Nonnegative matrix factorization (NMF) can be formulated as a minimization problem with bound constraints. Although bound-constrained optimization has been studied extensively in both theory and ...practice, so far no study has formally applied its techniques to NMF. In this letter, we propose two projected gradient methods for NMF, both of which exhibit strong optimization properties. We discuss efficient implementations and demonstrate that one of the proposed methods converges faster than the popular multiplicative update approach. A simple Matlab code is also provided.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Head and neck cancers, which affect 650,000 people and cause 350,000 deaths per year, is the sixth leading cancer by cancer incidence and eighth by cancer-related death worldwide. Oral cancer is the ...most common type of head and neck cancer. More than 90% of oral cancers are oral and oropharyngeal squamous cell carcinoma (OSCC). The overall five-year survival rate of OSCC patients is approximately 63%, which is due to the low response rate to current therapeutic drugs. In this review we discuss the possibility of using caffeic acid phenethyl ester (CAPE) as an alternative treatment for oral cancer. CAPE is a strong antioxidant extracted from honeybee hive propolis. Recent studies indicate that CAPE treatment can effectively suppress the proliferation, survival, and metastasis of oral cancer cells. CAPE treatment inhibits Akt signaling, cell cycle regulatory proteins, NF-κB function, as well as activity of matrix metalloproteinase (MMPs), epidermal growth factor receptor (EGFR), and Cyclooxygenase-2 (COX-2). Therefore, CAPE treatment induces cell cycle arrest and apoptosis in oral cancer cells. According to the evidence that aberrations in the EGFR/phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) signaling, NF-κB function, COX-2 activity, and MMPs activity are frequently found in oral cancers, and that the phosphorylation of Akt, EGFR, and COX-2 correlates to oral cancer patient survival and clinical progression, we believe that CAPE treatment will be useful for treatment of advanced oral cancer patients.
Transposable elements represent nearly half of mammalian genomes and are generally described as parasites, or “junk DNA.” The LINE1 retrotransposon is the most abundant class and is thought to be ...deleterious for cells, yet it is paradoxically highly expressed during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem cells (ESCs) and pre-implantation embryos. In ESCs, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a transcriptional program specific to the 2-cell embryo. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, promoting rRNA synthesis and ESC self-renewal. In embryos, LINE1 RNA is required for Dux silencing, synthesis of rRNA, and exit from the 2-cell stage. The results reveal an essential partnership between LINE1 RNA, Nucleolin, Kap1, and peri-nucleolar chromatin in the regulation of transcription, developmental potency, and ESC self-renewal.
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•LINE1 RNA is abundant and nuclear in mouse ESCs and pre-implantation embryos•LINE1 knockdown inhibits ESC self-renewal and induces transition to a 2C state•LINE1 RNA recruits Nucleolin/Kap1 to repress Dux and activate rRNA synthesis•In embryos, LINE1 inhibition causes persistence of the 2C program and impairs ZGA
RNA transcribed from LINE1 elements acts as a nuclear scaffold to direct gene expression programs essential for ESC self-renewal and pre-implantation embryo development.
LIBSVM Chang, Chih-Chung; Lin, Chih-Jen
ACM transactions on intelligent systems and technology,
04/2011, Letnik:
2, Številka:
3
Journal Article
Recenzirano
LIBSVM is a library for Support Vector Machines (SVMs). We have been actively developing this package since the year 2000. The goal is to help users to easily apply SVM to their applications. LIBSVM ...has gained wide popularity in machine learning and many other areas. In this article, we present all implementation details of LIBSVM. Issues such as solving SVM optimization problems theoretical convergence multiclass classification probability estimates and parameter selection are discussed in detail.
Truncated Newton (TN) methods have been a useful technique for large-scale optimization. Instead of obtaining the full Newton direction, a truncated method approximately solves the Newton equation ...with an inner conjugate gradient (CG) procedure (TNCG for the whole method). These methods have been employed to efficiently solve linear classification problems. However, even in this deeply studied field, various theoretical and numerical aspects were not completely explored. The first contribution of this work is to comprehensively study the global and local convergence when TNCG is applied to linear classification. Because of the lack of twice differentiability under some losses, many past works cannot be applied here. We prove various missing pieces of theory from scratch and clarify many proper references. The second contribution is to study the termination of the CG method. For the first time when TNCG is applied to linear classification, we show that the inner stopping condition strongly affects the convergence speed. We propose using a quadratic stopping criterion to achieve both robustness and efficiency. The third contribution is that of combining the study on inner stopping criteria with that of preconditioning. We discuss how convergence theory is affected by preconditioning and finally propose an effective preconditioned TNCG.
Indoxyl sulfate (IS) and p-cresyl sulfate (PCS) are protein-bound uremic toxins that increase in the sera of patients with chronic kidney disease (CKD), and are not effectively removed by dialysis. ...The purpose of this meta-analysis was to investigate the relationships of PCS and IS with cardiovascular events and all-cause mortality in patients with CKD stage 3 and above.
Medline, Cochrane, and EMBASE databases were searched until January 1, 2014 with combinations of the following keywords: chronic renal failure, end-stage kidney disease, uremic toxin, uremic retention, indoxyl sulfate, p-cresyl sulfate. Inclusion criteria were: 1) Patients with stage 1 to 5 CKD; 2) Prospective study; 3) Randomized controlled trial; 4) English language publication. The associations between serum levels of PCS and IS and the risks of all-cause mortality and cardiovascular events were the primary outcome measures. Of 155 articles initially identified, 10 prospective and one cross-sectional study with a total 1,572 patients were included. Free PCS was significantly associated with all-cause mortality among patients with chronic renal failure (pooled OR = 1.16, 95% CI = 1.03 to 1.30, P = 0.013). An elevated free IS level was also significantly associated with increased risk of all-cause mortality (pooled OR = 1.10, 95% CI = 1.03 to 1.17, P = 0.003). An elevated free PCS level was significantly associated with an increased risk of cardiovascular events among patients with chronic renal failure (pooled OR = 1.28, 95% CI = 1.10 to 1.50, P = 0.002), while free IS was not significantly associated with risk of cardiovascular events (pooled OR = 1.05, 95% CI = 0.98 to 1.13, P = 0.196).
Elevated levels of PCS and IS are associated with increased mortality in patients with CKD, while PCS, but not IS, is associated with an increased risk of cardiovascular events.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
With the growing air transport demand and concerns about its environmental impacts, alternative jet fuels derived from non-conventional sources have become an important strategy for achieving a ...sustainable and green aviation. In the past 10 years, governments around the world along with aviation industry have invested significant efforts into exploring all sorts of alternative jet fuels that can be used to power aircraft engines. Among all the alternative jet fuels explored, the aviation sector has agreed that hydrocarbon-based ‘drop-in’ replacement fuels, which are fully interchangeable and compatible with current conventional jet fuels, would be the best choice in the near future, as they can be used without any modifications to today׳s aircraft or fuel infrastructure. This paper reviews the current state of development of ‘drop-in’ alternative jet fuels including various Fisher–Tropsch synthetic jet fuels and bio-jet fuels. Recent advances in research activities on alternative jet fuels, including fuel property evaluations, combustor component tests, engine tests, and flight tests, are highlighted. Furthermore, basic research needs for understanding the combustion characteristics of alternative jet fuels are underlined and discussed by reviewing recent fundamental combustion studies on ignition, extinction, flame propagation, emissions, and species evolution of various conventional and alternative jet fuels. Recognizing that the use of ‘simpler’ surrogate fuels to emulate the behavior of ‘complex’ alternative jet fuels is of fundamental and practical importance for the development of physics-based models to enable quantitative emissions and performance predictions using combustion modeling, recent studies on surrogate formulation for alternative jet fuels are also reviewed and discussed. This review concludes with a brief discussion of future research directions.
With-no-lysine (WNK) kinases regulate renal sodium-chloride cotransporter (NCC) to maintain body sodium and potassium homeostasis. Gain-of-function mutations of WNK1 and WNK4 in humans lead to a ...Mendelian hypertensive and hyperkalemic disease pseudohypoaldosteronism type II (PHAII). X-ray crystal structure and in vitro studies reveal chloride ion (Cl⁻) binds to a hydrophobic pocket within the kinase domain of WNKs to inhibit its activity. The mechanism is thought to be important for physiological regulation of NCC by extracellular potassium. To test the hypothesis that WNK4 senses the intracellular concentration of Cl⁻ physiologically, we generated knockin mice carrying Cl⁻-insensitive mutant WNK4. These mice displayed hypertension, hyperkalemia, hyperactive NCC, and other features fully recapitulating human and mouse models of PHAII caused by gain-of-function WNK4. Lowering plasma potassium levels by dietary potassium restriction increased NCC activity in wild-type, but not in knockin, mice. NCC activity in knockin mice can be further enhanced by the administration of norepinephrine, a known activator of NCC. Raising plasma potassium by oral gavage of potassium inactivated NCC within 1 hour in wild-type mice, but had no effect in knockin mice. The results provide compelling support for the notion that WNK4 is a bona fide physiological intracellular Cl⁻ sensor and that Cl⁻ regulation of WNK4 underlies the mechanism of regulation of NCC by extracellular potassium.
One-Class SVM Probabilistic Outputs Que, Zhongyi; Lin, Chih-Jen
IEEE transaction on neural networks and learning systems,
05/2024, Letnik:
PP
Journal Article
One-class support vector machine (SVM) is an extension of SVM to handle unlabeled data. As a mature technique for outlier detection, one-class SVM has been widely used in many applications. However, ...similar to standard two-class SVM, the design of one-class SVM does not give probabilistic outputs. For two-class SVM, some methods have been proposed to effectively obtain probabilistic outputs, but due to the difficulty of no-label information, less attention has been paid to one-class SVM. Our aim in this work is to propose some practically viable techniques to generate probabilistic outputs for one-class SVM. We investigate existing methods for two-class SVM and explain why they may not be suitable for one-class SVM. Due to the lack of label information, we think a feasible setting is to have probabilities mimic to the decision values of training data. Based on this principle, we propose several new methods. Detailed experiments on both artificial and real-world data demonstrate the effectiveness of the proposed methods.
Given the enormous growth in user-generated videos, it is becoming increasingly important to be able to navigate them efficiently. As these videos are generally of poor quality, summarization methods ...designed for well-produced videos do not generalize to them. To address this challenge, we propose to use web-images as a prior to facilitate summarization of user-generated videos. Our main intuition is that people tend to take pictures of objects to capture them in a maximally informative way. Such images could therefore be used as prior information to summarize videos containing a similar set of objects. In this work, we apply our novel insight to develop a summarization algorithm that uses the web-image based prior information in an unsupervised manner. Moreover, to automatically evaluate summarization algorithms on a large scale, we propose a framework that relies on multiple summaries obtained through crowdsourcing. We demonstrate the effectiveness of our evaluation framework by comparing its performance to that of multiple human evaluators. Finally, we present results for our framework tested on hundreds of user-generated videos.
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