New Trends in Graph Mining

2010 ◽  
Vol 1 (1) ◽  
pp. 81-99 ◽  
Author(s):  
Francesco Bruno ◽  
Luigi Palopoli ◽  
Simona E. Rombo
Keyword(s):  
Computational Biology ◽  
Biological Networks ◽  
Graph Mining ◽  
Building Blocks ◽  
Biological Data ◽  
Future Research ◽  
Motif Extraction

Searching for repeated features characterizing biological data is fundamental in computational biology. When biological networks are under analysis, the presence of repeated modules across the same network (or several distinct ones) is shown to be very relevant. Indeed, several studies prove that biological networks can be often understood in terms of coalitions of basic repeated building blocks, often referred to as network motifs.This work provides a review of the main techniques proposed for motif extraction from biological networks. In particular, main intrinsic difficulties related to the problem are pointed out, along with solutions proposed in the literature to overcome them. Open challenges and directions for future research are finally discussed.

scholarly journals BioNetLink - An Architecture for Working with Network Data

2014 ◽  
Vol 11 (2) ◽  
pp. 68-79
Author(s):  
Matthias Klapperstück ◽  
Falk Schreiber
Keyword(s):  
Experimental Data ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Large Data ◽  
Biological Data ◽  
Network Data ◽  
Data Sets ◽  
Dynamic Views ◽  
Gene Regulatory ◽  
Multiple Network

Summary The visualization of biological data gained increasing importance in the last years. There is a large number of methods and software tools available that visualize biological data including the combination of measured experimental data and biological networks. With growing size of networks their handling and exploration becomes a challenging task for the user. In addition, scientists also have an interest in not just investigating a single kind of network, but on the combination of different types of networks, such as metabolic, gene regulatory and protein interaction networks. Therefore, fast access, abstract and dynamic views, and intuitive exploratory methods should be provided to search and extract information from the networks. This paper will introduce a conceptual framework for handling and combining multiple network sources that enables abstract viewing and exploration of large data sets including additional experimental data. It will introduce a three-tier structure that links network data to multiple network views, discuss a proof of concept implementation, and shows a specific visualization method for combining metabolic and gene regulatory networks in an example.

scholarly journals Simulated Breathing: Application of Molecular Dynamics Simulations to Pulmonary Lung Surfactant

Symmetry ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1259
Author(s):  
Maksymilian Dziura ◽  
Basel Mansour ◽  
Mitchell DiPasquale ◽  
P. Charukeshi Chandrasekera ◽  
James W. Gauld ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Pulmonary Surfactant ◽  
Lung Surfactant ◽  
Protein Composition ◽  
Md Simulations ◽  
Building Blocks ◽  
Future Research ◽  
Total Composition ◽  
Protein Components ◽  
Dynamics Simulations

In this review, we delve into the topic of the pulmonary surfactant (PS) system, which is present in the respiratory system. The total composition of the PS has been presented and explored, from the types of cells involved in its synthesis and secretion, down to the specific building blocks used, such as the various lipid and protein components. The lipid and protein composition varies across species and between individuals, but ultimately produces a PS monolayer with the same role. As such, the composition has been investigated for the ways in which it imposes function and confers peculiar biophysical characteristics to the system as a whole. Moreover, a couple of theories/models that are associated with the functions of PS have been addressed. Finally, molecular dynamic (MD) simulations of pulmonary surfactant have been emphasized to not only showcase various group’s findings, but also to demonstrate the validity and importance that MD simulations can have in future research exploring the PS monolayer system.

Temporal Dynamics of PERMA Building Blocks and Well-being in Daily Life: An Ecological Momentary Assessment

2021 ◽  
Author(s):  
Saeideh Heshmati ◽  
Zita Oravecz
Keyword(s):  
Ecological Momentary Assessment ◽  
Temporal Dynamics ◽  
Daily Life ◽  
Well Being ◽  
Building Blocks ◽  
Individual Variability ◽  
Future Research ◽  
Dynamical Features ◽  
Ecological Momentary ◽  
Momentary Assessment

Most assessments of well-being have relied on retrospective accounts, measured by global evaluative well-being scales. Following the recent debates focused on the assessment of hedonic and eudaimonic well-being based on the elements of the PERMA theory, the current study aimed to shed further light onto the measurement of PERMA elements in daily life and their temporal dynamics. Through an Ecological Momentary Assessment (EMA) design (N=160), we examined the dynamics of change (e.g., baselines and intra-individual variability) in the PERMA elements using the mPERMA measure, which is an EMA-adapted version of the PERMA Profiler. Findings revealed that momentary experiences of well-being, quantified via PERMA elements, map onto their corresponding hedonic or eudaimonic well-being components, and its dynamical features provide novel insights into predicting global well-being. This work offers avenues for future research to assess well-being in real-time and real-world contexts in ecologically valid ways, while eliminating recall bias.

scholarly journals Responsive and Adaptive Design for Survey Optimization

2018 ◽  
Vol 34 (3) ◽  
pp. 581-597 ◽  
Author(s):  
Asaph Young Chun ◽  
Steven G. Heeringa ◽  
Barry Schouten
Keyword(s):  
Adaptive Design ◽  
Survey Design ◽  
Special Section ◽  
Cost Optimization ◽  
Auxiliary Information ◽  
Building Blocks ◽  
Quality Data ◽  
Future Research ◽  
Efficient Production ◽  
Process Data

Abstract We discuss an evidence-based approach to guiding real-time design decisions during the course of survey data collection. We call it responsive and adaptive design (RAD), a scientific framework driven by cost-quality tradeoff analysis and optimization that enables the most efficient production of high-quality data. The notion of RAD is not new; nor is it a silver bullet to resolve all the difficulties of complex survey design and challenges. RAD embraces precedents and variants of responsive design and adaptive design that survey designers and researchers have practiced over decades. In this paper, we present the four pillars of RAD: survey process data and auxiliary information, design features and interventions, explicit quality and cost metrics, and a quality-cost optimization tailored to survey strata. We discuss how these building blocks of RAD are addressed by articles published in the 2017 JOS special issue and this special section. It is a tale of the three perspectives filling in each other. We carry over each of these three perspectives to articulate the remaining challenges and opportunities for the advancement of RAD. We recommend several RAD ideas for future research, including survey-assisted population modeling, rigorous optimization strategies, and total survey cost modeling.

Nano-Sized and Nanocrystalline Calcium Orhophosphates in Biomedical Engineering

2009 ◽  
Vol 3 ◽  
pp. 59-92 ◽  
Author(s):  
Sergey V. Dorozhkin
Keyword(s):  
Bone Repair ◽  
Dental Enamel ◽  
Building Blocks ◽  
Research Area ◽  
Future Research ◽  
Biological Origin ◽  
Current State ◽  
Calcium Orthophosphates ◽  
Recent Developments ◽  
Hard Tissue Engineering

There has been much recent activity in the research area of nanoparticles and nanocrystalline materials, in many fields of science and technology. This is due to their outstanding and unique physical, mechanical, chemical and biological characteristics. Recent developments in biomineralization have demonstrated that nano-sized particles play an important role in the formation of the hard tissues of animals. It is well established that the basic inorganic building blocks of bones and teeth of mammals are nano-sized and nanocrystalline calcium orthophosphates (in the form of apatites) of a biological origin. In mammals, tens to hundreds of nanocrystals of biological apatite are found to combine into self-assembled structures under the control of bio-organic matrixes. It was also confirmed experimentally that the structure of both dental enamel and bones could be mimicked by an oriented aggregation of nano-sized calcium orthophosphates, determined by the biomolecules. The application and prospective use of nano-sized and nanocrystalline calcium orthophosphates for clinical repair of damaged bones and teeth are also known. For example, a greater viability and a better proliferation of various cells were detected on smaller crystals of calcium orthophosphates. Furthermore, studies revealed that the differentiation of various cells was promoted by nano-sized calcium orthophosphates. Thus, the nano-sized and nanocrystalline forms of calcium orthophosphates have the potential to revolutionize the field of hard tissue engineering, in areas ranging from bone repair and augmentation to controlled drug delivery devices. This paper reviews the current state of knowledge and recent developments of various nano-sized and nanocrystalline calcium orthophosphates, covering topics from the synthesis and characterization to biomedical and clinical applications. This review also provides possible directions of future research and development.

Transcriptional Regulatory Network Topology with Applications to Bio-inspired Networking: A Survey

2022 ◽  
Vol 54 (8) ◽  
pp. 1-36
Author(s):  
Satyaki Roy ◽  
Preetam Ghosh ◽  
Nirnay Ghosh ◽  
Sajal K. Das
Keyword(s):  
Communication Networks ◽  
Biological Networks ◽  
Regulatory Network ◽  
Large Scale ◽  
Data Transfer ◽  
Transcriptional Regulatory Network ◽  
Future Research ◽  
Transcriptional Regulatory ◽  
Iot Devices ◽  
Networking Protocols

The advent of the edge computing network paradigm places the computational and storage resources away from the data centers and closer to the edge of the network largely comprising the heterogeneous IoT devices collecting huge volumes of data. This paradigm has led to considerable improvement in network latency and bandwidth usage over the traditional cloud-centric paradigm. However, the next generation networks continue to be stymied by their inability to achieve adaptive, energy-efficient, timely data transfer in a dynamic and failure-prone environment—the very optimization challenges that are dealt with by biological networks as a consequence of millions of years of evolution. The transcriptional regulatory network (TRN) is a biological network whose innate topological robustness is a function of its underlying graph topology. In this article, we survey these properties of TRN and the metrics derived therefrom that lend themselves to the design of smart networking protocols and architectures. We then review a body of literature on bio-inspired networking solutions that leverage the stated properties of TRN. Finally, we present a vision for specific aspects of TRNs that may inspire future research directions in the fields of large-scale social and communication networks.

Graph Mining Techniques

2013 ◽  
pp. 446-464 ◽  
Author(s):  
Ana Paula Appel ◽  
Christos Faloutsos ◽  
Caetano Traina Junior
Keyword(s):  
Social Networks ◽  
Communication Networks ◽  
Real World ◽  
Biological Networks ◽  
Graph Mining ◽  
Recommendation Systems ◽  
Computer Communication Networks ◽  
Computer Communication ◽  
Good Pattern ◽  
As Graph

Graphs appear in several settings, like social networks, recommendation systems, computer communication networks, gene/protein biological networks, among others. A large amount of graph patterns, as well as graph generator models that mimic such patterns have been proposed over the last years. However, a deep and recurring question still remains: “What is a good pattern?” The answer is related to finding a pattern or a tool able to help distinguishing between actual real-world and fake graphs. Here we explore the ability of ShatterPlots, a simple and powerful algorithm to tease out patterns of real graphs, helping us to spot fake/masked graphs. The idea is to force a graph to reach a critical (“Shattering”) point, randomly deleting edges, and study its properties at that point.

H.265 Video Streaming in Mobile Cloud Networks

Web Services ◽  
2019 ◽  
pp. 1007-1047
Author(s):  
Qi Wang ◽  
James Nightingale ◽  
Jose M. Alcaraz-Calero ◽  
Chunbo Luo ◽  
Zeeshan Pervez ◽  
...  
Keyword(s):  
Video Streaming ◽  
Video Processing ◽  
Building Blocks ◽  
Future Research ◽  
Mobile Cloud ◽  
Context Aware ◽  
Adaptive Streaming ◽  
Data Traffic ◽  
Cloud Networks ◽  
Cloud Networking

Mobile video applications have started to dominate the global mobile data traffic in recent years, and both opportunities and challenges have arisen when the emerging mobile cloud paradigm is introduced to support the resource-demanding video processing and networking services. This chapter offers in-depth discussions for content- and context-aware, adaptive, robust, secure, and real-time video applications in mobile cloud networks. The chapter describes and analyses the essential building blocks including the state-of-the-art technologies and standards on video encoding, adaptive streaming, mobile cloud computing, and resource management, and the associated security issues. The focus is context-aware adaptive streaming based on the latest video coding standard H.265 in the context of Internet-centric mobile cloud networking. Built upon selected building blocks underpinned by promising approaches and emerging standards, an integrated architecture is proposed towards achieving next-generation smart video streaming for mobile cloud users, with future research directions in this field identified.

An Overview of Biological Data Mining

Biotechnology ◽  
2019 ◽  
pp. 120-139
Author(s):  
Seetharaman Balaji
Keyword(s):  
Data Mining ◽  
Information Retrieval ◽  
Biological Networks ◽  
Web Mining ◽  
Biological Data ◽  
Biological Research ◽  
Digital Repository ◽  
Domain Specific ◽  
Novice Learner ◽  
Integration Data

The largest digital repository of information, the World Wide Web keeps growing exponentially and calls for data mining services to provide tailored web experiences. This chapter discusses the overview of information retrieval, knowledge discovery and data mining. It reviews the different stages of data mining and introduces the wide spread biological databanks, their explosion, integration, data warehousing, information retrieval, text mining, text repositories for biological research publications, domain specific search engines, web mining, biological networks and visualization, ontology and systems biology. This chapter also illustrates some technical jargon with picture analogy for a novice learner to understand the concepts clearly.

Secure Electronic Voting with Cryptography

Cyber Crime ◽  
2013 ◽  
pp. 918-935
Author(s):  
Xunhua Wang ◽  
Ralph Grove ◽  
M. Hossain Heydari
Keyword(s):  
Building Blocks ◽  
Electronic Voting ◽  
Future Research ◽  
Voting Systems ◽  
Research Directions ◽  
Security Challenges ◽  
Future Research Directions ◽  
Voting Scheme ◽  
Threshold Decryption

In recent years, computer and network-based voting technologies have been gradually adopted for various elections. However, due to the fragile nature of electronic ballots and voting software, computer voting has posed serious security challenges. This chapter studies the security of computer voting and focuses on a cryptographic solution based on mix-nets. Like traditional voting systems, mix-net-based computer voting provides voter privacy and prevents vote selling/buying and vote coercion. Unlike traditional voting systems, mix-net-based computer voting has several additional advantages: 1) it offers vote verifiability, allowing individual voters to directly verify whether their votes have been counted and counted correctly; 2) it allows voters to check the behavior of potentially malicious computer voting machines and thus does not require voters to blindly trust computer voting machines. In this chapter, we give the full details of the building blocks for the mix-net-based computer voting scheme, including semantically secure encryption, threshold decryption, mix-net, and robust mix-net. Future research directions on secure electronic voting are also discussed.

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