ELRUNA

Networks model a variety of complex phenomena across different domains. In many applications, one of the most essential tasks is to align two or more networks to infer the similarities between cross-network vertices and to discover potential node-level correspondence. In this article, we propose ELRUNA ( el imination ru le-based n etwork a lignment), a novel network alignment algorithm that relies exclusively on the underlying graph structure. Under the guidance of the elimination rules that we defined, ELRUNA computes the similarity between a pair of cross-network vertices iteratively by accumulating the similarities between their selected neighbors. The resulting cross-network similarity matrix is then used to infer a permutation matrix that encodes the final alignment of cross-network vertices. In addition to the novel alignment algorithm, we improve the performance of local search , a commonly used postprocessing step for solving the network alignment problem, by introducing a novel selection method RAWSEM ( ra ndom- w alk-based se lection m ethod) based on the propagation of vertices’ mismatching across the networks. The key idea is to pass on the initial levels of mismatching of vertices throughout the entire network in a random-walk fashion. Through extensive numerical experiments on real networks, we demonstrate that ELRUNA significantly outperforms the state-of-the-art alignment methods in terms of alignment accuracy under lower or comparable running time. Moreover, ELRUNA is robust to network perturbations such that it can maintain a close-to-optimal objective value under a high level of noise added to the original networks. Finally, the proposed RAWSEM can further improve the alignment quality with a smaller number of iterations compared with the naive local search method. Reproducibility : The source code and data are available at https://tinyurl.com/uwn35an.

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Delayed improvement local search

Journal of Heuristics ◽

10.1007/s10732-021-09479-9 ◽

2021 ◽

Author(s):

Heber F. Amaral ◽

Sebastián Urrutia ◽

Lars M. Hvattum

Keyword(s):

Local Search ◽

Heuristic Algorithms ◽

Travelling Salesman Problem ◽

Computation Time ◽

The Novel ◽

Local Optima ◽

New Strategy ◽

Max Cut Problem ◽

Novel Method ◽

FGF16 regulated by miR-520b enhances the cell proliferation of lung cancer

Open Medicine ◽

10.1515/med-2021-0232 ◽

2021 ◽

Vol 16 (1) ◽

pp. 419-427

Author(s):

Wenfeng He ◽

Xia Liu ◽

Zhijie Luo ◽

Longmei Li ◽

Xisheng Fang

Keyword(s):

Lung Cancer ◽

Cancer Progression ◽

Untranslated Region ◽

Target Gene ◽

Regulatory Mechanism ◽

The Novel ◽

Accelerated Growth ◽

High Level ◽

Cancer Tissues ◽

Great Damage

Abstract FGF16 is implicated in the progression of some specific types of cancers, such as embryonic carcinoma, ovarian cancer, and liver cancer. Yet, the function of FGF16 in the development of lung cancer remains largely unexplored. In this study, we present the novel function of FGF16 and the regulation of miR-520b on FGF16 in lung cancer progression. In clinical lung cancer tissues, FGF16 is overexpressed and its high level is negatively associated with the low level of miR-520b. Furthermore, both the transcription and translation levels of FGF16 are restrained by miR-520b in lung cancer cells. For the regulatory mechanism investigation, miR-520b is able to directly bind to the 3′-untranslated region (3′UTR) of FGF16 mRNA, leading to its mRNA cleavage in the cells. Functionally, miR-520b reduces the growth of lung cancer and its inhibitor anti-miR520b is able to promote the growth through competing endogenous miR-520b. Moreover, FGF16 silence using RNA interference is capable of doing great damage to anti-miR-520b-accelerated growth of lung cancer. Thus, our finding indicates that FGF16 is a new target gene of miR-520b in lung cancer. For lung cancer, FGF16 may serve as a novel biomarker and miR-520b/FGF16 may be useful in clinical treatment.

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Novel start codons introduce novel coding sequences in the human genomes

10.1101/2020.11.04.368936 ◽

2020 ◽

Author(s):

He Zhang ◽

Yang Xie

Keyword(s):

Translation Initiation ◽

Genomic Analysis ◽

Comparative Genomic ◽

Human Populations ◽

The Novel ◽

Coding Sequences ◽

Human Genomes ◽

High Level ◽

Selection Signal ◽

Human Specific

AbstractStart-gain mutations can introduce novel start codons and generate novel coding sequences that may affect the function of genes. In this study, we systematically investigated the novel start codons that were either polymorphic or fixed in the human genomes. 829 polymorphic start-gain SNVs were identified in the human populations, and the novel start codons introduced by these SNVs have significantly higher activity in translation initiation. Some of these start-gain SNVs were reported to be associated with phenotypes and diseases in previous studies. By comparative genomic analysis, we found 26 human-specific start codons that were fixed after the divergence between the human and chimpanzee, and high-level translation initiation activity was observed on them. The negative selection signal was detected in the novel coding sequences introduced by these human-specific start codons, indicating the important function of these novel coding sequences. This study reveals start-gain mutations are keeping appearing in the human genomes during the evolution and may be important sources altering the function of genes which may further affect the phenotypes or cause diseases.

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Iris Hanika's Treffen Sich Zwei: Reception, Analysis and Interpretation

10.26686/wgtn.17004778 ◽

2021 ◽

Author(s):

◽

Kerry Alistair Nitz

Keyword(s):

Quantitative Analysis ◽

Qualitative Approach ◽

The Other ◽

The Novel ◽

Quantitative Evidence ◽

Literary Context ◽

Narrative Functions ◽

The One ◽

High Level ◽

The Relationship

<p>Iris Hanika’s commercially and critically successful novel Treffen sich zwei makes use of several techniques in the characterisation of its protagonists. Many of its reviews focus on the author’s deliberate placement of links to a wider literary context. Their interest extends from questions of genre-mixing through to the identification of direct quotes from other authors’ works. The critical preoccupation with intertexts demonstrates their importance for the readers’ response to the novel. More specifically, certain reviews highlight the important role intertexts play in the characterisation of the protagonists. This study catalogues the intertexts, metaphors and parodies in Treffen sich zwei and, by means of quantitative analysis, identifies high-level patterns in the use of these techniques. In particular, patterns are identified between, on the one hand, the different narrative functions of the intertexts and, on the other hand, the different ways in which they are interwoven in the text. The data also shows that distinct patterns are associated with each of the two protagonists and that certain patterns change in the course of the novel in parallel with the changes in the relationship between them. This quantitative evidence is supported by a more detailed, qualitative approach, which examines how specific intertexts or metaphors are used for the purposes of characterisation. In addition, variations in voice are used to distinguish the two main protagonists in a manner consistent with the intertexts and metaphors. It is thanks to the combination of these techniques that the theme of meeting encapsulated in the title, Treffen sich zwei, is woven into the textual fabric of the novel.</p>

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Pulmonary Cavitation – An Under-recognized Late Complication of Severe COVID-19 Lung Disease

10.21203/rs.3.rs-62904/v1 ◽

2020 ◽

Author(s):

Zaid Zoumot ◽

Maria-Fernanda Bonilla ◽

Ali S. Wahla ◽

Irfan Shafiq ◽

Mateen Uzbeck ◽

...

Keyword(s):

Lung Disease ◽

Medical Records ◽

Late Complication ◽

Ground Glass ◽

The Novel ◽

Radiological Findings ◽

Imaging Characteristics ◽

Microbiological Parameters ◽

Novel Coronavirus ◽

High Level

Abstract Background: Pulmonary radiological findings of the novel coronavirus disease 2019 (COVID-19) have been well documented and range from scattered ground-glass infiltrates in milder cases to confluent ground-glass change, dense consolidation, and crazy paving in the critically ill. However, lung cavitation has not been commonly described in these patients. The objective of this study was to assess the incidence of pulmonary cavitation in patients with COVID-19 and describe its characteristics and evolution.Methods: We conducted a retrospective review of all patients admitted to our institution with COVID-19 and reviewed electronic medical records and imaging to identify patients who developed pulmonary cavitation.Results: Twelve out of 689 (1.7%) patients admitted to our institution with COVID-19 developed pulmonary cavitation, comprising 3.3% (n=12/359) of patients who developed COVID-19 pneumonia, and 11% (n=12/110) of those admitted to the intensive care unit. We describe the imaging characteristics of the cavitation and present the clinical, pharmacological, laboratory, and microbiological parameters for these patients. In this cohort six patients have died, two are recovering in hospital and four have been discharged home. Conclusion: Cavitary lung disease in patients with severe COVID-19 disease is not uncommon, and is associated with a high level of morbidity and mortality.

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TOPOLOGICAL INDICES – WHY AND HOW

10.46793/iccbi21.039g ◽

2021 ◽

Author(s):

Ivan Gutman ◽

Keyword(s):

Single Molecule ◽

Chemical Structure ◽

Chemical Reactivity ◽

Chemical Species ◽

Chemical Compounds ◽

Simple Calculation ◽

Topological Indices ◽

High Level ◽

Complex Phenomena ◽

Real World Problems

By means of presently available high-level computational methods, based on quantum theory, it is possible to determine (predict) the main structural, electronic, energetic, geometric, and thermodynamic properties of a particular chemical species (usually a molecule), as well as the ways in which it changes in chemical reactions. When one needs to estimate such properties of thousands or millions of chemical species, such high-level calculations are no more feasible. Then simpler, but less accurate, approaches are necessary. One such approach utilized so-called “topological indices”. According to IUPAC ‘s definition [Pure Appl. Chem. 69 (1997) 1137]: A topological index is a numerical value associated with chemical constitution for correlation of chemical structure with various physical properties, chemical reactivity or biological activity. In the first part of the lecture, we show that „numerical values“are associated with many other complex phenomena, encountered in various areas of human activity, implying that „topological indices“ are used far beyond chemistry. Next, we discuss the number of possible chemical compounds. Simple calculation shows that the number of possible compounds zillion times exceeds the number of those that have been experimentally characterized. Even worse, in the entire Universe, there is not enough matter to make at least a single molecule of each possible compound. In the second part of the lecture, a few most popular topological indices will be presented, as well as the way in which these can be (and are being) applied in treating real-world problems.

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The Automatic Basketball Rebound System

Volume 13: Design, Reliability, Safety, and Risk ◽

10.1115/imece2018-86715 ◽

2018 ◽

Author(s):

Thomas Smith ◽

Vidya K. Nandikolla

Keyword(s):

Inertial Measurement Unit ◽

High Efficiency ◽

Dead Reckoning ◽

Measurement Unit ◽

System Response ◽

The Novel ◽

Rotary Table ◽

Inertial Measurement ◽

Correct Orientation ◽

High Level

In the sport of basketball, it is important to practice shooting the ball to develop the skill of making the shot in the basket at a high efficiency. Making shots at a high efficiency allows the player to succeed at a high level in the sport. The main focus of the paper describes the design and development of an automatic basketball rebound (ABR) system. The developed ABR provides a system that will launch the ball back to the player at any position on the court within a 50-foot radius. This is accomplished by a variable spring loaded launching mechanism that will compress a spring, depending on the players location, to generate the appropriate force required to launch the ball back to the player. The novel launching mechanism developed is mounted to a rotary table that ensures the launching mechanism is in the correct orientation with the player once the ball is launched. The player is outfitted with an inertial measurement unit to track their position using a method known as dead reckoning. This information is relayed back to a microcontroller that determines the system response. The ABR system is made from lightweight materials and is compact such that it is easy to move around compared to its predecessors.

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MONACO: accurate biological network alignment through optimal neighborhood matching between focal nodes

Bioinformatics ◽

10.1093/bioinformatics/btaa962 ◽

2020 ◽

Author(s):

Hyun-Myung Woo ◽

Byung-Jun Yoon

Keyword(s):

Biological Network ◽

Protein Complexes ◽

Ground Truth ◽

Network Alignment ◽

Supplementary Information ◽

Alignment Algorithm ◽

Computationally Efficient ◽

Topological Similarity ◽

Alignment Algorithms ◽

Multiple Network

Abstract Motivation Alignment of protein–protein interaction networks can be used for the unsupervised prediction of functional modules, such as protein complexes and signaling pathways, that are conserved across different species. To date, various algorithms have been proposed for biological network alignment, many of which attempt to incorporate topological similarity between the networks into the alignment process with the goal of constructing accurate and biologically meaningful alignments. Especially, random walk models have been shown to be effective for quantifying the global topological relatedness between nodes that belong to different networks by diffusing node-level similarity along the interaction edges. However, these schemes are not ideal for capturing the local topological similarity between nodes. Results In this article, we propose MONACO, a novel and versatile network alignment algorithm that finds highly accurate pairwise and multiple network alignments through the iterative optimal matching of ‘local’ neighborhoods around focal nodes. Extensive performance assessment based on real networks as well as synthetic networks, for which the ground truth is known, demonstrates that MONACO clearly and consistently outperforms all other state-of-the-art network alignment algorithms that we have tested, in terms of accuracy, coherence and topological quality of the aligned network regions. Furthermore, despite the sharply enhanced alignment accuracy, MONACO remains computationally efficient and it scales well with increasing size and number of networks. Availability and implementation Matlab implementation is freely available at https://github.com/bjyoontamu/MONACO. Supplementary information Supplementary data are available at Bioinformatics online.

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An Improved Method for Completely Uncertain Biological Network Alignment

BioMed Research International ◽

10.1155/2015/253854 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 1

Author(s):

Bin Shen ◽

Muwei Zhao ◽

Wei Zhong ◽

Jieyue He

Keyword(s):

Biological Networks ◽

Biological Network ◽

Evaluation Criteria ◽

Network Alignment ◽

Global Network ◽

Uncertain Information ◽

Improved Method ◽

Network Comparison ◽

Probabilistic Network ◽

Alignment Problem

With the continuous development of biological experiment technology, more and more data related to uncertain biological networks needs to be analyzed. However, most of current alignment methods are designed for the deterministic biological network. Only a few can solve the probabilistic network alignment problem. However, these approaches only use the part of probabilistic data in the original networks allowing only one of the two networks to be probabilistic. To overcome the weakness of current approaches, an improved method called completely probabilistic biological network comparison alignment (C_PBNA) is proposed in this paper. This new method is designed for complete probabilistic biological network alignment based on probabilistic biological network alignment (PBNA) in order to take full advantage of the uncertain information of biological network. The degree of consistency (agreement) indicates that C_PBNA can find the results neglected by PBNA algorithm. Furthermore, the GO consistency (GOC) and global network alignment score (GNAS) have been selected as evaluation criteria, and all of them proved that C_PBNA can obtain more biologically significant results than those of PBNA algorithm.

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Fast Compass Alignment Algorithm of FOG SINS under Sway Condition

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.321-324.2171 ◽

2013 ◽

Vol 321-324 ◽

pp. 2171-2176 ◽

Cited By ~ 2

Author(s):

Bin Zhou ◽

Wei Wang

Keyword(s):

Fiber Optic ◽

Alignment Algorithm ◽

Test Results ◽

Fiber Optic Gyro ◽

Initial Alignment ◽

Variable Parameters ◽

Navigation Algorithm ◽

Alignment Problem ◽

Concrete Realization ◽

Instrument Accuracy

Through research on initial alignment problem of fiber optic gyro SINS in the sway condition, this paper proposed a rapid compass alignment scheme with variable parameters, which can accomplish rapid initial alignment. Firstly, analysted SINS compass alignment principle, and gave a concrete realization method which has the same calculation procedure with full damping navigation algorithm. This method makes the alignment and navigation to use the same set of algorithms, and can effectively reduce algorithm complexity. Simulation and repeatedly sway test results show that the alignment algorithm is effective. The alignment precision and instrument accuracy is consistent, it can meet the requirements of the initial alignment.

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