cholesterol homeostasis-related gene signature from the training cohort. Subsequently, Kaplan-Meier (KM) plot, receiver operating characteristic (ROC) curve and principal component analysis (PCA) were utilized to verify the predictive performance of the gene signature in two cohorts. Additionally, enrichment analysis and immune infiltration analysis were performed on differentially expressed genes (DEGs) between two risk groups.Results: Seven cholesterol homeostasis-related genes were selected to establish a gene signature. KM plot, ROC curve and PCA in two cohorts demonstrated that the gene signature was an efficient independent prognostic indicator. The enrichment analysis and immune infiltration analysis indicated that the high-risk group generally had lower immune infiltrating cells and immune function.Conclusion: We constructed and validated a cholesterol homeostasis-related gene signature to predict the prognosis of EC, which correlated to immune infiltration and expected to help the diagnosis and precision treatment of EC.

It has been observed that both cancer tissue cells and normal proliferating cells (NPCs) have the Warburg effect. Our goal here is to demonstrate that they do this for different reasons. To accomplish this, we have analyzed the transcriptomic data of over 7000 cancer and control tissues of 14 cancer types in TCGA and data of five NPC types in GEO. Our analyses reveal that NPCs accumulate large quantities of ATPs produced by the respiration process before starting the Warburg effect, to raise the intracellular pH from ∼6.8 to ∼7.2 and to prepare for cell division energetically. Once cell cycle starts, the cells start to rely on glycolysis for ATP generation followed by ATP hydrolysis and lactic acid release, to maintain the elevated intracellular pH as needed by cell division since together the three processes are pH neutral. The cells go back to the normal respiration-based ATP production once the cell division phase ends. In comparison, cancer cells have reached their intracellular pH at ∼7.4 from top down as multiple acid-loading transporters are up-regulated and most acid-extruding ones except for lactic acid exporters are repressed. Cancer cells use continuous glycolysis for ATP production as way to acidify the intracellular space since the lactic acid secretion is decoupled from glycolysis-based ATP generation and is pH balanced by increased expressions of acid-loading transporters. Co-expression analyses suggest that lactic acid secretion is regulated by external, non-pH related signals. Overall, our data strongly suggest that the two cell types have the Warburg effect for very different reasons. Keywords: Cancer, Warburg effect, Fenton reaction, Cell proliferation, pH homeostasis

Protein–protein interaction (PPI) plays key role in each cellular process of any living cell, however, almost all organisms’ PPIs are still incomplete. In this study, we firstly proposed a computational method Extended Local Path (ELP), which estimated links’ existence likelihood by integrating all their neighbours’ local paths in the network. In addition, on this basis, we extended it to Extended Local Path Gain (ELPG), which estimated gain effect when adding or deleting one potential link to the network. Applying both ELPG and ELP methods and other four recognized outstanding methods on four public PPI data of Yeast, E. coli, Fruit fly and Mouse, we demonstrated that ELPG and ELP obtained better performance under two standard measures: area under curve (AUC) and Precision. Besides, ELP and ELPG were identified as the best features for classifying existing and unknown links by using support vector machine-recursive feature elimination (SVM-RFE) for feature selection.

Three-phase induction motors (TPIMs) are prone to numerous faults due to their complicated stator and rotor conditions and require a fast response, accurate, and intelligent diagnostic system. Recently developed fault diagnostic systems for induction motors are based on machine learning approaches, but their complex structure typically results in long training time. Moreover, they need to be retrained from scratch if the system is not accurate. We apply incremental broad learning (IBL) method to the diagnosis of TPIM faults. The IBL can train and retrain the network efficiently due to its flexible structure. The new diagnostic framework also consists of feature extraction techniques (empirical mode decomposition and sample entropy) and a non-negative matrix factorization (NMF) IBL approach. The experimental results demonstrate that the IBL system is superior to some algorithms, such as deep belief networks, convolutional neural networks, and extreme learning machine. Moreover, the IBL simplified by NMF is more accurate than the IBL without NMF.

Knowledge extracted from the protein-protein interaction (PPI) network can help researchers reveal the molecular mechanisms of biological processes. With the rapid growth in the volume of the biomedical literature, manually detecting and annotating PPIs from raw literature has become increasingly difficult. Hence, automatically extracting PPIs by machine learning methods from raw literature has gained significance in the biomedical research. In this paper, we propose a novel PPI extraction method based on the residual convolutional neural network (CNN). This is the first time that the residual CNN is applied to the PPI extraction task. In addition, the previous state-of-the-art PPI extraction models heavily rely on parsing results from natural language processing tools, such as dependence parsers. Our model does not rely on any parsing tools. We evaluated our model based on five benchmark PPI extraction corpora, AIMed, BioInfer, HPRD50, IEPA, and LLL. The experimental results showed that our model achieved the best results compared with the previous kernel-based and CNN-based PPI extraction models. Compared with the previous recurrent neural network-based PPI extraction models, our model achieved better or comparable performance.

It is always difficult to evacuate crowds in public places like subway stations. The traditional crowd behavior simulation models often ignore two important issues in crowd evacuation: pedestrian tracking and individual differences. To solve the problem, this paper combines social force model (SFM) with deep learning into a novel pedestrian detection method. Firstly, several deep learning algorithms for pedestrian detection were compared, and the best ones for sparse and dense crowds were determined. Next, the pedestrian positions in a real video were acquired by the selected algorithms, and converted into actual coordinates in the scene. Then, the evacuation process was simulated with our method and the SFM based on these coordinates. The results show that our model output closer-to-reality results than the SFM. The research findings shed important new light on evacuation in crowded areas.

Abstract We present brief highlights and updates on some newer projects, both in operation/construction and in preparation stages, of astronomical research on Mainland China, with an emphasis on those involving international collaborations. Limited by the scope of this paper, this sample is not meant to be uniform nor comprehensive, and in some cases it may not be fully up to date. For more specific and detailed information on these or other projects, we refer the readers to the official websites of these projects and those of the National Astronomical Observatories, Chinese Academy of Sciences.

Oil drilling is the core process of oil and natural gas resources exploitation. Well overflow is one of the biggest threats to safety drilling. Prediction of the overflow in advance can effectively avoid the occurrence of this kind of accident. However, the drilling history has unbalanced distribution, and labeling data is a time-consuming and laborious job. To address this issue, an overflow-prediction algorithm based on semi-supervised learning is designed in this paper, which can accurately predict overflow 10 min in advance when the labeled data are limited. Firstly, a three-step feature-selection algorithm is conducted to extract 22 features, and the time series samples are constructed through a 500-width sliding window with step size 1. Then, the Mean Teacher model with Jitter noise is employed to train the labeled and unlabeled data at the same time, in which a fused CNN-LSTM network is built for time-series prediction. Compared with supervised learning and other semi-supervised learning frameworks, the results show that the proposed model based on only 200 labeled samples is able to achieve the same effect as supervised learning method using 1000 labeled samples, and the prediction accuracy can reach 87.43% 10 min in advance. With the increase in the proportion of unlabeled samples, the performance of the model can sustain a rise within a certain range.

Under the idea of low carbon economy, natural gas has drawn widely attention all over the world and becomes one of the fastest growing energies because of its clean, high calorific value, and environmental protection properties. However, policy and political factors, supply-demand relationship and hurricanes can cause the jump in natural gas prices volatility. To address this issue, a deep learning model based on oil and gas news is proposed to predict natural gas price trends in this paper. In this model, news text embedding is conducted by BERT-Base, Uncased on natural gas-related news. Attention model is adopted to balance the weight of the news vector. Meanwhile, corresponding natural gas price embedding is conducted by a BiLSTM module. The Attention-weighted news vectors and price embedding are the inputs of the fused network with transformer is built. BiLSTM is used to extract used price information related with news features. Transformer is employed to capture time series trend of mixed features. Finally, the network achieves an accuracy as 79%, and the performance is better than most traditional machine learning algorithms.

Introduction. Purkinje system and false tendons (FTs) are related to ventricular arrhythmia, but the association between Purkinje fibers and FTs is not clear. This study investigated the associations of anatomical and electrophysiological characteristics between Purkinje fibers and FTs. Methods and Results. We optimized the protocol of Lugol’s iodine solution staining of Purkinje fibers to study the anatomical structure and originated a novel electrophysiological mapping method, named the direct visual mapping (DVM) method, to study the electrophysiological characteristics. By using the above-mentioned innovations in 12 dogs, we found the following. (1) There was no Purkinje fiber found 0.5 cm–1.0 cm below the valve annulus or on the leaflets or chordae tendineae of the mitral valve or adjacent to the top 1/3 of the papillary muscle. (2) Purkinje fibers existed in all FTs, including smaller and tiny FTs. (3) The Purkinje fibers contained in the FTs extended from the proximal to the distal end, and their electrophysiological characteristics were similar to the fibers on the endocardium, including anterograde, retrograde, and decremental conduction and automaticity. Conclusions. Purkinje fibers are commonly found in FTs. The electrophysiological characteristics of the Purkinje fibers contained in FTs are similar to the fibers on the endocardium. FTs might have an anatomical and electrophysiological basis for ventricular arrhythmia.

Abstract Endometriosis is a complex and heterogeneous disorder with unknown etiology. Dysregulation of macrophages and innervation are important factors influencing the pathogenesis of endometriosis-associated pain. It is known to be an estrogen-dependent disease, estrogen can promote secretion of chemokines from peripheral nerves, enhancing the recruitment and polarization of macrophages in endometriotic tissue. Macrophages have a role in the expression of multiple nerve growth factors (NGF), which mediates the imbalance of neurogenesis in an estrogen-dependent manner. Under the influence of estrogen, co-existence of macrophages and nerves induces an innovative neuro-immune communication. Persistent stimulation by inflammatory cytokines from macrophages on nociceptors of peripheral nerves aggravates neuroinflammation through the release of inflammatory neurotransmitters. This neuro-immune interaction regulated by estrogen sensitizes peripheral nerves, leading to neuropathic pain in endometriosis. The aim of this review is to highlight the significance of estrogen in the interaction between macrophages and nerve fibers, and to suggest a potentially valuable therapeutic target for endometriosis-associated pain.

Abstract The aberrant alterations of biological functions are well known in tumorigenesis and cancer development. Hence, with advances in high-throughput sequencing technologies, capturing and quantifying the functional alterations in cancers based on expression profiles to explore cancer malignant process is highlighted as one of the important topics among cancer researches. In this article, we propose an algorithm for quantifying biological processes by using gene expression profiles over a sample population, which involves the idea of constructing principal curves to condense information of each biological process by a novel scoring scheme on an individualized manner. After applying our method on several large-scale breast cancer datasets in survival analysis, a subset of these biological processes extracted from corresponding survival model is then found to have significant associations with clinical outcomes. Further analyses of these biological processes enable the study of the interplays between biological processes and cancer phenotypes of interest, provide us valuable insights into cancer biology in biological process level and guide the precision treatment for cancer patients. And notably, prognosis predictions based on our method are consistently superior to the existing state of art methods with the same intention.

Machine learning models can automatically discover biomedical research trends and promote the dissemination of information and knowledge. Text feature representation is a critical and challenging task in natural language processing. Most methods of text feature representation are based on word representation. A good representation can capture semantic and structural information. In this paper, two fusion algorithms are proposed, namely, the Tr-W2v and Ti-W2v algorithms. They are based on the classical text feature representation model and consider the importance of words. The results show that the effectiveness of the two fusion text representation models is better than the classical text representation model, and the results based on the Tr-W2v algorithm are the best. Furthermore, based on the Tr-W2v algorithm, trend analyses of cancer research are conducted, including correlation analysis, keyword trend analysis, and improved keyword trend analysis. The discovery of the research trends and the evolution of hotspots for cancers can help doctors and biological researchers collect information and provide guidance for further research.

A community in a complex network refers to a group of nodes that are densely connected internally but with only sparse connections to the outside. Overlapping community structures are ubiquitous in real-world networks, where each node belongs to at least one community. Therefore, overlapping community detection is an important topic in complex network research. This paper proposes an overlapping community detection algorithm based on membership degree propagation that is driven by both global and local information of the node community. In the method, we introduce a concept of membership degree, which not only stores the label information, but also the degrees of the node belonging to the labels. Then the conventional label propagation process could be extended to membership degree propagation, with the results mapped directly to the overlapping community division. Therefore, it obtains the partition result and overlapping node identification simultaneously and greatly reduces the computational time. The proposed algorithm was applied to a synthetic Lancichinetti–Fortunato–Radicchi (LFR) dataset and nine real-world datasets and compared with other up-to-date algorithms. The experimental results show that our proposed algorithm is effective and outperforms the comparison methods on most datasets. Our proposed method significantly improved the accuracy and speed of the overlapping node prediction. It can also substantially alleviate the computational complexity of community structure detection in general.

With the development of Internet of Things technology, radio-frequency identification localization methods have been widely applied due to their low cost and ease of deployment. The indoor radio-frequency identification localization algorithm based on received signal strength indication technology is a currently hot topic. Because the received signal strength is highly dependent on environments, the classic algorithms may result in large errors in localization accuracy. This article proposed a new radio-frequency identification localization algorithm, named BP_LANDMARC, by utilizing the back propagation neural network, which is designed to address nonlinear changes in radio-frequency signals. A strategy for selecting different working parameters in variable environments is presented. The evaluation methods of root mean square error and cumulative distribution function are used to compare the proposed algorithm with some existing algorithms. Experimental results show that the proposed algorithm remarkably improves the localization accuracy of both absolute distance and cumulative probability. Moreover, the proposed algorithm performs effectively and efficiently when it is applied to a logistics warehouse management system.

The flexible job shop scheduling problem (FJSP) is one of the most important problems in the field of production scheduling, which is the abstract of some practical production processes. It is a complex combinatorial optimization problem due to the consideration of both machine assignment and operation sequence. In this paper, an efficient artificial fish swarm model with estimation of distribution (AFSA-ED) is proposed for the FJSP with the objective of minimizing the makespan. Firstly, a pre-principle and a post-principle arranging mechanism that operate by adjusting machine assignment and operation sequence with different orders are designed to enhance the diversity of population. Following this, the population is divided into two sub-populations and then two arranging mechanisms are applied. In AFSA-ED, a preying behavior based on estimation of distribution is proposed to improve the performance of algorithm. Moreover, an attracting behavior is proposed to improve the global exploration ability and a public factor based critical path search strategy is proposed to enhance the local exploitation ability. Simulated experiments are carried on BRdata, BCdata and HUdata benchmark sets. The computational results validate the performance of the proposed algorithm in solving the FJSP, as compared with some other state of the art algorithms.

More and more studies have demonstrated that long noncoding RNAs (lncRNAs) play critical roles in diversity of biological process and are also associated with various types of disease. How to rapidly identify lncRNAs and messenger RNA is the fundamental step to uncover the function of lncRNAs identification. Here, we present a novel method for rapid identification of lncRNAs utilizing sequence intrinsic composition features and open reading frame information based on support vector machine model, named as Lncident (LncRNAs identification). The 10-fold cross-validation and ROC curve are used to evaluate the performance of Lncident. The main advantage of Lncident is high speed without the loss of accuracy. Compared with the exiting popular tools, Lncident outperforms Coding-Potential Calculator, Coding-Potential Assessment Tool, Coding-Noncoding Index, and PLEK. Lncident is also much faster than Coding-Potential Calculator and Coding-Noncoding Index. Lncident presents an outstanding performance on microorganism, which offers a great application prospect to the analysis of microorganism. In addition, Lncident can be trained by users’ own collected data. Furthermore, R package and web server are simultaneously developed in order to maximize the convenience for the users. The R package “Lncident” can be easily installed on multiple operating system platforms, as long as R is supported.

Previous studies have demonstrated the involvement of nerve repellent factors in regulation of the imbalanced innervation of endometriosis. This prospective study aims to explore the role of Sema 3A in regulating aberrant sympathetic innervation in peritoneal and deep infiltrating endometriosis. Ectopic endometriotic lesion were collected from patients with peritoneal endometriosis (n = 24) and deep infiltrating endometriosis of uterosacral ligament (n = 20) undergoing surgery for endometriosis. Eutopic endometrial samples were collected from patients with endometriosis (n = 22) or without endometriosis (n = 26). Healthy peritoneum (n = 13) from the lateral pelvic wall and healthy uterosacral ligament (n = 13) were obtained from patients who had no surgical and histological proof of endometriosis during hysterectomy for uterine fibroids. Firstly, we studied the immunostaining of Sema 3A, Plexin A1 and NRP-1 in all the tissues described above. Then we studied the nerve fiber density (NFD) of endometriosis-associated (sympathetic) nerve and para-endometriotic (sympathetic) nerve by double immunofluorescence staining. Finally we analyzed the relationship between expression of Sema 3A in stromal cells of endometriotic lesion and the aberrant innervation of endometriosis. Semi-quantitative immunostaining demonstrated that (1) Higher immunostaining of Sema 3A were found in the eutopic endometrial glandular epithelial cells from patients with endometriosis (p = 0.041) than those without endometriosis; (2) Sema 3A immunostaining was higher in glandular epithelial cells of peritoneal endometriosis (P