Efficient Low Rank Tensor Ring Completion Wenqi Wang; Aggarwal, Vaneet; Aeron, Shuchin
2017 IEEE International Conference on Computer Vision (ICCV),
2017-Oct.
Conference Proceeding
Open access
Using the matrix product state (MPS) representation of the recently proposed tensor ring (TR) decompositions, in this paper we propose a TR completion algorithm, which is an alternating minimization ...algorithm that alternates over the factors in the MPS representation. This development is motivated in part by the success of matrix completion algorithms that alternate over the (low-rank) factors. We propose a novel initialization method and analyze the computational complexity of the TR completion algorithm. The numerical comparison between the TR completion algorithm and the existing algorithms that employ a low rank tensor train (TT) approximation for data completion shows that our method outperforms the existing ones for a variety of real computer vision settings, and thus demonstrates the improved expressive power of tensor ring as compared to tensor train.
Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. Accumulating investigations have identified the aberrant expression of miRNAs (microRNAs) in UM, such as miR‐181, ...miR‐20a, miR‐144, miR‐146a. The purpose of this study is to investigate the biological function of miR‐224‐5p in UM. The expression of miR‐224‐5p, PIK3R3, and AKT3 in 30 tumor tissues and paired adjacent noncancerous tissues were analyzed using Western blot analysis and quantitative real‐time polymerase chain reaction (qRT‐PCR) assays. Cell proliferation assay, transwell assay, and wound healing assay were used to measure the effects of miR‐224‐5p on the motility of UM in vitro. Western blot analysis and luciferase assays were used to detect the expression of PIK3R3 and AKT3 as miR‐224‐5p downstream targets. The results of Western blot analysis and qRT‐PCR assays indicated that the expression of miR‐224‐5p was lower in UM tissues compared to normal tissue, while the expression of PIK3R3 and AKT3 were simultaneously increased. Upregulation of miR‐224‐5p significantly inhibited capacities of proliferation, invasion, and migration of OCM‐1A cells and decreased expression of PIK3R3 and AKT3. Luciferase assay demonstrated PIK3R3 and AKT3 as downstream targets of miR‐224‐5p. Moreover, upregulating PIK3R3 and AKT3 restrained miR‐224‐5p‐induced inhibition of the motility of OCM‐1A cells. Thus, our study proved that miR‐224‐5p was involved in proliferation, invasion, and migration of UM cells via regulation the expression of PIK3R3 and AKT3. And the results also established a miR‐224‐5p/PIK3R3/PI3K/AKT axis in the regulation of UM progression, providing an experimental basis for further exploring the miR‐224‐5p as a therapeutic and diagnosis target for patients with UM.
1. Upregulation of miR‐224‐5p significantly inhibited capacities of proliferation, invasion, and migration of OCM‐1A cells. 2. Upregulation of miR‐224‐5p decreased expression of PIK3R3 and AKT3. 3. Established a miR‐224‐5p/PIK3R3/PI3K/AKT axis in the regulation of uveal melanoma progression.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Under the backdrop of the pandemic of COVID-19, people have different predictions of the future condition and understanding of the current status. In this paper, findings from an online experiment ...show how overconfidence can play an important role in terms of decision-making of the pandemic: among the main findings from data analysis, self overconfidence significantly increases donations. Also, with the growth of age, people tend to donate more while as they advance the education level, people prefer to donate less. The results of this research can further inform policymakers on individuals’ behaviors during a negative economic shock.
BRCA1 promotes homologous recombination repair and antagonizes 53BP1-dependent nonhomologous end joining (NHEJ) pathway. However, the molecular basis of the competition between BRCA1 and 53BP1 ...pathways remains elusive. Here we report that RIF1 protein translocates to damage sites via ATM-dependent 53BP1 phosphorylation. Strikingly, loss of RIF1 rescues initial DNA end resection and checkpoint activation in BRCA1-depleted cells. Interestingly RIF1 accumulation at damage sites is antagonized by BRCA1 in S and G2 phases. Conversely, the translocation of BRCA1 to damage sites is inhibited by RIF1 in G1 phase. However, loss of RIF1 differs from that of 53BP1 deficiency, as it cannot fully rescue RAD51 foci formation, homologous recombination defect, and radio-hypersensitivity in BRCA1-deficient cells. This is likely because RIF1, but not 53BP1, also regulates the foci formation and chromatin loading of BLM (the Bloom syndrome helicase). Thus, RIF1 not only acts downstream of 53BP1 and counteracts BRCA1-mediated end resection but also has a secondary role in promoting BLM function in DNA repair.
Background: 53BP1 counteracts BRCA1 in DNA repair.
Results: RIF1 acts downstream of 53BP1 and counteracts BRCA1 in DNA end resection. It also has a 53BP1-independent role in regulating BLM chromatin association.
Conclusion: RIF1 is the major downstream effector of 53BP1.
Significance: These results reveal that RIF1 antagonizes BRCA1, functions in DNA end protection, and prevents homologous recombination repair.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Proteins are the key players in many cellular processes. Their composition, trafficking, and interactions underlie the dynamic processes of life. Furthermore, diseases are frequently accompanied by ...malfunction of proteins at multiple levels. Understanding how biological processes are regulated at the protein level is critically important to understanding the molecular basis for diseases and often shed light on disease prevention, diagnosis, and treatment. With rapid advances in mass spectrometry (MS) instruments and experimental methodologies, MS-based proteomics has become a reliable and essential tool for elucidating biological processes at the protein level. Over the past decade, we have witnessed great expansion of knowledge of human diseases with the application of MS-based proteomic technologies, which has led to many exciting discoveries. Herein we review the recent progress in MS-based proteomics in biomedical research, including that in establishing disease-related proteomes and interactomes. We also discuss how this progress will benefit biomedical research and clinical diagnosis and treatment of disease.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Growing evidence has suggested that immune-related genes play crucial roles in the development and progression of hepatocellular carcinoma (HCC). Nevertheless, the utility of immune-related genes for ...evaluating the prognosis of HCC patients are still lacking. The study aimed to explore gene signatures and prognostic values of immune-related genes in HCC.
We comprehensively integrated gene expression data acquired from 374 HCC and 50 normal tissues in The Cancer Genome Atlas (TCGA). Differentially expressed genes (DEGs) analysis and univariate Cox regression analysis were performed to identify DEGs that related to overall survival. An immune prognostic model was constructed using the Lasso and multivariate Cox regression analyses. Furthermore, Cox regression analysis was applied to identify independent prognostic factors in HCC. The correlation analysis between immune-related signature and immune cells infiltration were also investigated. Finally, the signature was validated in an external independent dataset.
A total of 329 differentially expressed immune-related genes were detected. 64 immune-related genes were identified to be markedly related to overall survival in HCC patients using univariate Cox regression analysis. Then we established a TF-mediated network for exploring the regulatory mechanisms of these genes. Lasso and multivariate Cox regression analyses were applied to construct the immune-based prognostic model, which consisted of nine immune-related genes. Further analysis indicated that this immune-related prognostic model could be an independent prognostic indicator after adjusting to other clinical factors. The relationships between the risk score model and immune cell infiltration suggested that the nine-gene signature could reflect the status of tumor immune microenvironment. The prognostic value of this nine-gene prognostic model was further successfully validated in an independent database.
Together, our study screened potential prognostic immune-related genes and established a novel immune-based prognostic model of HCC, which not only provides new potential prognostic biomarkers and therapeutic targets, but also deepens our understanding of tumor immune microenvironment status and lays a theoretical foundation for immunotherapy.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Degradable vinyl polymers by radical ring‐opening polymerization are promising solutions to the challenges caused by non‐degradable vinyl plastics. However, achieving even distributions of labile ...functional groups in the backbone of degradable vinyl polymers remains challenging. Herein, we report a photocatalytic approach to degradable vinyl random copolymers via radical ring‐opening cascade copolymerization (rROCCP). The rROCCP of macrocyclic allylic sulfones and acrylates or acrylamides mediated by visible light at ambient temperature achieved near‐unity comonomer reactivity ratios over the entire range of the feed compositions. Experimental and computational evidence revealed an unusual reversible inhibition of chain propagation by in situ generated sulfur dioxide (SO2), which was successfully overcome by reducing the solubility of SO2. This study provides a powerful approach to degradable vinyl random copolymers with comparable material properties to non‐degradable vinyl polymers.
A general approach to degradable vinyl random copolymers via photocontrolled radical ring‐opening cascade copolymerization (rROCCP) is developed. A variety of acrylates or acrylamides can be copolymerized with the macrocyclic allylic sulfone with near‐unity comonomer reactivity ratios at all feed compositions. The unusual reversible inhibition of chain propagation by sulfur dioxide in rROCCP was resolved by reducing the solubility of sulfur dioxide.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Long non-coding RNAs (lncRNAs) have emerged as critical regulators in various cellular processes. However, the potential involvement of lncRNAs in kinase signalling remains largely unknown. ...AMP-activated protein kinase (AMPK) acts as a critical sensor of cellular energy status. Here we show that the lncRNA NBR2 (neighbour of BRCA1 gene 2) is induced by the LKB1-AMPK pathway under energy stress. On energy stress, NBR2 in turn interacts with AMPK and promotes AMPK kinase activity, thus forming a feed-forward loop to potentiate AMPK activation during energy stress. Depletion of NBR2 attenuates energy-stress-induced AMPK activation, resulting in unchecked cell cycling, altered apoptosis/autophagy response, and increased tumour development in vivo. NBR2 is downregulated and its low expression correlates with poor clinical outcomes in some human cancers. Together, the results of our study uncover a mechanism coupling lncRNAs with metabolic stress response, and provides a broad framework to understand further the regulation of kinase signalling by lncRNAs.
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IJS, NUK, SBMB, UL, UM, UPUK
The Hippo pathway was discovered as a conserved tumour suppressor pathway restricting cell proliferation and apoptosis. However, the upstream signals that regulate the Hippo pathway in the context of ...organ size control and cancer prevention are largely unknown. Here, we report that glucose, the ubiquitous energy source used for ATP generation, regulates the Hippo pathway downstream effector YAP. We show that both the Hippo pathway and AMP-activated protein kinase (AMPK) were activated during glucose starvation, resulting in phosphorylation of YAP and contributing to its inactivation. We also identified glucose-transporter 3 (GLUT3) as a YAP-regulated gene involved in glucose metabolism. Together, these results demonstrate that glucose-mediated energy homeostasis is an upstream event involved in regulation of the Hippo pathway and, potentially, an oncogenic function of YAP in promoting glycolysis, thereby providing an exciting link between glucose metabolism and the Hippo pathway in tissue maintenance and cancer prevention.
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DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SBMB, UILJ, UKNU, UL, UM, UPUK
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