As a promising way for analyzing data, sparse modeling has achieved great success throughout science and engineering. It is well known that the sparsity/low-rank of a vector/matrix can be rationally ...measured by nonzero-entries-number (l 0 norm)/nonzerosingular-values-number (rank), respectively. However, data from real applications are often generated by the interaction of multiple factors, which obviously cannot be sufficiently represented by a vector/matrix, while a high order tensor is expected to provide more faithful representation to deliver the intrinsic structure underlying such data ensembles. Unlike the vector/matrix case, constructing a rational high order sparsity measure for tensor is a relatively harder task. To this aim, in this paper we propose a measure for tensor sparsity, called Kronecker-basis-representation based tensor sparsity measure (KBR briefly), which encodes both sparsity insights delivered by Tucker and CANDECOMP/PARAFAC (CP) low-rank decompositions for a general tensor. Then we study the KBR regularization minimization (KBRM) problem, and design an effective ADMM algorithm for solving it, where each involved parameter can be updated with closed-form equations. Such an efficient solver makes it possible to extend KBR to various tasks like tensor completion and tensor robust principal component analysis. A series of experiments, including multispectral image (MSI) denoising, MSI completion and background subtraction, substantiate the superiority of the proposed methods beyond state-of-the-arts.
Seed plants have evolved to maintain the dormancy of freshly matured seeds until the appropriate time for germination. Seed dormancy and germination are distinct physiological processes, and the ...transition from dormancy to germination is not only a critical developmental step in the life cycle of plants but is also impor- tant for agricultural production. These processes are precisely regulated by diverse endogenous hormones and environmental cues. Although ABA （abscisic acid） and GAs （gibberellins） are known to be the primary phytohormones that antagonistically regulate seed dormancy, recent findings demonstrate that another phytohormone, auxin, is also critical for inducing and maintaining seed dormancy, and therefore might act as a key protector of seed dormancy. In this review, we summarize our current understanding of the sophisticated molecular networks involving the critical roles of phytohormones in regulating seed dormancy and germination, in which AP2-domain-containing transcription factors play key roles. We also discuss the interactions （crosstalk） of diverse hormonal signals in seed dormancy and germination, focusing on the ABA/GA balance that constitutes the central node.
This study aimed to find potential diagnostic markers for osteoarthritis (OA) and analyze the role of immune cells infiltration in this pathology. We used OA datasets from the Gene Expression Omnibus ...database. First, R software was used to identify differentially expressed genes (DEGs) and perform functional correlation analysis. Then least absolute shrinkage and selection operator (LASSO) logistic regression and support vector machine-recursive feature elimination algorithms were used to screen and verify the diagnostic markers of OA. Finally, CIBERSORT was used to evaluate the infiltration of immune cells in OA tissues, and the correlation between diagnostic markers and infiltrating immune cells was analyzed. A total of 458 DEGs were screened in this study. GRB10 and E2F3 (AUC = 0.962) were identified as diagnostic markers of OA. Immune cell infiltration analysis found that resting mast cells, T regulatory cells, CD4 memory resting T cells, activated NK cells, and eosinophils may be involved in the OA process. In addition, GRB10 was correlated with NK resting cells, naive CD4 + T cells, and M1 macrophages, while E2F3 was correlated with resting mast cells. In conclusion, GRB10 and E2F3 can be used as diagnostic markers of osteoarthritis, and immune cell infiltration plays an important role in the occurrence and progression of OA.
Cancer stem cells (CSCs) proactively remodel their microenvironment to maintain a supportive niche. Viewed through the lens of an ecosystem, numerous tumor components have multi-directional ...interactions involving CSCs, supporting the complexity of tumors to maintain growth in a dynamic host. In this Perspective, we discuss how CSCs are active architects of their microenvironment and drive interactions with other tumor components, such as immune cells, cancer-associated fibroblasts and differentiated cells, blood vessels, and other extracellular cues to engineer a sustainable niche. We also highlight considerations for modeling this dynamic tumor ecology and discuss potential therapeutic strategies for targeting these multifaceted interactions.
In this Perspective, Prager et al. discuss how cancer stem cells are active architects of their microenvironment and drive interactions with a myriad of other tumor components to engineer a sustainable niche. They also highlight considerations for modeling this dynamic tumor ecology and discuss potential niche-targeting therapeutic strategies.
Osteoarthritis (OA) is a chronic degenerative disease of the bone and joints. Immune-related genes and immune cell infiltration are important in OA development. We analyzed immune-related genes and ...immune infiltrates to identify OA diagnostic markers. The datasets GSE51588, GSE55235, GSE55457, GSE82107, and GSE114007 were downloaded from the Gene Expression Omnibus database. First, R software was used to identify differentially expressed genes (DEGs) and differentially expressed immune-related genes (DEIRGs), and functional correlation analysis was conducted. Second, CIBERSORT was used to evaluate infiltration of immune cells in OA tissue. Finally, the least absolute shrinkage and selection operator logistic regression algorithm and support vector machine-recurrent feature elimination algorithm were used to screen and verify diagnostic markers of OA. A total of 711 DEGs and 270 DEIRGs were identified in this study. Functional enrichment analysis showed that the DEGs and DEIRGs are closely related to cellular calcium ion homeostasis, ion channel complexes, chemokine signaling pathways, and JAK-STAT signaling pathways. Differential analysis of immune cell infiltration showed that M1 macrophage infiltration was increased but that mast cell and neutrophil infiltration were decreased in OA samples. The machine learning algorithm cross-identified 15 biomarkers (BTC, PSMD8, TLR3, IL7, APOD, CIITA, IFIH1, CDC42, FGF9, TNFAIP3, CX3CR1, ERAP2, SEMA3D, MPO, and plasma cells). According to pass validation, all 15 biomarkers had high diagnostic efficacy (AUC > 0.7), and the diagnostic efficiency was higher when the 15 biomarkers were fitted into one variable (AUC = 0.758). We developed 15 biomarkers for OA diagnosis. The findings provide a new understanding of the molecular mechanism of OA from the perspective of immunology.
As a convex relaxation of the rank minimization model, the nuclear norm minimization (NNM) problem has been attracting significant research interest in recent years. The standard NNM regularizes each ...singular value equally, composing an easily calculated convex norm. However, this restricts its capability and flexibility in dealing with many practical problems, where the singular values have clear physical meanings and should be treated differently. In this paper we study the weighted nuclear norm minimization (WNNM) problem, which adaptively assigns weights on different singular values. As the key step of solving general WNNM models, the theoretical properties of the weighted nuclear norm proximal (WNNP) operator are investigated. Albeit nonconvex, we prove that WNNP is equivalent to a standard quadratic programming problem with linear constrains, which facilitates solving the original problem with off-the-shelf convex optimization solvers. In particular, when the weights are sorted in a non-descending order, its optimal solution can be easily obtained in closed-form. With WNNP, the solving strategies for multiple extensions of WNNM, including robust PCA and matrix completion, can be readily constructed under the alternating direction method of multipliers paradigm. Furthermore, inspired by the reweighted sparse coding scheme, we present an automatic weight setting method, which greatly facilitates the practical implementation of WNNM. The proposed WNNM methods achieve state-of-the-art performance in typical low level vision tasks, including image denoising, background subtraction and image inpainting.
Background:
Knee osteoarthritis (KOA) is one of the most common chronic musculoskeletal disorders worldwide, for which exosomes derived from stem cells may provide an effective treatment.
Purpose:
To ...assess the effect of exosomes derived from human urine–derived stem cells (hUSCs) overexpressing miR-140-5p (miR means microRNA) on KOA in an in vitro interleukin 1β (IL-1β)–induced osteoarthritis (OA) model and an in vivo rat KOA model.
Study Design:
Controlled laboratory study.
Methods:
Exosomes derived from hUSCs (hUSC-Exos) were isolated and validated. The hUSCs were transfected with miR-140s using lentivirus, and exosomes secreted from such cells (hUSC-140-Exos) were collected. The roles of hUSC-Exos and hUSC-140-Exos in protecting chondrocytes against IL-1β treatment were compared by analyzing the proliferation, migration, apoptosis, and secretion of extracellular matrix (ECM) in chondrocytes. After vascular endothelial growth factor A (VEGFA) was identified as a target of miR-140, the mechanism by which VEGFA can mediate the beneficial effect of miR-140 on OA was investigated using small interfering RNA transfection or chemical drugs. The expression of VEGFA in cartilage and synovial fluid from patients with KOA was measured and compared with that of healthy controls. Surgery for anterior cruciate ligament transection and destabilization of the medial meniscus were performed on the knee joints of Sprague-Dawley rats to establish an animal model of OA, and intra-articular (IA) injection of hUSC-Exos or hUSC-140-Exos was conducted at 4 to 8 weeks after the surgery. Cartilage regeneration and subchondral bone remodeling were evaluated through histological staining and micro–computed tomography analysis.
Results:
Proliferation and migration ability were enhanced and apoptosis was inhibited in chondrocytes treated with IL-1β via hUSC-Exos, with the side effect of decreased ECM secretion. hUSC-140-Exos not only retained the advantages of hUSC-Exos but also increased the secretion of ECM by targeting VEGFA, including collagen II and aggrecan. Increased expression of VEGFA during the progression of KOA was also confirmed in cartilage and synovial fluid samples obtained from patients with OA. In the rat OA model, IA injection of hUSC-140-Exos enhanced cartilage regeneration and subchondral bone remodeling.
Conclusion:
Our results demonstrated the superiority of hUSC-Exos overexpressing miR-140-5p for treating OA compared with the hUSC-Exos. The effect of hUSC-140-Exos for suppressing the progression of KOA is in part mediated by VEGFA.
Clinical Relevance:
Exosomes derived from stem cells may provide a promising treatment for KOA, and our study can advance the related basic research.
Snoring is common in children and is associated with many adverse consequences. One must study the relationships between pharyngeal morphology and snoring physics to understand snoring progression. ...Although some model studies have provided fluid–structure interaction dynamic descriptions for the correlation between airway size and snoring physics, the descriptions still need to be further investigated in patient-specific airway models. Fluid-structure interaction studies using patient-specific airway structures complement the above model studies. Based on reported cephalometric measurement methods, this study quantified and preset the size of the palatopharynx airway in a patient-specific airway and investigated how the palatopharynx size affects the pharyngeal airflow fluctuation, soft palate vibration, and glossopharynx vibration with the help of a verified FSI method. The results showed that the stenosis anterior airway of the soft palate increased airway resistance and airway resistance fluctuations, which can lead to increased sleep effort and frequent snoring. Widening of the anterior airway can reduce airflow resistance and avoid obstructing the anterior airway by the soft palate vibration. The pharyngeal airflow resistance, mouth inflow proportion, and soft palate apex displacement have components at the same frequencies in all airway models, and the glossopharynx vibration and instantaneous inflow rate have components at the same frequencies, too. The mechanism of this same frequency fluctuation phenomenon can be explained by the fluid–structure interaction dynamics of an ideal coupled model consisting of a flexible plate model and a collapsible tube model. The results of this study demonstrate the potential of FSI in studying snoring physics and clarify to some degree the mechanism of airway morphology affecting airway vibration physics.
Cold stress is a major environmental factor that limits plant growth and development. The C-repeat-binding factor (CBF)-dependent cold signaling pathway is extensively studied in Arabidopsis; ...however, the specific protein kinases involved in this pathway remain elusive. Here we report that OST1 (OPEN STOMATA 1), a well-known Ser/Thr protein kinase in ABA signaling, acts upstream of CBFs to positively regulate freezing tolerance. The ost1 mutants show freezing hypersensitivity, whereas transgenic plants overexpressing OST1 exhibit enhanced freezing tolerance. The OST1 kinase is activated by cold stress. Moreover, OST1 interacts with both the transcription factor ICE1 and the E3 ligase HOS1 in the CBF pathway. Cold-activated OST1 phosphorylates ICE1 and enhances its stability and transcriptional activity. Meanwhile, OST1 interferes with the interaction between HOS1 and ICE1, thus suppressing HOS1-mediated ICE1 degradation under cold stress. Our results thus uncover the unexpected roles of OST1 in modulating CBF-dependent cold signaling in Arabidopsis.
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•OST1 is a positive regulator in CBF-dependent cold signaling•OST1 interacts with and phosphorylates the ICE1 protein•OST1 interferes with the interaction between ICE1 and HOS1•OST1 suppresses HOS1-mediated ICE1 degradation
The ICE1 transcription factor integrates different signals to regulate cold tolerance in Arabidopsis. Ding et al. demonstrate that the protein kinase OST1, a key component in ABA signaling, is also activated by cold stress. In response to cold, OST1 phosphorylates and stabilizes ICE1, promoting the expression of downstream cold-tolerance genes.
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