Non-negative Matrix Factorization Method Research Articles

Investigating radial gradient variations of nanostructure of cellulose microfibrils in bamboo culm by synchrotron X-ray scattering

Bamboo is a swiftly renewable natural material. A thorough exploration of its functional hierarchical structure is helpful to improve its utilization efficiency. Previous studies have found that there are notable structural distinctions in bamboo fibers and parenchyma cell wall at the nanoscale. The fluctuation in cellulose microfibrils (CMF) within bamboo has been verified as a critical factor significantly impacting the mechanical properties of bamboo fibers. This study systematically examines the radial gradient variation in the cellulose supramolecular structures of bamboo culms through synchrotron X-ray scattering. The measured cellulose crystallinity index (CrI), the diameter and packing distance of CMF, the orientation parameter, and the distribution of microfibril angle (MFA) were found to be correlated with the radial distribution of fibers and parenchyma cells. In the radial direction, the relative CrI values of 004 reflection increased from 26 % for the innermost layer to 51 % for the outermost layer; the CMF diameter decreased from 2.75 nm to 2.66 nm; the packing distance of CMF’ cylinders was reduced from 3.68 nm to 3.35 nm. The measured mean MFA values exhibit a decrease from approximately 70° to around 5°. Moreover, the azimuthal X-ray scattering signals were effectively segregated from fiber and parenchyma cell wall using the non-negative matrix factorisation (NNMF) method. This methodology holds promise for nanostructure analysis in complex plant stems comprising fiber and parenchyma cells, including but not limited to wheat, corn stalks, and other biomaterials.

Integrating topology and content equally in non-negative matrix factorization for community detection

Non-negative matrix factorization (NMF) is widely used in analyzing the community structure of complex networks. However, most of the current related efforts only focus on the network structural topology, while neglecting the node content. Although there have been efforts to integrate topology and content, inefficient strategies balancing their contributions can also lead to unsatisfactory results. In this work, we treat topology and content equally and propose two novel NMF-based methods to finely balance topology and content to improve the performance of community detection. We first propose a double encoder–decoder-based NMF (DEDNMF) method that employs two NMF-based encoder–decoders to integrate topology and content adaptively. Experimental results show that DEDNMF outperforms the baseline methods with average improvements of 50.69% and 46.93% in terms of normalized mutual information (NMI) and adjusted rand index (ARI) on all experimental networks, respectively. Moreover, we propose a double-decoder-based NMF (DDNMF) method that uses only two decoders for both topology and content, imposing sparsity constraints on NMF. Experimental results show that DDNMF outperforms the baseline methods with average improvements of 72.11% and 77.00% in terms of NMI and ARI on all experimental networks. Experimental results also show that the proposed two methods have good convergence and robustness.

Clinically relevant immune subtypes based on alternative splicing landscape of immune-related genes for lung cancer advanced PPPM approach.

Alternative splicing (AS) occurs in the process of gene post-transcriptional process, which is very important for the correct synthesis and function of protein. The change of AS pattern may lead to the change of expression level or function of lung cancer-related genes, and then affect the occurrence and development of lung cancers. The specific AS pattern might be used as a biomarker for early warning and prognostic assessment of a cancer in the framework of predictive, preventive, and personalized medicine (PPPM; 3PM). AS events of immune-related genes (IRGs) were closely associated with tumor progression and immunotherapy. We hypothesize that IRG-AS events are significantly different in lung adenocarcinomas (LUADs) vs. controls or in lung squamous cell carcinomas (LUSCs) vs. controls. IRG-AS alteration profiling was identified to construct IRG-differentially expressed AS (IRG-DEAS) signature models. Study on the selective AS events of specific IRGs in lung cancer patients might be of great significance for further exploring the pathogenesis of lung cancer, realizing early detection and effective monitoring of lung cancer, finding new therapeutic targets, overcoming drug resistance, and developing more effective therapeutic strategies, and better used for the prediction, diagnosis, prevention, and personalized medicine of lung cancer. The transcriptomic, clinical, and AS data of LUADs and LUSCs were downloaded from TCGA and its SpliceSeq databases. IRG-DEAS events were identified in LUAD and LUSC, followed by their functional characteristics, and overall survival (OS) analyses. OS-related IRG-DEAS prognostic models were constructed for LUAD and LUSC with Lasso regression, which were used to classify LUADs and LUSCs into low- and high-risk score groups. Furthermore, the immune cell distribution, immune-related scores, drug sensitivity, mutation status, and GSEA/GSVA status were analyzed between low- and high-risk score groups. Also, low- and high-immunity clusters and AS factor (SF)-OS-related-AS co-expression network and verification of cell function of CELF6 were analyzed in LUAD and LUSC. Comprehensive analysis of transcriptomic, clinical, and AS data of LUADs and LUSCs identified IRG-AS events in LUAD (n = 1607) and LUSC (n = 1656), including OS-related IRG-AS events in LUAD (n = 127) and LUSC (n = 105). A total of 66 IRG-DEAS events in LUAD and 89 IRG-DEAS events in LUSC were identified compared to controls. The overlapping analysis between IRG-DEASs and OS-related IRG-AS events revealed 14 OS-related IRG-DEAS events for LUAD and 16 OS-related IRG-DEAS events for LUSC, which were used to identify and optimize a 12-OS-related-IRG-DEAS signature prognostic model for LUAD and an 11-OS-related-IRG-DEAS signature prognostic model for LUSC. These two prognostic models effectively divided LUAD or LUSC samples into low- and high-risk score groups that were closely associated with OS, clinical characteristics, and tumor immune microenvironment, with significant gene sets and pathways enriched in the two groups. Moreover, weighted gene co-expression network (WGCNA) and nonnegative matrix factorization method (NMF) analyses identified four OS-relevant subtypes of LUAD and six OS-relevant subtypes of LUSC, and ssGSEA identified five immunity-relevant subtypes of LUAD and five immunity-relevant subtypes of LUSC. Interestingly, splicing factors-OS-related-AS network revealed hub molecule CELF6 was significantly related to the malignant phenotype in lung cancer cells. This study established two reliable IRG-DEAS signature prognostic models and constructed interesting splicing factor-splicing event networks in LUAD and LUSC, which can be used to construct clinically relevant immune subtypes, patient stratification, prognostic prediction, and personalized medical services in the PPPM practice. The online version contains supplementary material available at 10.1007/s13167-024-00366-4.

Non-apoptotic regulatory cell death scoring system to predict the clinical outcome and drug choices in breast cancer

BackgroundBreast cancer (BC), the most common cancer among women globally, has been shown by numerous studies to significantly involve non-apoptotic regulatory cell death (RCD) in its pathogenesis and progression. MethodsWe obtained the RNA sequences and clinical data of BC patients from The Cancer Genome Atlas (TCGA) database for the training set, while datasets GSE96058, GSE86166, and GSE20685 from The Gene Expression Omnibus (GEO) database were utilized as validation cohorts. Initially, we performed non-negative matrix factorization (NMF) clustering analysis on the BC samples from the TCGA database to discern non-apoptotic RCD-related molecular subtypes. To identify prognostically-relevant non-apoptotic RCD genes (NRGs) and construct a prognostic model, we implemented three machine learning algorithms: lasso regression, random forest, and XGBoost analysis. The expression of selected genes was verified using real-time quantitative polymerase chain reaction (RT-qPCR), single-cell RNA-sequencing (scRNA-seq) analysis, and The Human Protein Atlas (HPA) database. The risk signature was evaluated concerning clinical characteristics and drug sensitivity. Furthermore, we developed a nomogram to predict BC patient survival. ResultsThe NMF method successfully compartmentalized patients from the TCGA database into three distinct non-apoptotic RCD-related subtypes, with significant variations observed in immune characteristics and prognostic stratification across these subtypes. We identified 5 differentially expressed NRGs used in establishing the risk signature. Patients with different risk groups exhibited distinct clinicopathological features, drug sensitivity, and prognostic outcomes. A nomogram was subsequently developed, incorporating the NRGs-related risk signature, age, T stage, and N stage, to aid clinical decision-making. ConclusionWe identified a novel NRGs-related risk signature, which was expected to become a potential prognostic marker in BC.

Utilizing data-driven algorithms for blind modal parameter identification of structures from output-only video measurements

In structural dynamics and vibration analysis, modal identification plays a pivotal role in understanding and characterizing the dynamic behavior of complex systems. Traditional modal analysis techniques heavily rely on accurate sensor placement and knowledge of the excitation forces, which may not always be feasible or practical in real-world scenarios. Recently, non-contact video-based modal analysis methods for structures with arbitrary complexity using computer vision techniques have gained much importance. But these methods need to know ahead of time where the structure's natural frequency ranges are, and they use steerable pyramids, which are complicated multi-scale image decomposition filters. To address these issues, a blind modal identification technique is suggested to extract the modal parameters (modal frequency and mode shapes) from the recorded structural vibration video signal. The proposed algorithm for unsupervised machine learning is the Non-Negative Matrix Factorization (NNMF) method, which is combined with the Generalized Complexity Pursuit (GCP) method for blind source separation. The NNMF algorithm is directly applied to the raw pixel-time series made from the video data to get the temporal components, which are then separated using GCP to find the individual modal frequencies and mode shapes. The above algorithm is first validated on a numerical model and then implemented on laboratory scale models (cantilever, single-degree, and multi-degree frame models). Finally, the proposed methodology is implemented on real-world recorded structural vibration videos to determine its noise sensitivity, such as the Tacoma Narrows bridge and the London Millennium footbridge. The modal parameters extracted are compared with those from the available literature for validation. The estimation errors obtained from all the validations are well below 1%, which makes the technique quite suitable and reliable for structural vibration monitoring by identifying and reproducing complex vibration modes.

Symmetry and Graph Bi-Regularized Non-Negative Matrix Factorization for Precise Community Detection

Community is a fundamental and highly desired pattern in a Large-scale Undirected Network (LUN). Community detection is a vital issue when LUN representation learning is performed. Owing to its good scalability and interpretability, a Symmetric and Non-negative Matrix Factorization model is frequently utilized to tackle this issue. It adopts a unique Latent Factor (LF) matrix for precisely representing LUN’s symmetry, which, unfortunately, leads to a reduced LF space that decreases its representation learning ability to a target LUN. Motivated by this discovery, this study proposes a Symmetry and Graph Bi-regularized Non-negative Matrix Factorization (B-NMF) method that: a) leverages multiple LF matrices when representing LUN, thereby boosting the representation learning ability; b) constructs a symmetry regularization term that implies the equality constraint among its multiple LF matrices, thereby illustrating LUN’s intrinsic symmetry; and c) incorporates graph regularization into its learning objective, thereby illustrating LUN’s local geometry. A theoretical proof is given to theoretically validate B-NMF’s convergence ability. The regularization hyperparameters are selected by validating model modularity, thereby guaranteeing B-NMF’s practicability in addressing real application issues. Extensive experimental results on ten LUNs from real applications demonstrate that the proposed B-NMF-based community detector significantly outperforms several baseline and state-of-the-art models in achieving highly-accurate community detection results. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —LUNs are very-commonly seen in real applications like a social network system. Communities in LUNs are vital for various knowledge discovery-related applications. For accurately detecting them, a detector should guarantee its high representation learning ability to a target LUN. To do so, this paper presents a B-NMF model that is able to perform precise representation learning to LUNs, thereby achieving accurate community detection results. In comparison with conventional Symmetric and Non-negative Matrix Factorization-based community detectors, a B-NMF-based community detector enjoys its enlarged latent feature space, which ensures its higher representation ability to a target LUN. It depends on two regularization hyperparameters, which can be selected by performing grid-search on the target LUN via its modularity evaluation. This paper gives the empirical values of B-NMF’s regularization hyperparameters based on the parametersensitivity tests on the involved experimental datasets. The proposed B-NMF model is shown to be highly suitable for addressing community detection and clustering tasks on LUNs from real applications.

Deep Nonnegative Matrix Factorization with Joint Global and Local Structure Preservation

Deep Non-Negative Matrix Factorization (DNMF) methods provide an efficient low-dimensional representation of given data through their layered architecture. A limitation of such methods is that they cannot effectively preserve the local and global geometric structures of the data in each layer. Consequently, a significant amount of the geometrical information within the data, present in each layer of the employed deep framework, can be overlooked by the model. This can lead to an information loss and a subsequent drop in performance. In this paper, we propose a novel deep non-negative matrix factorization method, Deep Non-Negative Matrix Factorization with Joint Global and Local Structure Preservation (dubbed Dn2MFGL), that ensures the preservation of both global and local structures within the data space. Dn2MFGL performs representation learning through a sequential embedding procedure which involves both the global data structure by accounting for the data variance, and the local data relationships by utilizing information from neighboring data points. Moreover, a regularization term that promotes sparsity by utilizing the concept of the inner product is applied to the matrices representing the lower dimensions. This aims to retain the fundamental data structure while discarding less crucial features. Simultaneously, the residual matrix of Dn2MFGL is subjected to the L2,1 norm, which ensures the robustness of the model against noisy data samples. An effective and multiplicative updating process also facilitates Dn2MFGL in solving the employed objective function. The clustering performance of the proposed deep NMF method is explored across various benchmarks of face datasets. The results point to Dn2MFGL outperforming several existing classical and state-of-the-art NMF methods. The source code is available at https://github.com/FaridSaberi/Dn2MFGO.git.

Advances in cancer DNA methylation analysis with methPLIER: use of non-negative matrix factorization and knowledge-based constraints to enhance biological interpretability

DNA methylation is an epigenetic modification that results in dynamic changes during ontogenesis and cell differentiation. DNA methylation patterns regulate gene expression and have been widely researched. While tools for DNA methylation analysis have been developed, most of them have focused on intergroup comparative analysis within a dataset; therefore, it is difficult to conduct cross-dataset studies, such as rare disease studies or cross-institutional studies. This study describes a novel method for DNA methylation analysis, namely, methPLIER, which enables interdataset comparative analyses. methPLIER combines Pathway Level Information Extractor (PLIER), which is a non-negative matrix factorization (NMF) method, with regularization by a knowledge matrix and transfer learning. methPLIER can be used to perform intersample and interdataset comparative analysis based on latent feature matrices, which are obtained via matrix factorization of large-scale data, and factor-loading matrices, which are obtained through matrix factorization of the data to be analyzed. We used methPLIER to analyze a lung cancer dataset and confirmed that the data decomposition reflected sample characteristics for recurrence-free survival. Moreover, methPLIER can analyze data obtained via different preprocessing methods, thereby reducing distributional bias among datasets due to preprocessing. Furthermore, methPLIER can be employed for comparative analyses of methylation data obtained from different platforms, thereby reducing bias in data distribution due to platform differences. methPLIER is expected to facilitate cross-sectional DNA methylation data analysis and enhance DNA methylation data resources.

A method for detecting spatiotemporal patterns of cancer biomarkers-evoked activity using radial basis function network extracted time-domain features from calcium imaging data

BackgroundTwo-photon calcium imaging is widely used to study the odor-evoked glomerular activity in the dorsal olfactory bulb of macrosmatic animals. The nonstationary character of activated patterns sets a limit on the use of a traditional image processing approaches. New methodThe developed method makes it possible to automatically map cancer biomarkers-activated glomeruli in the rat dorsal olfactory bulb. We interpolated fluorescence intensity of calcium dynamics based on the Gaussian RBF network and synthesized the physiological fluorescence model of the receptive glomerular field. ResultsThe experiments on 5 rats confirmed the correctness of the developed approach. Patterns evoked by the 6-methyl-5-hepten-2-one (stomach cancer biomarker) and benzene (lung cancer biomarker) were correctly identified. Comparison with existing methodsThe proposed method was compared with the nonnegative matrix factorization method and with the method based on computer vision algorithms. The developed approach showed better accuracy in experiments and provided the mathematical models of the odor-evoked patterns synthesis. These models can be used to generate synthetic images of odor-evoked glomerular activity and thus to overcome the problem of small experimental data collected in calcium imaging. ConclusionsThe proposed method should be considered part of the toolkit for fully automatic analysis of calcium imaging-based studies. Currently available methodology is not able to use breath biomarkers to reliably discriminate between cancer patients and healthy controls. Nevertheless, the effective identification of the spatial patterns of cancer biomarkers-evoked glomerular activity can serve as the foundation for highly sensitive biohybrid systems for cancer screening.

Direction-Specific Changes in Trunk Muscle Synergies in Individuals With Extension-Related Low Back Pain.

Background Identifying altered trunk control is critical for treating extension-related low back pain (ERLBP), a common subgroup classified by clinical manifestations. The changed coordination of trunk muscles within this group during particular trunk tasks is still not clearly understood. Objectives The objective of this study is to investigate trunk muscle coordination during 11 trunk movement and stability tasks in individuals with ERLBP compared to non-low back pain (LBP) participants. Methods Thirteen individuals with ERLBP and non-LBP performed 11 trunk movement and stability tasks. We recorded the electromyographic activities of six back and abdominal muscles bilaterally. Trunk muscle coordination was assessed using the non-negative matrix factorization (NMF) method to identify trunk muscle synergies. Results The number of synergies in the ERLBP group during the cross-extension and backward bend tasks was significantly higher than in the non-LBP group (p<0.05). The cluster analysis identified the two trunk synergies for each task with strikingly similar muscle activation patterns between groups. In contrast, the ERLBP group exhibited additional trunk muscle synergies that were not identified in the non-LBP group. The number of synergies in the other tasks did not differ between groups (p>0.05). Conclusion Individuals with ERLBP presented directionally specific alterations in trunk muscle synergies that were considered as increased coactivations of multiple trunk muscles. These altered patterns may contribute to the excessive stabilization of and the high frequency of hyperextension in the spine associated with the development and persistence of ERLBP.

Extracted Spectral Signatures from the Water Column as a Tool for the Prediction of the Structure of a Marine Microbial Community

In this communication, we present an innovative approach leveraging advanced Machine Learning (ML) and Artificial Intelligence (AI) techniques, specifically the Non-Negative Matrix Factorization (NMF) method, to analyze downward and upward light spectra collected by Hyperspectral Ocean Color Radiometer (HyperOCR, HOCR) sensors in the water column. Our work focuses on the development of a robust and efficient tool for unraveling the structure and activities of natural microbial assemblages in the ocean. By applying the NMF method to HyperOCR data, we successfully extracted five spectral signatures, representing unique patterns in the data. These signatures were instrumental in predicting the abundances of various microbial components, including bacteria, heterotrophic nanoflagellates, and picoeukaryotes, showcasing the potential of ML and AI in advancing oceanographic studies. To validate these methods, the study area included a shallow coastal area under the influence of freshwater inflow and an open offshore area with a depth of 100 m. The study sites in coastal and offshore waters (Kaštela Bay and Stončica Vis, respectively) had significantly different hydrographic and microbiological characteristics. Kaštela Bay had lower temperatures and salinity than the site on Vis. We have demonstrated prediction of the structure of the microbial community through application of different AI and ML methods with specific HOCR sensors.

A Novel High-Dimensional Kernel Joint Non-Negative Matrix Factorization With Multimodal Information for Lung Cancer Study.

Judging and identifying biological activities and biomarkers inside tissues from imaging features of diseases is challenging, so correlating pathological image data with genes inside organisms is of great significance for clinical diagnosis. This paper proposes a high-dimensional kernel non-negative matrix factorization (NMF) method based on muti-modal information fusion. This algorithm can project RNA gene expression data and pathological images (WSI) into a common feature space, where the heterogeneous variables with the largest coefficient in the same projection direction form a co-module. In addition, the miRNA-mRNA and miRNA-lncRNA interaction networks in the ceRNA network are added to the algorithm as a priori information to explore the relationship between the images and the internal activities of the gene. Furthermore, the radial basis kernel function is used to calculate the feature proportion between different kinds of genes mapped in the high-dimensional feature space and projected into the common feature space to explore the gene interaction in the high-dimensional situation. The original feature matrix is regularized to improve biological correlation, and the feature factors are sparse by orthogonal constraints to reduce redundancy. Experimental results show that the proposed NMF method is better than the traditional NMF method in stability, decomposition accuracy, and robustness. Through data analysis applied to lung cancer, genes related to tissue morphology are found, such as COL7A1, CENPF and BIRC5. In addition, gene pairs with a correlation degree exceeding 0.8 are found, and potential biomarkers of significant correlation with survival are obtained such as CAPN8. It has potential application value for the clinical diagnosis of lung cancer.

LUSTC: A Novel Approach for Predicting Link States on Dynamic Attributed Networks

Predicting link states on dynamic attributed networks is one of the most fundamental problems for network analysis. To accurately predict the formations and disappearances of links, we need to utilize three types of information, that is, structural information, node content information, and temporal information, simultaneously. To this end, we propose a novel approach called LUSTC for predicting links and unlinks with structural information, temporal information, and node content information on dynamic attributed networks. For each snapshot, LUSTC first randomly chooses some sets of active nodes whose degree changes between adjacent snapshots and collects higher-order structural information using a random walk method based on the active nodes. Then, LUSTC generates two global matrices containing the temporal structural information and temporal node content information, respectively, as well as a sequence of auxiliary matrices for reconstructing the structural information and node content information of snapshots. These generated matrices are optimized using a nonnegative matrix factorization (NMF) method based on the structural information and node content information of snapshots. Finally, LUSTC estimates the similarity matrix for future snapshots to predict the links that are more likely to be formed or broken. The experimental results on various dynamic attributed networks demonstrate the effectiveness of LUSTC on the link prediction and unlink prediction tasks.

Prognostic model development and molecular subtypes identification in bladder urothelial cancer by oxidative stress signatures.

Mounting studies indicate that oxidative stress (OS) significantly contributes to tumor progression. Our study focused on bladder urothelial cancer (BLCA), an escalating malignancy worldwide that is growing rapidly. Our objective was to verify the predictive precision of genes associated with overall survival (OS) by constructing a model that forecasts outcomes for bladder cancer and evaluates the prognostic importance of these genetic markers. Transcriptomic data were obtained from TCGA-BLCA and GSE31684, which are components of the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), respectively. To delineate distinct molecular subtypes, we employed the non-negative matrix factorization (NMF)method. The significance of OS-associated genes in predicting outcomes was assessed using lasso regression, multivariate Cox analysis, and univariate Cox regression analysis. For external validation, we employed the GSE31684 dataset. CIBERSORT was utilized to examine the tumor immune microenvironment (TIME). A nomogram was created and verified using calibration and receiver operating characteristic (ROC) curves, which are based on risk signatures. We examined variations in clinical characteristics and tumor mutational burden (TMB) among groups classified as high-risk and low-risk. To evaluate the potential of immunotherapy, the immune phenomenon score (IPS) was computed based on the risk score. In the end, the pRRophetic algorithm was employed to forecast the IC50 values of chemotherapy medications. In our research, we examined the expression of 275 genes associated with OS in 19 healthy and 414 cancerous tissues of the bladder obtained from the TCGA database. As a result, a new risk signature was created that includes 4 genes associated with OS (RBPMS, CRYAB, P4HB, and PDGFRA). We found two separate groups, C1 and C2, that showed notable variations in immune cells and stromal score. According to the Kaplan-Meier analysis, patients classified as high-risk experienced a considerably reduced overall survival in comparison to those categorized as low-risk (P<0.001). The predictive capability of the model was indicated by the area under the curve (AUC) of the receiver operating characteristic (ROC) curve surpassing 0.6. Our model showed consistent distribution of samples from both the GEO database and TCGA data. Both the univariate and multivariate Cox regression analyses validated the importance of the risk score in relation to overall survival (P < 0.001). According to our research, patients with a lower risk profile may experience greater advantages from using a CTLA4 inhibitor, whereas patients with a higher risk profile demonstrated a higher level of responsiveness to Paclitaxel and Cisplatin. In addition, methotrexate exhibited a more positive outcome in patients with low risk compared to those with high risk. Our research introduces a novel model associated with OS gene signature in bladder cancer, which uncovers unique survival results. This model can assist in tailoring personalized treatment approaches and enhancing patient therapeutic effect in the management of bladder cancer.

Modified nonmonotonic projection Barzilai-Borwein gradient method for nonnegative matrix factorization

&lt;p&gt;In this paper, an active set recognition technique is suggested, and then a modified nonmonotonic line search rule is presented to enhance the efficiency of the nonmonotonic line search rule, in which we introduce a new parameter formula to attempt to control the nonmonotonic degree of the line search, and thus improve the chance of discovering the global minimum. By using a modified linear search and an active set recognition technique, a global convergence gradient solution for nonnegative matrix factorization (NMF) based on an alternating nonnegative least squares framework is proposed. We used a Barzilai-Borwein step size and greater step-size tactics to speed up the convergence. Finally, a large number of numerical experiments were carried out on synthetic and image datasets, and the results showed that our presented method was effective in calculating the speed and solution quality.&lt;/p&gt;

Exploring 2-D temporal patterns of individual mobility using non-negative matrix factorization

Understanding human mobility patterns is important for sustainable mobility development. One practical issue is about observing individual mobility regularity and variability over time and space. After the extraction of pre-treated travel attributes from a geolocation dataset, a further exploration of individual mobility profiles with multiple features is always required. The big challenge on this is to deal with a large number of mobility variables in order to find fine-grained temporal patterns. This paper aims to identify temporal mobility patterns with the two-dimensional (i.e., 2-D) trip attributes, i.e., departure time and distance. We use the three-month journey data from thousands of mobile phone users in the Paris region, France. For the pattern detection, the non-negative matrix factorization (NMF) method is suggested. According to the decompositions of our observation matrix, five types of temporal mobility patterns are obtained. The users’ mobility profiles represented by the impact ratios of these patterns are then interpreted. Beyond these, individual mobility variability is measured correspondingly by the day-to-day and week-to-week mobility divergences. Based on our findings, the impacts of the Covid-19 pandemic and the importance of time-to-time mobility variability are discussed with special concerns on mobility modeling.

Large-Scale Cortical Network Analysis and Classification of MI-BCI Tasks Based on Bayesian Nonnegative Matrix Factorization.

Motor imagery (MI) is a high-level cognitive process that has been widely applied to clinical rehabilitation and brain-computer interfaces (BCIs). However, the decoding of MI tasks still faces challenges, and the neural mechanisms underlying its application are unclear, which seriously hinders the development of MI-based clinical applications and BCIs. Here, we combined EEG source reconstruction and Bayesian nonnegative matrix factorization (NMF) methods to construct large-scale cortical networks of left-hand and right-hand MI tasks. Compared to right-hand MI, the results showed that the significantly increased functional network connectivities (FNCs) mainly located among the visual network (VN), sensorimotor network (SMN), right temporal network, right central executive network, and right parietal network in the left-hand MI at the β (13-30Hz) and all (8-30Hz) frequency bands. For the network properties analysis, we found that the clustering coefficient, global efficiency, and local efficiency were significantly increased and characteristic path length was significantly decreased in left-hand MI compared to right-hand MI at the β and all frequency bands. These network pattern differences indicated that the left-hand MI may need more modulation of multiple large-scale networks (i.e., VN and SMN) mainly located in the right hemisphere. Finally, based on the spatial pattern network of FNC and network properties, we propose a classification model. The proposed model achieves a top classification accuracy of 78.2% in cross-subject two-class MI-BCI tasks. Overall, our findings provide new insights into the neural mechanisms of MI and a potential network biomarker to identify MI-BCI tasks.

Multiomics analysis reveals metabolic subtypes and identifies diacylglycerol kinase α (DGKA) as a potential therapeutic target for intrahepatic cholangiocarcinoma.

Intrahepatic cholangiocarcinoma (iCCA) is a highly heterogeneous and lethal hepatobiliary tumor with few therapeutic strategies. The metabolic reprogramming of tumor cells plays an essential role in the development of tumors, while the metabolic molecular classification of iCCA is largely unknown. Here, we performed an integrated multiomics analysis and metabolic classification to depict differences in metabolic characteristics of iCCA patients, hoping to provide a novel perspective to understand and treat iCCA. We performed integrated multiomics analysis in 116 iCCA samples, including whole-exome sequencing, bulk RNA-sequencing and proteome analysis. Based on the non-negative matrix factorization method and the protein abundance of metabolic genes in human genome-scale metabolic models, the metabolic subtype of iCCA was determined. Survival and prognostic gene analyses were used to compare overall survival (OS) differences between metabolic subtypes. Cell proliferation analysis, 5-ethynyl-2'-deoxyuridine (EdU) assay, colony formation assay, RNA-sequencing and Western blotting were performed to investigate the molecular mechanisms of diacylglycerol kinase α (DGKA) in iCCA cells. Three metabolic subtypes (S1-S3) with subtype-specific biomarkers of iCCA were identified. These metabolic subtypes presented with distinct prognoses, metabolic features, immune microenvironments, and genetic alterations. The S2 subtype with the worst survival showed the activation of some special metabolic processes, immune-suppressed microenvironment and Kirsten rat sarcoma viral oncogene homolog (KRAS)/AT-rich interactive domain 1A (ARID1A) mutations. Among the S2 subtype-specific upregulated proteins, DGKA was further identified as a potential drug target for iCCA, which promoted cell proliferation by enhancing phosphatidic acid (PA) metabolism and activating mitogen-activated protein kinase (MAPK) signaling. Via multiomics analyses, we identified three metabolic subtypes of iCCA, revealing that the S2 subtype exhibited the poorest survival outcomes. We further identified DGKA as a potential target for the S2 subtype.

Few sex-specific effects of fatigue on muscle synergies in a repetitive pointing task

Previous studies have identified some sex differences in how individual muscles change their activation during repetitive multi-joint arm motion-induced fatigue. However, little is known about how indicators of multi-muscle coordination change with fatigue in males and females. Fifty-six (29 females) asymptomatic young adults performed a repetitive, forward-backward pointing task until scoring 8/10 on a Borg CR10 scale while surface electromyographic activity of upper trapezius, anterior deltoid, biceps brachii, and triceps brachii was recorded. Activation coefficient, synergy structure, and relative weight of each muscle within synergies were calculated using the non-negative matrix factorization method. Two muscle synergies were extracted from the fatiguing task. The synergy structures were mostly preserved after fatigue, while the activation coefficients were altered. A significant Sex × Fatigue interaction effect showed more use of the anterior deltoid in males especially before fatigue in synergy 1 during shoulder stabilization (p = 0.04). As for synergy 2, it was characterized by variations in the relative weight of biceps, which was higher by 16 % in females compared to males (p = 0.04), and increased with fatigue (p = 0.03) during the elbow flexion acceleration phase and the deceleration phase of the backward pointing movement. Findings suggest that both sexes adapted to fatigue similarly, using fixed synergy structures, with alterations in synergy activation patterns and relative weights of individual muscles. Results support previous findings of an important role for the biceps and anterior deltoid in explaining sex differences in patterns of repetitive motion-induced upper limb fatigue.

Establishment of novel ferroptosis-related prognostic subtypes correlating with immune dysfunction in prostate cancer patients

BackgroundWe aimed to identify two new prognostic subtypes and create a predictive index for prostate cancer (PCa) patients based on ferroptosis database. MethodsThe nonnegative matrix factorization approach was used to identify molecular subtypes. We investigate the differences between cluster 1 and cluster 2 in terms of clinical features, functional pathways, tumour stemness, tumour heterogeneity, gene mutation and tumour immune microenvironment score after identifying the two molecular subtypes. Colony formation assay and flow cytometry assay were performed. ResultsThe stratification of two clusters was closely connected to BCR-free survival using the nonnegative matrix factorization method, which was validated in the other three datasets. Furthermore, multivariate Cox regression analysis revealed that this classification was an independent risk factor for patients with PCa. Ribosome, aminoacyl tRNA production, oxidative phosphorylation, and Parkinson's disease-related pathways were shown to be highly enriched in cluster 1. In comparison to cluster 2, patients in cluster 1 exhibited significantly reduced CD4+ T cells, CD8+ T cells, neutrophils, dendritic cells and tumor immune microenvironment scores. Only HHLA2 was more abundant in cluster 1. Moreover, we found that P4HB downregulation could significantly inhibit the colony formation ability and contributed to cell apoptosis of C4-2B and DU145 cell lines. ConclusionsWe discovered two new prognostic subtypes associated with immunological dysfunction in PCa patients based on ferroptosis-related genes and found that P4HB downregulation could significantly inhibit the colony formation ability and contributed to cell apoptosis of PCa cell lines.