bluuebunny/crossref_metadata_2025 huggingface dataset:
Societal metamorphosis via authentic democracy principles
Authors: Georgantzas Nicholas C. , Contogeorgis Georges D.
Published: December 2019

Without suggesting our modernity's return to antiquity, this article looks at the principles behind Athenians' authentic democracy, which can help our modern temporality metamorphose for the benefit of all concerned. Democracy's multiple equality, liberty and civic-accountability dimension bundles take their role in a multi-perspective dialectic about their dynamic societal implications. The article also shows a couple of small system dynamics (SD) models of political corruption, in order to showcase a major problem that Athenians' authentic democracy de-solved rather effectively; particularly when compared to the vast failures of our postmodern temporality's ‘gated’ business, economic, societal and political systems. The juxtaposition of an acute problematic situation – such as political corruption is in our modernity – and the principles behind the multi-dimensional political structure that managed this problematic effectively in the past points to the systemic leverage required for the metamorphosis needed in our postmodern business, economic, societal and political systems worldwide.
The role of information technology in e-learning systems success
Authors: Eom Sean , Ashill Nicholas J. , Arbaugh J.B. , Stapleton James L.
Published: December 2019

This study empirically tested the DeLone and McLean model of information systems success model (the DM model) in a university e-learning context using structural equation modeling. The results indicated that system quality, information quality, all affected the two mediating constructs, system use and user satisfaction, which in turn, influences the e-learning systems success. The nature of e-learning systems is fundamentally different from the environment in which the DeLone and McLean model is developed and tested, either voluntary or quasi-voluntary environments. However, e-learning systems are to be used in a mandatory environment. For that reason, the DeLone and McLean model has a limited explanatory power for explaining the role of e-learning systems on the outcomes of e-learning. Consequently, we conclude that the primary focus of the e-learning system empirical research should shift from the system factor toward human and design factors. E-learning systems empirical research is focusing on the critical success factors of e-learning outcomes that are comparable to or superior than traditional face-to-face learning system.
Corporate social responsibility: A concern among employees
Authors: Hsieh Yi-Hua , Chan Jui-Ying
Published: December 2019

In the past, the extant research of CSR was mainly focused on the relations of CSR to organizational performance, financial performance, social responsibility investment, and firm competitiveness. In this paper, from employees' perspective, we used social identity theory, organizational justice theory, and empirical researches to develop our hypotheses. We acquired 278 valid questionnaires and exercise multiple regression and hierarchical regression. These findings revealed that employee perception of the organization's CSR effort has a positive effect on organizational commitment; employee perception of the organization's CSR effort has a positive effect on job satisfaction; job satisfaction has a positive effect on organizational commitment; and partial mediation of job satisfaction in the relationship between employee perception of the organization's CSR effort and organizational commitment.
In silico Analysis of Evolutionary Patterns in	Restriction Endonucleases
Authors: Singh Tiratha Raj , Pardasani Kamal Raj
Published: December 2019

Restriction endonucleases represent one of the best studied examples of DNA binding proteins. Type II restriction endonucleases recognize short sequences of foreign DNA and cleave the target on both strands with remarkable sequence specificity. Type II restriction endonucleases are part of restriction modification systems. Restriction modification systems occur ubiquitously among bacteria and archaea. Restriction endonucleases are indispensable tools in molecular biology and biotechnology. They are important model system for specific protein-nucleic acid interactions and also serve as good example for investigating structural, functional and evolutionary relationships among various biomolecules. The interaction between restriction endonucleases and their recognition sequences plays a crucial role in biochemical activities like catalytic site/metal binding, DNA repair and recombination etc. We study various patterns in restriction endonucleases type II and analyzed their structural, functional and evolutionary role. Our studies support X-ray crystallographic studies, arguing for divergence and molecular evolution. Conservation patterns of the nuclease superfamily have also been analyzed by estimating site-specific evolutionary rates for the analyzed structures related to respective chains in this study.
Analysis of n-Gram based Promoter Recognition Methods and	Application to Whole Genome Promoter Prediction
Authors: Rani T. Sobha , Bapi Raju S.
Published: December 2019

Promoter prediction is an important and complex problem. Pattern recognition algorithms typically require features that could capture this complexity. A special bias towards certain combinations of base pairs in the promoter sequences may be possible. In order to determine these biases n-grams are usually extracted and analyzed. An n-gram is a selection of n contiguous characters from a given character stream, DNA sequence segments in this case. Here a systematic study is made to discover the efficacy of n-grams for n = 2, 3, 4, 5 in promoter prediction. A study of n-grams as features for a neural network classifier for E. coli and Drosophila promoters is made. In case of E. coli n = 3 and in case of Drosophila n = 4 seem to give optimal prediction values. Using the 3-gram features, promoter prediction in the genome sequence of E. coli is done. The results are encouraging in positive identification of promoters in the genome compared to software packages such as BPROM, NNPP, and SAK. Whole genome promoter prediction in Drosophila genome was also performed but with 4-gram features.
Numerical Characterization of Protein Sequences and Application to	Voltage-Gated Sodium Channel α Subunit Phylogeny
Authors: Nandy Ashesh , Ghosh Ambarnil , Nandy Papiya
Published: December 2019

We propose a new method to compare sequences of protein families by generating numerical characterizations through a 20D representation. Using a walk along the axes representing the amino acids we generate a vector for each sequence whose components can be used to derive distance matrices between sequences and whose magnitudes can be used to compare the similarities/dissimilarities between the different sequences. The distance matrices enable creation of phylogenetic trees without need for multiple alignments or any other model dependencies. In this paper we test this technique with human globin gene sequences and then apply the method to a contemporary issue of evolutionary relationships of rat and human voltage-gated sodium channel α subunits and compare with published literature. The close match of the results demonstrates the reliability and ease of use of this method.
Systematic Analysis of Disease-Related Regulatory Mutation Classes	Reveals Distinct Effects on Transcription Factor Binding
Authors: Laurila Kirsti , Lähdesmäki Harri
Published: December 2019

Detailed knowledge of the mechanisms of transcriptional regulation is essential in understanding the gene expression in its entirety. Transcription is regulated, among other things, by transcription factors that bind to DNA and can enhance or repress the transcription process. If a transcription factor fails to bind to DNA or binds to a wrong DNA region that can cause severe effects to the gene expression, to the cell and even to the individual. The problems in transcription factor binding can be caused by alterations in DNA structure which often occurs when parts of the DNA strands are mutated. An increasing number of the identified disease-related mutations occur in gene regulatory sequences. These regulatory mutations can disrupt transcription factor binding sites or create new ones. We have studied effects of mutations on transcription factor binding affinity computationally. We have compared our results with experimentally verified cases where a mutation in a gene regulatory region either creates a new transcription factor binding site or deletes a previously existing one. We have investigated the statistical properties of the changes on transcription factor binding affinity according to the mutation type. Our analysis shows that the probability of a loss of a transcription factor binding site and a creation of a new one varies remarkably by the mutation type. Our results demonstrate that computational analysis provides valuable information about the effect of mutations on transcription factor binding sites. The analysis results also give a useful test set for in vitro studies of regulatory mutation effects.
In silico Identification of Candidate Drug and	Vaccine Targets from Various Pathways in Neisseria gonorrhoeae
Authors: Barh Debmalya , Kumar Anil
Published: December 2019

Neisseria gonorrhoeae is responsible for causing gonorrhea, one of the most common sexually transmitted diseases prevailing globally. Although extensive researches are in progress in order to control the transmission of the disease and to develop drug(s) against the pathogen, till date no effective vaccine or specific drug could be developed and only antibiotic treatment is in use. Perhaps, due to excess use of antibiotics, several resistant strains have been found. In the present study, metabolic pathways-related candidate drug and vaccine targets have been identified in N. gonorrhoeae virulent strain FA 1090 using an in silico subtractive genomics approach. 106 putative drug targets out of 537 essential genes have been predicted. 67 cytoplasmic and 9 membrane enzymes, along with 10 membrane transporters are found to be the potential drug targets from the host-pathogen common metabolic pathways. Among these targets, competence lipoproteins (NGO0277) and cysW have been identified as candidate vaccine targets. 20 drug targets have been identified from pathogen specific unique metabolic pathways. Out of these, 6 enzymes are involved in dual metabolic pathways and 2 are expressed in cell wall and fimbrium. These gonococci-specific proteins are expected to be better possible drug targets. Screening of the functional inhibitors against these novel targets may result in discovery of novel therapeutic compounds that can be effective against antibiotic resistant strains.
Development of a Database and Ontology for Pathogenic Pathways in	Periodontitis
Authors: Suzuki Asami , Takai-Igarashi Takako , Numabe Yukihiro , Tanaka Hiroshi
Published: December 2019

It is getting familiar that pathway information greatly contributes to elucidate the molecular basis of human disease with large-scale biological data. We developed a pathway database for molecular pathology in periodontitis named 'Pathogenic Pathway Database for Periodontitis'. Periodontitis is an inflammation disease in periodontal tissue and associated with an increased health risk of angina, myocardial infarction, and fetal cardiovascular events. Despite accumulation of biomedical research on periodontitis pathology at the molecular level, there has been no systematization for biological pathways in periodontitis. We checked 185 reference papers and extracted causal relationships among molecules as well as pathways representing molecular etiology. We also built an ontology that systematizes conceptual terms associated with the pathways. Besides pathways, our ontology provides cellular and tissue specific contextual information that is required to represent pathology at the cellular and tissue specific levels. We implemented in our database an integrated viewer for the association between pathways and ontology. Pathogenic Pathway Database for Periodontitis is freely available at http://bio-omix.tmd.ac.jp/disease/perio/.
GEN-SNiP: An Online Tool to Find Polymorphisms in a Genome
Authors: Whyte David B. , Nair Gopakumar Gopalakrishnan , Nair Achuthsankar S. , Oommen Oommen V.
Published: December 2019

An online tool named GEN-SNiP that identifies variations in a set of test DNA sequences with respect to a standard reference sequence is developed and deployed successfully. The tool generates a list of substitutions, insertions and deletions for each test sequences, determined by the reference sequence. In the key batch mode feature, the tool allows multiple sequences to be compared and contrasted even when small insertions and deletions are present, with results sent to the user via email. Other distinguishing features of the tool are grouping of continuous deletions or insertions in the test sequence into a single entity for better output handling, displaying of the alignment of test and reference sequence and the input sequence. The tool has been reported as unique in recent literature.
Conformational Dynamics and Thermal Stabilities of the	αβ-Tubulin Dimer: A Molecular Dynamics Simulation Study
Authors: Wu Xiaomin , Yang Gang , Zu Yuangang , Yang Zhiwei , Zhou Lijun
Published: December 2019

Molecular dynamics simulations were employed to study the conformational dynamics and thermal stabilities of the large αβ-tubulin dimer systems under various conditions. The αβ-tubulin dimer at ambient and cryogenic temperatures remains stable around the native conformations, and the water solvent molecules tend to stabilize the native conformations through the formation of complex hydrogen-bonding networks. The elevation of temperature severely destroys the native conformations and the bioactivities, especially in aqueous solution. It was caused by the lack of intra- and inter-molecular interactions and the decrease of water polarity at higher temperatures. The conformational analysis of the selected segment (β15-QIGAKFWEVIS) provides detailed information on the whole proteins. It was revealed that the local structures of proteins at ambient and cryogenic temperatures have obvious differences albeit the overall structures are close to each other. The selected segments under high temperatures are dominated by random coils instead of native helix at ambient and cryogenic temperatures, accompanied by more diversities and faster conversions of conformations. In addition, the temperature or/and the solvent are capable of altering the secondary structures and further the conformations of the segments and the whole proteins. At ambient temperatures, the water solvent helps the proteins to achieve the native conformation with bioactivities. Different from the corresponding segments in proteins, the truncated peptides are endowed with higher structural flexibilities and characterized by random coils even at ambient temperatures, along with the disappearance of helical hydrogen bonds.
HIV1 V3 Loop Hypermutability is Enhanced by the Guanine Usage Bias	in the Part of env Gene Coding for it
Authors: Khrustalev Vladislav Victorovich
Published: December 2019

Guanine is the most mutable nucleotide in HIV genes because of frequently occurring G to A transitions, which are caused by cytosine deamination in viral DNA minus strands catalyzed by APOBEC enzymes. Distribution of guanine between three codon positions should influence the probability for G to A mutation to be nonsynonymous (to occur in first or second codon position). We discovered that nucleotide sequences of env genes coding for third variable regions (V3 loops) of gp120 from HIV1 and HIV2 have different kinds of guanine usage biases. In the HIV1 reference strain and 100 additionally analyzed HIV1 strains the guanine usage bias in V3 loop coding regions (2G>1G≫3G) should lead to elevated nonsynonymous G to A transitions occurrence rates. In the HIV2 reference strain and 100 other HIV2 strains guanine usage bias in V3 loop coding regions (3G>2G>1G) should protect V3 loops from hypermutability. According to the HIV1 and HIV2 V3 alignment, insertion of the sequence enriched with 2G (21 codons in length) occurred during the evolution of HIV1 predecessor, while insertion of the different sequence enriched with 3G (19 codons in length) occurred during the evolution of HIV2 predecessor. The higher is the level of 3G in the V3 coding region, the lower should be the immune escaping mutation occurrence rates. This hypothesis was tested in this study by comparing the guanine usage in V3 loop coding regions from HIV1 fast and slow progressors. All calculations have been performed by our algorithms "VVK In length", "VVK Dinucleotides" and "VVK Consensus" (www.barkovsky.hotmail.ru).
Evaluation of Accuracy and Applicability of Protein Models:	Retrospective Analysis of Biological and Biomedical Predictions
Authors: Khan Sofia , Vihinen Mauno
Published: December 2019

In order to study protein function and activity structural data is required. Since experimental structures are available for just a small fraction of all known protein sequences, computational methods such as protein modelling can provide useful information. Over the last few decades we have predicted, with homology modelling methods, the structures for numerous proteins. In this study we assess the structural quality and validity of the biological and medical interpretations and predictions made based on the models. All the models had correct scaffolding and were ranked at least as correct or good by numerical evaluators even though the sequence identity with the template was as low as 8%. The biological explanations made based on models were well in line with experimental structures and other experimental studies. Retrospective analysis of homology models indicates the power of protein modelling when made carefully from sequence alignment to model building and refinement. Modelling can be applied to studying and predicting different kinds of biological phenomena and according to our results it can be done so with success.
Interface of Apoptotic Protein Complexes Has Distinct Properties
Authors: Mitra Pralay , Dhar Riddhiman , Pal Debnath
Published: December 2019

Apoptosis is a programmed mechanism of cell death that is a normal component of development and health of multi-cellular organisms. In this study, we ask if interface properties of apoptotic protein complexes are different from protein complexes in general. We find that although in apoptotic protein complexes the overall distribution of interface size, surface complementarity, hydrogen bonding, hydrophobicity are similar to general interface properties, apoptotic complexes tend to have more fragmented interfaces and different secondary structural preferences. The statistics on the number of interfaces where specific amino acid(s) occur with significantly enhanced frequency suggest that Arg, Met and Asp are most important functional residues. The role of Met is believed to be unique, as evidenced from the existing data on hot spot potential of residues. These findings together provide insight into the possible role of various physico-chemical attributes at the protein interface in regulation of the apoptosis process.
Mutational Bias and Gene Expression Level Shape Codon Usage in Thermobifida fusca YX
Authors: Nayak Kinshuk C.
Published: December 2019

In this study major factors shaping codon and amino acid usage variation in Thermobifida fusca YX are reported. It is a major degrader of plant cell walls. It produces spores that can be allergenic and has been associated with a condition called farmers lung. For comparison, two other closely related Actinobacteria, S. coelicolor and N. farcinica were considered. Correspondence analysis on RSCU (Relative Synonymous Codon Usage) showed significant correlation between the major trend of codon usage variation and gene expression level assessed by the "Codon Adaptation Index" (CAI) values. The result was further confirmed from distribution of genes along the first axis. In addition, N $_{c}$ (effective number of codons) plot, SCUO (synonymous codon usage order) plot and correlation analyses showed that base composition and mutational bias have a dominant role in codon usage variation. Furthermore, gene expression level, hydrophobicity and aromaticity have played a significant role in the source of variations for amino acid usage. In addition, codon preference for genes at higher expression level was found to be similar among three different genera. Notably, 14 codons optimally used by Thermobifida fusca YX and its comparative study with S. coelicolor and N. farcinica might provide some useful information for their further study of molecular evolution and genetic engineering.
A Combination of Evolutionary Trace Method, Molecular Surface	Accessibility and Hydrophobicity Analysis to Design a High Hydrophobicity Laccase
Authors: Mohamad Saharuddin Bin , Ong Ai Ling , Khairuddin Raja Farhana , Ripen Adiratna Mat
Published: December 2019

Laccases are industrially attractive enzymes and their applications have expanded to the field of bioremediation. The challenge of today's biotechnology in enzymatic studies is to design enzymes that not only have a higher activity but are also more stable and could fit well with the condition requirements. Laccases are known to oxidize non-natural substrates like polycyclic aromatic hydrocarbons (PAHs). We suppose by increasing the hydrophobicity of laccase, it would increase the chance of the enzyme to meet the hydrophobic substrates in a contamination site, therefore increasing the bioremediation efficacy of PAHs from environment. In this attempt, the applications of evolutionary trace (ET), molecular surface accessibility and hydrophobicity analysis on laccase sequences and laccase's crystal structure (1KYA) are described for optimal design of an enzyme with higher hydrophobicity. Our analysis revealed that Q23A, Q45I, N141A, Q237V, N262L, N301V, N331A, Q360L and Q482A could be promising exchanges to be tested in mutagenesis experiments.
POODLE-I: Disordered Region Prediction by Integrating POODLE	Series and Structural Information Predictors Based on a Workflow Approach
Authors: Hirose Shuichi , Shimizu Kana , Noguchi Tamotsu
Published: December 2019

Under physiological conditions, many proteins that include a region lacking well-defined three-dimensional structures have been identified, especially in eukaryotes. These regions often play an important biological cellular role, although they cannot form a stable structure. Therefore, they are biologically remarkable phenomena. From an industrial perspective, they can provide useful information for determining three-dimensional structures or designing drugs. For these reasons, disordered regions have attracted a great deal of attention in recent years. Their accurate prediction is therefore anticipated to provide annotations that are useful for wide range of applications.

POODLE-I (where "I" stands for integration) is a web-based disordered region prediction system. POODLE-I integrates prediction results obtained from three kinds of disordered region predictors (POODLEs) developed from the viewpoint that the characteristics of disordered regions change according to their length. Furthermore, POODLE-I combines that information with predicted structural information by application of a workflow approach. When compared with server teams that showed best performance in CASP8, POODLE-I ranked among the top and exhibited the highest performance in predicting unfolded proteins.

POODLE-I is an efficient tool for detecting disordered regions in proteins solely from the amino acid sequence. The application is freely available at http://mbs.cbrc.jp/poodle/poodle-i.html.
Three Dimensional Model for N-Terminal A Domain of DmpR	(2-Dimethylphenol) Protein Based on Secondary Structure Prediction and Fold Recognition
Authors: Suresh Panneer Selvam , Kumar Rita , Kumar Anil
Published: December 2019

DmpR (dimethylphenol regulatory protein) is a member of the NtrC family of transcriptional activators and controls the transcription of the dmp operons in response to aromatic effector compounds. Secondary structure and fold recognition prediction of N-terminal A domain of this protein (210 amino acid) was performed in Genesilico Metaserver and 3DJury. The consensus result from these servers suggested MJ_1460 as a template. Three dimensional structures were generated from the sequence structure alignments of the template and target protein with MODELLER. The results suggested that the N-terminal A domain of DmpR belongs to Muramoyl pentapeptide carboxypeptidase domain family. The binding interaction sites of the known effectors were predicted using protein-ligand docking. The proposed active site of N-terminal A domain of DmpR comprises of key residues such as Phe93, Glu127, Phe132, Ser160, Phe163, Met164, Arg166 and Pro189. The findings provide some direction to the experimental studies that aim to broaden the range of phenolic derivative which can be sensed by N-DmpR in order to improve the biodegradation potential.
In Silico Characterization of Thermoactive, Alkaline and	Detergent-Stable Lipase from a Staphylococcus Aureus Strain
Authors: Parameswaran Saravanan , Dubey Vikash Kumar , Patra Sanjukta
Published: December 2019

Bacterial true lipases having thermo and alkaline stability are highly attractive for their industrial production of pharmaceuticals, agrochemicals, cosmetics, and flavour. Staphylococcus aureus lipase (SAL3) remains active at temperatures 40–60°C, with an optimum temperature of 55°C and an optimum pH of 9.5 stable over a range of 5–12. Detailed understanding of the structure and insight into the activity of such lipase would aid in engineering lipases that would function in the desired extreme industrial environments. In the present study, we carried out in silico characterization and structural modeling of SAL3 which is thermoactive, alkaline and detergent-stable. Comparison of SAL3 with other staphylococcal lipases indicates that SAL3 is a true lipase having the catalytic triad (residues Ser119, Asp310 & His352) and the calcium binding site (residues Asp351, Asp354, Asp359, Asp362 and Gly286). Conservation in sequence implies that interfacial activation mechanism is possible in SAL3 with the lid formed by helix (residues 180–196) and loop (residues 197–206). Three dimensional (3D) structure model of SAL3 has been predicted for the first time and aims at understanding its function and biochemical characteristics of possessing relatively high thermal and pH stability.
A scalable anonymous protocol for heterogeneous wireless ad hoc networks
Authors: Durresi Mimoza , Paruchuri Vamsi , Durresi Arjan , Barolli Leonard , Takizawa Makoto
Published: December 2019

Ensuring anonymity in wireless and hoc networks is a major security goal. Using traffic analysis, the attacker can compromise the network functionality by correlating data flow patterns to event locations/active areas. In this paper we present a novel Scalable Anonymous Protocol that hides the location of nodes and obscure the correlation between event zones and data flow from snooping adversaries. We quantify the anonymity strength of our protocol by introducing a new anonymity metric: Degree of Exposure Index. Our protocol is designed to offer flexible tradeoffs between degree of anonymity and communication-delay overhead.
RTL power modeling and estimation of sleep transistor based power gating
Authors: Rosinger Sven , Helms Domenik , Nebel Wolfgang
Published: December 2019

We present an accurate RT level estimation methodology describing the power consumption of a component under power gating. By developing separate models for the on- and off-state and the transition cost between them, we can limit errors to below 10% compared to SPICE. The models support several implementation styles of power gating as NMOS/PMOS or Super-Cutoff. Additionally the models can be used to size the sleep transistors more accurate. We show, how the models can be integrated into a high level power estimation framework supporting design space exploration for several design for leakage methodologies.
Caching in green IP over WDM networks
Authors: Osman Niemah I. , El-Gorashi Taisir , Elmirghani Jaafar M.H.
Published: December 2019

Increasing popularity of media-rich Internet content and the associated growth in power consumption have highlighted the need for energy efficient content distribution schemes. This paper investigates the power savings introduced by caching content in IP over WDM networks. To carry out the study, we develop a MILP model to minimize the power consumption of cache-based services over an IP over WDM network by optimizing the cache sizes of the network nodes at different times of the day. A Constraint-Based Genetic Algorithm (CBGA) is developed to validate the optimum cache sizes obtained from the MILP model and a simulation based on lightpath bypass validates the power consumption of routing traffic demands. We consider different popularity distributions including the Zipf, Pareto and Bimodal content popularity distributions to exemplify different types of IPTV services. Our results reveal that deploying the optimum variable cache sizes at the nodes reduces the overall network power consumption by up to 42%, 68% and 72% using Zipf, Pareto and Bimodal distributions for content popularity, respectively. We further study the impact of regular cache updates on power efficiency. The results show that removing the 10 most popular objects from caches increases the network power consumption by up to 20%.
Self-organized node coordination scheme based on a biological inter-cell signaling system for wireless sensor networks
Authors: Byun Heejung , Yu Junglok
Published: December 2019

In this paper, we propose an energy efficient and delay guaranteed node coordination scheme inspired by biological systems, which have gained considerable attention as a computing and problem solving technique. With the identification of analogies between biological cellular signaling systems and WSN systems, we formulate a new mathematical model that considers the networking challenges of WSNs. The proposed bio-inspired scheme determines the state of the sensor node, as required by each mission-critical application and as determined by the local environmental conditions. A control analysis and simulation results show that the proposed bio-inspired scheme guarantees the system stability and provides significant energy savings, as well as reliable delay guarantees.
A metric for dynamic routing based on variational principles
Authors: Sukhov A.M. , Chemodanov D.Yu.
Published: December 2019

In this paper, variational principles from theoretical physics are used to describe the process of routing in computer networks as an alternate approach to the traditional graph theory principles. The total traffic currently served on all hops of the route has been chosen as the quantity to minimize. A universal metric has been found for dynamic routing, taking into account the packet loss effect. An attempt was made to derive the metrics of the most popular dynamic routing protocols such as RIP, OSPF, EIGRP from the universal metric.
Analysis and evaluation of the maximum throughput for data streaming over IEEE 802.15.4 wireless networks
Authors: Mikhaylov Konstantin , Tervonen Jouni
Published: December 2019

Recently, multiple novel applications have been developed using IEEE 802.15.4-based radio modules. In this paper, we focus on the maximum throughput that one can obtain with IEEE 802.15.4-based transceivers that operate in the license-free 2.4 GHz band using the 2450 direct-sequence spread spectrum physical layer. The results of the thorough maximum throughput analysis for single-hop and multi-hop data streaming scenarios in the beacon-enabled (with both contention access and contention-free periods) and nonbeacon-enabled networks are presented. The results of the analysis are compared with the results of the experiments, which were performed using contemporary IEEE 802.15.4 hardware transducers. Aside from defining the maximum possible throughput for the different scenarios, the presented data disclose the effect of various parameters on communication throughput and latency. The presented results reveal the capabilities of the IEEE 802.15.4 technology and enable one to estimate the feasibility of using the technology for particular applications.
Smart social architecture for green distributed networks
Authors: Vizziello Anna , Favalli Lorenzo
Published: December 2019

Nowadays, the energy consumption and efficiency of wireless networks have become a societal challenge. In this paper a novel system architecture is proposed to achieve green communications. The proposed smart social architecture exploits the flexibility and adaptability of cognitive radio (CR) technology to interact with the environment and achieve eco-sustainability by means of finding the best transmission opportunities. However, the effort required for CR nodes to obtain sensing measurements might make less effective the potential energy efficiency gain obtainable in CR networks. We thus propose to combine CR and social network technologies to maximize the energy efficiency and the associated context awareness in terms of energy and radio knowledge. In this way it is also possible to reduce the sensing burden of CR devices. Through the proposed approach, a greater awareness of environmental impacts by CR paradigm can be instilled in participating users, devices and backbones. This is based on a novel extension of the concept of social network, and specifically by allowing socialization among all the network actors, both users (as it is already done today) and cognitive devices to develop a much lighter and more flexible distributed infrastructure. The functionalities of the network elements and their interfaces are described in detail.
Improving energy efficiency in distributed intrusion detection systems
Authors: Migliardi Mauro , Merlo Alessio
Published: December 2019

Recent studies show that malicious traffic has a significant impact on the behavior of networks, thus early dropping of malicious packets could enhance network performance. Furthermore, recent developments in the field of green networking show that it is possible to modulate power consumption according to the traffic level. Intrusion Detection Systems burden the basic routing task with packets inspection; however, traffic reduction could have beneficial results both on network performance and, with next generation routing devices, in network energy consumption. In this paper, we focus on energy consumption and we present an approach to distribute packet inspection over the network nodes, a model to evaluate the changes in network energy consumption according to early or late discovery and discard of rogue packets, and we adopt our technique and model to evaluate by means of simulation how aggressive distributed intrusion detection could be beneficial in terms of network energy savings.
Performance-Driven Robust Video Multicast over broadband wireless access networks
Authors: Shieh Ce-Kuen , Yu Chia-Yu , Lin Cheng-Han , Ke Chih-Heng
Published: December 2019

In performing video multicast over WiMAX networks, AMC enables the BSs to be able to select an appropriate modulation method in accordance with the transmission objective, namely to improve the video quality or to maximize the bandwidth utilization efficiency. However, by choosing the modulation method which maximizes the video quality at all of the SSs, the bandwidth utilization efficiency is reduced and vice versa. In addition, because wireless channels are noisy, FEC is always employed for video multicast. However, by choosing high FEC ratio, the video quality is improved but the bandwidth utilization efficiency is degraded and vice versa. In other words, a tradeoff exists between the video quality and the bandwidth utilization efficiency for video multicast over WiMAX networks. Accordingly, the present study proposes a scheme designated as Performance-Driven Robust Video Multicast (PDRVM), in which both the modulation method and the FEC ratio are determined adaptively in accordance with the network status by mathematical analyses. Simulation results show that PDRVM not only ensures that most of the SSs acquire a good video quality, but also makes the best possible use of the available transmission resources.
A directional MAC for switchable directional antennas to enhance throughput in crowded infrastructure wireless networks
Authors: Oh Seoungyoul , Lee Ki-Seok , Ko Hyeonmok , Kim Cheeha
Published: December 2019

In conventional infrastructure wireless networks, access points and nodes use omni-directional antennas. In a crowded situation, users have experienced throughput degradation due to various reasons. In this paper, we propose wireless LANs equipped with switchable directional antennas and a directional MAC protocol designed for them. In the proposed wireless LAN, every node including access point is always engaged in directional transmission and reception, but a node is allowed to receive omni-directionally only for association process. This new system enhances throughput in overlapped multiple basic service sets by reducing interference, increasing spatial reuse, and avoiding transmission loss phenomenon (TLP). The simulation results show that the proposed protocol outperforms conventional IEEE 802.11 DCF, in terms of throughput in crowded infrastructure wireless networks.
Route optimization in mobile IPv6 NEMO
Authors: ul Haq Zia , Baig Adeel
Published: December 2019

Network Mobility (NEMO) gives us network communication when whole network is on the move. The need for mobile networks is addressed by NEMO Basic Support Protocol (BSP) proposed by IETF. Although, the proposed protocol gives us network mobility but there are some disadvantages in using NEMO BSP. These disadvantages include inefficiency in routing the data packets, delay and high latency rate. The latest research in NEMO is mainly focuses on providing solution for efficient routing of data packets. In general scenario of mobile network; a hierarchy is formed with the multiple mobile routers with their mobile nodes which are joined together in hierarchical way with a top level mobile router. The nesting of mobile network increases when new mobile routers join it. The inefficient routing becomes more vital if the nesting of mobile network is high. One feature of NEMO BSP is that the mobile network maintains location privacy for the mobile network nodes. Recent research for optimizing the route tries to solve the issue with a compromise made to location privacy of mobile network nodes. In this paper ROMIN (Route Optimization in Mobile IPv6 NEMO) we proposed a solution to solve inefficiency of routing with location privacy. The proposed solution is simulated in NS2 and achieves better throughput and less end to end delay as compared to NEMO BSP.
Petri net based evaluation of energy consumption in wireless sensor nodes
Authors: D'Arienzo Maurizio , Iacono Mauro , Marrone Stefano , Nardone Roberto
Published: December 2019

Wireless Sensor Networks have proven their capability to deal with problems where wide and hardly accessible areas need to be monitored. Among the other systems there are also sensor networks in which nodes can (voluntarily) modify their positions to better adapt to changes of monitored phenomenon. One of the major issues arising in these situations is the energy consumption: as all the movements affect the batteries lifetime, the life of a sensor can be extended by equipping the device with power generators that exploit renewable sources, albeit this solution does not always avoid a full battery discharge. In this paper a Fluid Stochastic Petri Net modelling framework is presented to provide a wide evaluation of all the factors that contribute to the energy dissipation in mobile wireless sensor nodes. The framework allows the generation of extensible and composable models capable to evaluate the energy consumption due to sensing, communication and movement functions as well as the impact of power saving mechanisms on the energetical balance of the node. The approach is applied to a marine sensing problem and is validated by comparing the model analysis results with experimental results achieved through an existing off-the-shelf sensor network simulator.
On efficient replication-based routing in vehicular networks
Authors: Deng Zuoxiang , Zhu Yanmin , Li Minglu
Published: December 2019

Efficient routing in vehicular networks is one of the most challenging problems because of frequent network disruption and fast topological change. Some replication-based routing protocols such as epidemic routing have been proposed. However, these existing replication-based routing protocols cannot achieve high delivery ratio, low end-to-end delay and low delivery cost. In this paper, we design an efficient replication-based routing protocol called ERR for efficient routing in vehicular networks. ERR is a fully distributed protocol, and it has the following three desirable design objectives: first, ERR delivers the majority of the messages generated in time-to-live; second, ERR achieves low end-to-end delay; third, ERR introduces as little delivery cost as possible. To achieve these design objectives, ERR adopts an adaptive strategy for the number of copies of a message in a distributed fashion. In addition, we propose two forwarding rules for a message carrier with some copies to decide whether it should forward the message when it meets a vehicle. Based on real traces of vehicles, we have conducted real trace-driven simulations. Performance results demonstrate that ERR can increase delivery ratio, decrease end-to-end delay, and decrease delivery cost, when compared with four other alternative protocols.
A comparison study of Hill Climbing, Simulated Annealing and Genetic Algorithm for node placement problem in WMNs
Authors: Sakamoto Shinji , Kulla Elis , Oda Tetsuya , Ikeda Makoto , Barolli Leonard , Xhafa Fatos
Published: December 2019

One of the key advantages of Wireless Mesh Networks (WMNs) is their importance for providing cost-efficient broadband connectivity. There are issues for achieving the network connectivity and user coverage, which are related with the node placement problem. In this work, we compare Hill Climbing (HC), Simulated Annealing (SA) and Genetic Algorithm (GA) by simulations for node placement problem. We want to find the optimal distribution of router nodes in order to provide the best network connectivity and provide the best coverage in a set of randomly distributed clients. From the simulation results, all algorithms converge to the maximum size of Giant Component (GC). However, according to the number of covered mesh clients, HC and SA converge faster.
A multi-point transmission scheme for cross-tier interference mitigation in downlink heterogeneous networks
Authors: Hameed Atif , Yang Da-cheng , Wang Xian-ling , Zhang Weiwei
Published: December 2019

Heterogeneous network (HetNet) deployment comprising of high power macro nodes overlaid with pico nodes and various other types of low power nodes has been considered as one of the key enabling technology in 3GPP LTE-Advanced. HetNet can significantly enhance the capacity and coverage of cellular networks. However, severe inter-cell interference (ICI) between high power macro and low power pico nodes is a critical performance limiting factor for cell-edge users in HetNet. Coordinated multipoint transmission (CoMP) has been recognized as an effective technique to mitigate ICI in LTE-A. However, backhaul overhead and complexity are critical issues in CoMP. In this paper we propose a novel scheme that utilizes the benefits of HetNet to improve the system capacity and coverage. Moreover it exploits coordinated multi-point transmission to effectively mitigate ICI with reduced feedback overhead and complexity. In our scheme the users with high signal to interference plus noise ratio are served by the respective macro and pico cells. However, for users in high interference region, coordinated multi-point joint transmission is adopted to increase the radio signal strength and effectively mitigate ICI. The proposed scheme outperforms the conventional system with reduced backhaul overhead and complexity. System level simulations illustrate that the proposed scheme attains higher performance as compared to conventional schemes.
EDMA-based schemes for cognitive radio systems with channel state information
Authors: Salvo Rossi Pierluigi , Ciuonzo Domenico
Published: December 2019

In this paper we explore the possibility of using Energy-Division Multiple Access (EDMA) scheme for uplink communications in a cognitive radio context in order to allow transmission to unlicensed users overlapping with the primary user in both time and frequency domains. The proposed solution is energy consuming for unlicensed users, thus represents a viable solution when spectral efficiency and/or latency are more crucial than energy constraints. Simulation results in scenarios with Orthogonal Frequency Division Multiplexing (OFDM) transmissions, both uncoded and coded cases, are presented.
Design of a secure communication and handoff protocol for VANETs
Authors: Chen Chin-Ling , Kuo Tsung-Min , Shih Tzay-Farn
Published: December 2019

Vehicular communications have become an increasingly important communication technique worldwide. The current limitations of vehicular communications are not determined by capability or authentication but by security infrastructure. In 2005, a proposal for vehicular network security was discussed by Raya and Hubaux. However, such protocol is not practical and is unsafe for use in VANETs. In addition, handoff has become a relevant issue for vehicles moving from one region to another. For these reasons, we propose a secure communication and handoff protocol. In our protocol, a vehicle can enjoy seamless service between heterogeneous vehicular networks. Furthermore, vehicular communication is made more secure and ubiquitous.
Optical Distribution Channel: An Almost-All Optical LAN Based on the Field-coding Technique
Authors: Haas Zygmunt , Gitlin Richard D.
Published: December 2019

The very high-speed access requirement that characterizes interactive and real-time high-performance applications like parallel processing, compressed video, or high-quality imaging, initiated a considerable interest in networks that provide a single user with a very high-speed network access. Coupled with this effort is the belief that optical networking can provide very high speed access, in addition to already utilized large aggregated bandwidth. In this paper, we examine the possibility of harvesting the optical spectrum to provide high-speed access networking capability in local-area environment in a way that is economically justifiable. In particular, we describe a design of the physical layer of an “almost-all” optical local-area network that is capable of providing gigabit per second network access. The network design is based on the dual-bus topology, the field-coding technique that was reported by us earlier (in which the header and the data fields are encoded at different rates), and the principle of “almost-all” optical switching. The field-coding technique allows integration of several subnets on the same physical medium. Moreover, we show that because of the field-coding technique, the maximal number of stations on the bus before signal amplification is required is doubled in the limit. Furthermore, we discuss various implementation issues in the design of ODC, like opto-electronic amplification, clock distribution and clock-data synchronization, and reduction in the receiver dynamic range.