bluuebunny/crossref_metadata_2025 huggingface dataset:
Rational, emotional and normfollowing actors and liberal free trade in the Norwegian electricity market
Authors: Midttun Atle , Bakken Bent Erik , Wenstøp Fred
Published: December 2019

This article explores the implications of different behavioral assumptions for market outcomes. This is done by modeling emotionally and normatively oriented actors alongside the ‘rational’ economic ideal type in a system dynamics simulation of a free trade market. The simulation exercise has a concrete case focus, as the model incorporates stylized elements of the Norwegian electricity market, which is a free trade market with a large number of buyers and sellers. The article has three sections. The first section gives a short overview of the three ideal type actors and the behavioral assumptions behind them. The second section presents a simulation model of the Norwegian electricity market, a free trade market with more than 130 actors. One of the peculiarities of this market is its exposure to seasonal and yearly variations in rainfall, as Norwegian electricity production is almost exclusively hydropower based. This exogenously generated variation in production capacity creates distortions that trigger endogenous behavioral reactions in our model. The third section presents the results of the modeling exercise, showing that actor rationality does matter for price generation in a competitive market. Moving from a market dominated by calculative behavior towards a market dominated by emotional behavior causes greater volatility in market prices and more pronounced price cycles.
Supply chain control: trade-offs and system requirements
Authors: Leach N.P. , Makatsoris C. , Richards H.D.
Published: December 2019

This paper describes the underlying forces which drive change in manufacturing enterprises and supply chains. It sets out the complexities in modern capitalism and global economics and illustrates the trade-offs that can be made. IT systems which are required to assist improvements to both customer service and enterprise manufacturing performance are explained alluding to the special case for the semiconductor industry. Finally it shows how the new tools being developed with the ESPRIT project 20544, X-CITTIC, will satisfy the control needs for a virtual enterprise.
Technology management and international cooperation: several success stories
Authors: Filip F.G. , Alexandru Adriana , Socol Irina
Published: December 2019

Innovation processes represent a decisive factor for success in the severe competition of today. The cooperation with Central and Eastern Europe Countries gives significant opportunities and presents many challenges. This paper presents three case studies: (a) a series of EU-PECO projects on the use of Information Technology in renewable energy resources, (b) the cooperation in R&D between an EU-based innovative group and Romanian organizations, and (c) how the transition of a Romanian public R&D institution is influenced by its participation in European joint research projects. Each of the three cases has its own story told and comments made on it, which are quite explanatory to technology management issues and models.
General management: back to the future
Authors: Warner Malcolm , Witzel Morgen
Published: December 2019

This article examines the role and function of the general manager in the light of historical evidence which suggests that general management may be an integral part of the Western way of doing business. Although management as a discipline is relatively recent in origin, management as a function is probably as old as organised business itself. The paper suggests that the development of management as a function coincided with the rise of scientific thinking, leading to undue emphasis on scientific management; more recently the pendulum has swung back the other way, but there is a lack of consensus about both the nature of general management and the best way of developing general managers. The paper suggests that revisiting the principles of general mananagement as they developed historically can provide insights into the role and character of the general manager.
The successful adoption of groupware: perceptions of the users
Authors: Kline Theresa J.B. , Gardiner Helen
Published: December 2019

This study was conducted to allow the end-users of groupware systems to voice their opinions about the systems. Thirty one-on-one interviews were carried out with members of different organizations and who used different groupware systems. The qualitative data was analyzed and several consistent themes emerged in response to the questions we asked regarding the expectations of the system and the variables that fostered or hindered the successful adoption of the system. Results indicated that many expectations of the users had not been met by the system, and that the variables of enough training and technical support while in the initial stages of learning to use the systems were by far the most important in the adoption process.
Empirical assessment of ERP learning effects
Authors: Chen Kuanchin , Razi Muhammad , Tarn J. Michael
Published: December 2019

ERP-based business curriculum or inclusion of ERP components in some business courses is relatively new in high education. There are discussions in the literature about the pedagogical and epistemological issues surrounding today's business education. Examples of ERP-based framework for curriculum development in business education are also available in the literature. However, the literature is scarce in empirical assessments of different ERP teaching pedagogies and how they are related to student learning. This study provides a conceptual model and a framework for an empirical assessment of ERP learning effects. Relationships of three factors, attitude toward behavior, subjective norm and perceived behavioral control with the intention to learn ERP, are measured for two cognitive styles, intuition and analysis.
Extracting Signature Motifs from Promoter Sets of Differentially	Expressed Genes
Authors: Mitašiūnaitė Ieva , Rigotti Christophe , Schicklin Stéphane , Meyniel Laurène , Boulicaut Jean-François , Gandrillon Olivier
Published: December 2019

There is a critical need for new and efficient computational methods aimed at discovering putative transcription factor binding sites (TFBSs) in promoter sequences. Among the existing methods, two families can be distinguished: statistical or stochastic approaches, and combinatorial approaches. Here we focus on a complete approach incorporating a combinatorial exhaustive motif extraction, together with a statistical Twilight Zone Indicator (TZI), in two datasets: a positive set and a negative one, which represents the result of a classical differential expression experiment. Our approach relies on the existence of prior biological information in the form of two sets of promoters of differentially expressed genes. We describe the complete procedure used for extracting either exact or degenerated motifs, ranking these motifs, and finding their known related TFBSs. We exemplify this approach using two different sets of promoters. The first set consists in promoters of genes either repressed or not by the transforming form of the v-erbA oncogene. The second set consists in genes the expression of which varies between self-renewing and differentiating progenitors. The biological meaning of the found TFBSs is discussed and, for one TF, its biological involvement is demonstrated. This study therefore illustrates the power of using relevant biological information, in the form of a set of differentially expressed genes that is a classical outcome in most of transcriptomics studies. This allows to severely reduce the search space and to design an adapted statistical indicator. Taken together, this allows the biologist to concentrate on a small number of putatively interesting TFs.
Gene Set Enrichment Analyses Revealed Differences in Gene	Expression Patterns between Males and Females
Authors: Zhang Wei , Huang R. Stephanie , Duan Shiwei , Dolan M. Eileen
Published: December 2019

Men and women differ not only in their physical attributes and reproductive functions but also in many other characteristics, including the risks for some diseases as well as response to certain therapeutic treatments. Though genetically-identical for autosomal chromosomes, males and females could have gender-specific transcriptional or translational regulation, leading to differential mRNAs or protein products for some genes. To illustrate the gender-specific differences in mRNA-level expression, we compared gene expression patterns between males and females using a whole-genome microarray dataset on the unrelated HapMap lymphoblastoid cell lines derived from individuals of European (58 individuals) and African (59 individuals) ancestry. We applied the Gene Set Enrichment Analysis to identify any overrepresented predefined gene sets in either men or women. Distinct patterns of upregulation and downregulation of certain chromosomal regions and other gene sets such as targets for certain microRNAs and transcription factors were identified in males or females, suggesting their potential roles in defining the gender-specific phenotypes. Gender-specific patterns of gene expression also appeared to be different between these two populations.
Classification of Information Fusion Methods in Systems	Biology
Authors: Synnergren Jane , Olsson Björn , Gamalielsson Jonas
Published: December 2019

Biological systems are extremely complex and often involve thousands of interacting components. Despite all efforts, many complex biological systems are still poorly understood. However, over the past few years high-throughput technologies have generated large amounts of biological data, now requiring advanced bioinformatic algorithms for interpretation into valuable biological information. Due to these high-throughput technologies, the study of biological systems has evolved from focusing on single components (e.g. genes) to encompassing large sets of components (e.g. all genes in an entire genome), with the aim to elucidate their interdependences in various biological processes. In addition, there is also an increasing need for integrative analysis, where knowledge about the biological system is derived by data fusion, using heterogeneous data sets as input. We here review representative examples of bioinformatic methods for fusion-oriented interpretation of multiple heterogeneous biological data, and propose a classification into three categories of tasks that they address: data extraction, data integration and data fusion. The aim of this classification is to facilitate the exchange of methods between systems biology and other information fusion application areas.
Determinants for Psychrophilic and Thermophilic Features of	Metallopeptidases of the M4 Family
Authors: Khan Mahmud Tareq Hassan , Sylte Ingebrigt
Published: December 2019

Naturally occurring peptidases from organisms living under extreme conditions are adapted to function in environmental extremes, including temperature, salinity, pH, or pressure. These organisms represent unique sources for new bio-molecules that have both industrial and medicinal application. Adaptive strategies for functioning under extreme conditions are reflected at the enzyme sequence and structural level. Understanding the determinants responsible for unique functional features can be used to enhance the functional features of known proteins. In the present study, the amino acid sequences of 81 peptidases of the thermolysin (M4) family were analyzed for possible determinants of psychrophilic and thermophilic features, by comparing with thermolysin from Bacillus thermoproteolyticus, the prototype enzyme of the family. The analysis indicated that M4 peptidases from cold-adapted species have fewer arginines and more lysines, and also fewer tyrosines and more phenylalanines than the prototype thermolysin. However, the opposite was true for M4 peptidases from thermophilic species. For sequences from thermophilic species the ratio of the seven amino acids I,V,Y,W,R,E,L were correlated to optimal growth temperature.
Evolutionary Origin of the Tumor Suppressor Hyperplastic Discs	Protein
Authors: Omelyanchuk Leonid V. , Pertseva Julya A. , Saul John M.
Published: December 2019

Previous evolutionary study of the tumor suppressor Merlin revealed that this protein family was produced by very early metazoans with the exception of some or all flatworm lineages [Golovnina et al., 2005]. We ask whether other tumor-suppressor proteins had also been in existence in these times and focus our attention on Hyperplastic Discs (Hyd) protein, a classic tumor suppressor in Drosophila melanogaster which, when mutated, may cause over-proliferation and malignancy. Phylogenetic analysis of the Hyd protein indicates that it was present among metazoa by the time Trichoplax adhaerens had emerged from the common unicellular ancestor of the Animalia.
Assessment of the Evolutionary Origin and Possibility of	CRISPR-Cas (CASS) Interference Pathway in Vibrio cholerae O395
Authors: Chakraborty Sajib , Waise T.M. Zaved , Hassan Faizule , Kabir Yearul , Smith Mark A. , Arif Mohammad
Published: December 2019

Bacteria have developed several defense mechanisms against bacteriophages over evolutionary time, but the concept of prokaryotic RNA interference mediated defense mechanism against phages and other invading genetic elements has emerged only recently. Clustered regularly interspaced short palindromic repeats (CRISPR) together with closely associated genes (cas genes) constitute the CASS system that is believed to provide a RNAi-like defense mechanism against bacteriophages within the host bacterium. However, a CASS mediated RNAi-like pathway in enteric pathogens such as Vibrio cholerae O395 or Escherichia coli O157 have not been reported yet. This study specifically was designed to investigate the possibility and evolutionary origin of CASS mediated RNAi-like pathway in the genome of a set of enteric pathogens, especially V. cholerae. The results showed that V. cholerae O395 and also other related enteric pathogens have the essential CASS components (CRISPR and cas genes) to mediate a RNAi-like pathway. The functional domains of a V. cholerae Cas3 protein, which is believed to act as a prokaryotic Dicer, was revealed and compared with the domains of eukaryotic Dicer proteins. Extensive homology in several functional domains provides significant evidence that the Cas3 protein has the essential domains to play a vital role in RNAi like pathway in V. cholerae. The secondary structure of the pre-siRNA for V. cholerae O395 was determined and its thermodynamic stability also reinforced the previous findings and signifies the probability of a RNAi-like pathway in V. cholerae O395.
PlasmoID: A P. falciparum Information Discovery Tool
Authors: Rao Aditya , Yeleswarapu Sri Jyothsna , Raghavendra Gudladona , Srinivasan Rajgopal , Bulusu Gopalakrishnan
Published: December 2019

Plasmodium falciparum is the parasite responsible for more than 90% of deaths that occur due to malaria. Organization and mining of 'omic' (genomic, proteomic, transcriptomic, interactomic) data can improve our understanding of P. falciparum biology and help in the fight against malaria. PlasmoID (Plasmodium Information Discovery) is a tool developed for the dynamic exploration of the parasite's 'omic' landscape. Diverse computational and curated P. falciparum protein-protein interaction datasets, as well as binary relationships involving protein-small molecule entities, manually curated protein-protein relationships derived from the published literature and protein-protein interactions based on metabolic pathways are included in the PlasmoID database. The graphical user interface is designed as a plug-in to Cytoscape, an open-source network visualization tool. Important features of this plug-in include a synchronized tabular representation of any network loaded on the canvas, ability to find the shortest path between a pair of nodes in the database, search and expansion of entities from the database, and the ability to add new entities to the database through the interface. Malaria researchers can now seamlessly interrogate heterogeneous 'omic' datasets as well as add proprietary data to generate and visualize P. falciparum pathway and cell process network models. PlasmoID can be downloaded from http://pfalciparum.atc.tcs.com/PlasmoID.
Prediction of Proteins Putatively Involved in the Thiol: Disulfide	Redox Metabolism of a Bacterium (Listeria): The CXXC Motif as Query Sequence
Authors: Gopal Shubha , Srinivas Vanishree , Zameer Farhan , Kreft Jürgen
Published: December 2019

Thiol:disulfide redox metabolism (TDRM) is a central metabolic network in all living cells. However, numerous proteins with different biochemical functions and several structural domains are involved, making it not trivial to identify and annotate its constituents in sequenced genomes. We developed an uncomplicated approach to solve the problem using existing web-based tools and public databases with the gram-positive bacterium Listeria monocytogenes EGD-e as a model organism. A pattern search for the Cys-Xaa-Xaa-Cys (CXXC) motif – a hallmark of TDRM proteins – in the genome sequence of the bacterium yielded 156 proteins. After initial refinement by protein and domain analysis, 14 candidate proteins remained. Subsequent detailed analyses, supported by modeling of 3D structures and data integration yielded 6 thioredoxin-like proteins plus thioredoxin reductase, glutaredoxin, one redox-sensitive regulator, one peptide methionine reductase – all typical TDRM constituents – and three putative novel components of the TDRM. For all 14 proteins orthologues were found in other Listeria species. Homology searches and phylogenetic analyses showed that related proteins are present mainly in other Firmicutes. This fast approach required minimal resources. It is immediately applicable to any genome with appropriate modifications and should be practicable also for other conserved, functionally important amino acid motifs.
In silico Analysis of T-bet Activity in	Peripheral Blood Mononuclear Cells in Patients with Inflammatory Bowel Disease (IBD)
Authors: Fernandez-Becker Nielsen Q. , Moss Alan C.
Published: December 2019

T-bet (TBX21) is a transcription factor that regulates T-cell differentiation, and has recently been implicated in the pathogenesis of Crohn's disease (CD). The regulatory networks through which T-bet affects immune function are unknown.

An NCBI gene expression profile from patients with CD and controls was analyzed. T-bet transcription factor binding sites and promoter modules were identified using promoter analysis software. Functional correlations between T-bet-containing promoters were determined using data mining and ontological analysis.

T-bet expression in CD peripheral blood mononuclear cells (PBMCs) (n=59) was significantly reduced compared to control (n=42) (p<0.0001) and ulcerative colitis PBMCs (n=26), (p=0.005). The promoter regions of all genes differentially-expressed in CD were probed for T-bet Transcription Factor Binding Sites (TFBSs). Twenty-three genes contained transcription-factor binding sites for T-bet; 8 were down-regulated, and 15 were up-regulated in CD-PBMCs. Three genes (S100A16, ABHD3 and EZH1) that were down-regulated in CD-PBMCs contained a complex promoter module consisting of T-bet and EGRF transcription-factor binding sites. Ontological analysis revealed that a significant number of differentially-expressed genes that contain T-bet binding sites are involved in innate immunity (8 genes, Z-score 4.11) and signal transduction (5 genes, Z-score 2.65).

This combination of gene expression datasets and promoter analysis has identified a network of genes that contain simple T-bet binding sites, and complex T-bet promoter modules, in their promoter regions. These results implicate a mechanism through which T-bet may influence innate immunity in CD.
sRNAbase: A Web Resource for Small RNAs in	Enterobacteriaceae\m{1}
Authors: Sathesh-Kumar Sivasankaran , Sridhar Jayavel , Rafi Ziauddin Ahamed
Published: December 2019

Bacterial small RNAs (sRNAs) have gained considerable attention due to their multivalent roles in the survival and pathogenesis of bacteria and mostly identified through bio-computational methods. A manually curated web-resource, sRNAbase has been constructed to give comprehensive and exhaustive information on non-coding small RNAs excluding tRNAs and rRNAs in Enterobacteriaceae family. The sRNA entries curated in sRNAbase contain experimentally verified small RNAs available in the literature and their partial/non-homologs reported within the related genomes from our earlier studies. The sRNAbase aims to facilitate the scientific community by providing information on the physical genomic location of the non-coding small RNAs, its alias names, sequences, strand orientation, gene identification numbers of the conserved genes that sandwiches the particular sRNA with possible functional role and a link to the PubMed literatures. Currently, sRNAbase holding information on 1986 entries belongs to 80 sRNA families spread over 45 Enterobacteriaceae genomes. The sRNAbase is accessible on the web at http://bicmku.in:8081/srnabase/.
Evolution of Regulatory Motifs of Bacterial Transcription	Factors
Authors: Gorbunov Konstantin Y. , Laikova Olga N. , Rodionov Dmitry A. , Gelfand Mikhail S. , Lyubetsky Vassily A.
Published: December 2019

Unlike evolution of genes and proteins, evolution of regulatory systems is a relatively new area of research. In particular, little systematic study has been done on evolution of DNA binding motifs in transcription factor families. We suggest an algorithm that reconstructs the most parsimonious scenario for changes in DNA binding motifs along an evolutionary tree of transcription factor binding sites. The algorithm was validated on several artificial datasets and then applied to reconstruct the evolutionary history of the NrdR, MntR, LacI, FNR, Irr, Fur and Rrf2 transcription factor families. The algorithm seems to be sufficiently robust to be applicable in realistic situations. In most transcription factor families the changes in binding motifs are limited to several branches. Changes in consensus nucleotides proceed via an intermediate stage when the respective position is not conserved.
A Comparison of Database Systems for XML-Type Data
Authors: Risse Judith E. , Leunissen Jack A.M.
Published: December 2019

Background: In the field of bioinformatics interchangeable data formats based on XML are widely used. XML-type data is also at the core of most web services. With the increasing amount of data stored in XML comes the need for storing and accessing the data. In this paper we analyse the suitability of different database systems for storing and querying large datasets in general and Medline in particular.

Results: All reviewed database systems perform well when tested with small to medium sized datasets, however when the full Medline dataset is queried a large variation in query times is observed.

Conclusions: There is not one system that is vastly superior to the others in this comparison and, depending on the database size and the query requirements, different systems are most suitable. The best all-round solution is the Oracle 11~g database system using the new binary storage option. Alias-i's Lingpipe is a more lightweight, customizable and sufficiently fast solution. It does however require more initial configuration steps. For data with a changing XML structure Sedna and BaseX as native XML database systems or MySQL with an XML-type column are suitable.
Theory and practice in visual interfaces for semi-structured document discovery and selection
Authors: Loizides Fernando , Buchanan George , Mavri Keti
Published: December 2019

With the increase in electronic publications, and indeed the availability of existing publications in digital form, as well as the encouragement of open access publication, comes a challenge. That challenge is to create assistive software to aid in the discovery and selection of relevant documents to one’s information need. Visual interfaces have begun to address the need of information seekers in finding publications and wading through the large result sets that are returned from search engines. There is currently, little evidence to suggest that these interfaces are based on systematic research on requirements. In this article, we examine areas which contribute to the theory and practice of visual interfaces directly relating to the discovery and selection of publications. We bring together work from different fields in a targeted approach to assist the future creation of these interfaces.
Optimizing parallelism for nested loops with iterational and instructional retiming
Authors: Xue Chun Jason , Shao Zili , Liu MeiLin , Qiu Mei Kang , Sha Edwin H.-M.
Published: December 2019

Embedded systems have strict timing and code size requirements. Retiming is one of the most important optimization techniques to improve the execution time of loops by increasing the parallelism among successive loop iterations. Traditionally, retiming has been applied at instruction level to reduce cycle period for single loops. While multi-dimensional (MD) retiming can explore the outer loop parallelism, it introduces large overheads in loop index generation and code size due to loop transformation. In this paper, we propose a novel approach, that combines iterational retiming with instructional retiming to satisfy any given timing constraint by achieving full parallelism for iterations in a partition with minimal code size. The experimental results show that combining iterational retiming and instructional retiming, we can achieve 37% code size reduction comparing to applying iteration retiming alone.
A framework for managing the life-cycle of event-driven, embedded applications
Authors: Reason Johnathan M. , Chen Han , Jung ChangWoo , Kim SooYeon , Chou Paul B. , Lee KangYoon
Published: December 2019

Event-driven, embedded applications that embody the composition of many disparate components are emerging as an important class of pervasive applications. Realizing such applications often requires a breadth of expertise across many disciplines; consequently, managing the life cycle for this class of applications can be a very complex, time-intensive process. In this paper, we present a framework that eases the complexity of managing the life cycle of event-driven, embedded applications. We call this framework Rapid Integrated Solution Enablement or RISE. For solution creation, component composition and software reuse are two central concepts of RISE. Solutions in RISE are graphically composed from reusable components using a visual editor. For deployment and management of solutions, we exploit the concept of dynamic and remote deployment of components from the Open Service Gateway Initiative (OSGi). We describe the RISE architecture and discuss our prototype implementation, which follows the model-driven methodology and leverages open source technologies, such as Eclipse. Additionally, we illustrate the efficacy of RISE with an example solution for RFID supply chain logistics.
Energy minimization for heterogeneous wireless sensor networks
Authors: Qiu Meikang , Xue Chun , Shao Zili , Liu Meilin , Sha Edwin H.-M.
Published: December 2019

Lifetime is very important to wireless sensor networks since most sensors are equipped with non-rechargeable batteries. Therefore, energy and delay are critical issues for the research of sensor networks that have limited lifetime. Due to the uncertainties in execution time of some tasks, this paper models each varied execution time as a probabilistic random variable with the consideration of applications’ performance requirements to solve the MAP (Mode Assignment with Probability) problem. Using probabilistic design, we propose an optimal algorithm to minimize the total energy consumption while satisfying the timing constraint with a guaranteed confidence probability. The experimental results show that our approach achieves significant energy saving than previous work. For example, our algorithm achieves an average improvement of 32.6% on total energy consumption.
Asymmetry-aware link layer services in wireless sensor networks
Authors: Du Junzhao , Shi Weisong , Sha Kewei
Published: December 2019

Recent studies in wireless sensor networks (WSNs) have observed that the irregular link quality is a common phenomenon, rather than an anomaly. The irregular link quality, especially link asymmetry, has significant impacts on the design of WSN protocols. In this paper, we propose two asymmetry-aware link layer services, including the neighborhood link quality service (NLQS) and the link relay service (LRS). The novelty of the NLQS service is taking the link asymmetry into consideration, providing timeliness link quality and distinguishing the inbound and outbound neighbors with the support of LRS, which builds a relay framework to alleviate the effects of link asymmetry. To demonstrate the proposed link layer service, we design and implement two example applications, building the shortest-hop routing path (SHRT) and the best path reliability routing path (BRRT), on the TinyOS platform. We found that the performance of two example applications is improved substantially. More than 40% of nodes identify more outbound neighbors and the percentage of increased outbound neighbors is between 14% and 100%. In SHRT, more than 15% of nodes reduce hops of the routing path and the percentage of reduced hops is between 14% and 100%. In BRRT, more than 16% of nodes improve the path reliability of the routing path and the percentage of the improved path reliability is between 2% to 50%.
Online energy-saving algorithm for sensor networks in dynamic changing environments
Authors: Qiu Meikang , Chen Min , Liu Meiqin , Liu Shaobo , Li Jiayin , Liu Xue , Zhu Yongxin
Published: December 2019

How to save energy is a critical issue for the life time of sensor networks. Under continuously changing environments, sensor nodes have varying sampling rates. In this paper, we present an online algorithm to minimize the total energy consumption while satisfying sampling rate with guaranteed probability. We model the sampling rate as a random variable, which is estimated over a finite time window. An efficient algorithm, EOSP (Energy-aware Online algorithm to satisfy Sampling rates with guaranteed Probability), is proposed. Our approach can adapt the architecture accordingly to save energy. Experimental results demonstrate the effectiveness of our approach.
Combined effects of structure and partial saturation in natural soils
Authors: Pereira Jean-Michel , Rouainia Mohamed , Manzanal Diego
Published: December 2019

The mechanical behaviour of natural clays is significantly affected by their in situ or initial structure in the form of cementation or interparticle bonding. This behaviour can differ substantially from the behaviour of reconstituted clays. Suction as well as plastic volumetric strains drive isotropic hardening/softening as this is a simple way to account for the phenomenon of volumetric collapse upon wetting and the stiffening effect that suction has on the soil skeletal response. A model that combines unsaturated and structured behavior is presented and then used to simulate stress strain behaviour observed for an unsaturated natural clay subjected to isotropic load paths. A parametric analysis is performed to observe the influence suction hardening has on mobilized strengths. It is also shown that the model can predict the maximum of collapse of unsaturated soils.
Consolidation of unsaturated lumpy clays
Authors: Salimzadeh Saeed , Khalili Nasser
Published: December 2019

Coupled flow-deformation analysis of consolidation in unsaturated lumpy clays is presented. The governing differential equations are discretised using the Galerkin method and the finite difference technique for space and time, respectively. Particular attention is given to the cross coupling coefficients arising from the pore scale deformation compatibility between micro and macro voids. Two examples are analysed: a one-dimensional soil column, and a strip footing acting on a two-dimensional medium of lumpy clay. A range of sensitivity analyses are preformed using different values of degree of saturation and volume fraction of macro voids. All results are carefully analysed and salient features of consolation in lumpy clays are highlighted. The significance of the cross coupling coefficients in the numerical results obtained are also examined.
Suction effects on the residual shear strength of clays
Authors: Romero Enrique , Vaunat Jean , Merchán Vladimir
Published: December 2019

The paper presents an experimental study on the residual shear strength of different clayey soils at varying total suctions. In a first part of the paper some insight into the behaviour of residual shear strength of a filled rock discontinuity is presented to bring into light the sensitivity to hydraulic states of a clayey gouge material subjected to shearing along large displacements. An adapted Bromhead ring shear apparatus, in which the sample is enclosed in a controlled relative humidity chamber, has been used to control total suction during shearing. Afterwards, results on different types of clayey materials are presented to discuss the importance of the plasticity of the clay on the residual friction angle changes. These changes show an important increase in the residual friction angle with imposed total suction that may reach 15° for medium plastic clay and without cohesion component. The reasons for this increase have been explained by the more granular character of the dry clay as a result of aggregate densification and desaturation during strong drying. The changes have been interpreted using a simple model inspired in both macroscopic and microstructural observations, which is based on the stiffness of the soil (or aggregates) and depends on the product of the total suction applied and the degree of saturation. A microstructural model, already developed to take into account microstructural aspects on water retention and following an equivalent behavioural response to the macroscopic shrinkage curve, has been used to estimate the degree of saturation at the microstructural level (inside aggregates). To highlight its applicability in geotechnical practice, the different parameters used in the water retention and residual shear strength models have been shown to depend on the plasticity index of the different clayey soils studied.
Assessment of Chloroquine Treatment for Modulating Autophagy Flux in Brain of WT and HD Mice
Authors: Vodicka Petr , Lim Junghyun , Williams Dana T. , Kegel Kimberly B. , Chase Kathryn , Park Hyunsun , Marchionini Deanna , Wilkinson Stephen , Mead Tania , Birch Helen , Yates Dawn , Lyons Kathy , Dominguez Celia , Beconi Maria , Yue Zhenyu , Aronin Neil , DiFiglia Marian
Published: December 2019

Background: Increasing mutant huntingtin (mHTT) clearance through the autophagy pathway may be a way to treat Huntington's disease (HD). Tools to manipulate and measure autophagy flux in brain in vivo are not well established. Objective: To examine the in vivo pharmacokinetics and pharmacodynamics of the lysosomal inhibitor chloroquine (CQ) and the levels of selected autophagy markers to determine usefulness of CQ as a tool to study autophagy flux in brain. Methods: Intraperitoneal injections of CQ were administered to WT and HDQ175/Q175 mice. CQ levels were measured by LC-MS/MS in WT brain, muscle and blood at 4 to 24 hours after the last dose. Two methods of tissue preparation were used to detect by Western blot levels of the macroautophagy markers LC3II and p62, the chaperone mediated autophagy receptor LAMP-2A and the late endosome/lysosomal marker RAB7. Results: Following peripheral administration, CQ levels were highest in muscle and declined rapidly between 4 and 24 hours. In the brain, CQ levels were greater in the cortex than striatum, and levels persisted up to 24 hours post-injection. CQ treatment induced changes in LC3II and p62 that were variable across regions and tissue preparations. HDQ175/Q175 mice exposed to CQ had variable but diminished levels of LC3II, p62 and LAMP-2A, and increased levels of RAB7. Higher levels of mHTT were found in the membrane compartment of CQ treated HD mice. Conclusion: Our findings suggest that the response of brain to CQ treatment, a blocker of autophagy flux, is variable and not as robust as it has been demonstrated in vitro, suggesting that CQ treatment has limitations for modulating autophagy flux in vivo. Alternative methods, compounds, and technologies need to be developed to further investigate autophagy flux in vivo, especially in the brain.
Energy-efficiency of protected IP-over-WDM networks with sleep-mode devices
Authors: Musumeci Francesco , Tornatore Massimo , Lopez Vizcaino Jorge , Ye Yabin , Pattavina Achille
Published: December 2019

Recently, the need for energy-efficient and sustainable capacity growth has become stringent for telecommunication networks and great efforts have been produced to reduce their power consumption. Optical technologies based on Wavelength Division Multiplexing are well-recognized as a promising solution for greening the future Internet. One relevant approach to achieve such power savings consists in aggregating traffic flows in few network links, so that power can be saved by switching-off some unused network devices. However, the need to ensure network resiliency against link and/or node failures imposes that still the resources reserved to protect connections become available immediately after a failure occurs. Therefore, a possible solution is to set some devices into low-power sleep-mode, so that they can be rapidly re-activated and provide fast connection recovery.

In this paper we focus on the power-efficiency of protected IP-over-WDM networks and provide a comprehensive comparison of four different protection strategies, namely Shared-Link, Shared-Path, Dedicated-Link and Dedicated-Path Protection (SLP, SPP, DLP and DPP respectively) in a sleep-mode scenario. In the proposed design strategies we assume that low-power sleep-mode is enabled for devices used for protection. Mathematical models for a power-aware design with sleep-mode is proposed for the four protection strategies. We show that relevant power savings (up to about 60%) can be obtained for all the protection strategies by setting protection devices into sleep-mode.
Scalable and energy-efficient packet switches based on multi-granular forwarding operations
Authors: Testa Patrizia , Germoni Angelo , Listanti Marco
Published: December 2019

Telecommunication networks are evolving due to rapid growth of internet traffic and the necessity to satisfy the new requirements of emerging packet services. Upgrading of network devices so as they can allow scalable and full line rate traffic aggregation and eliminate any internal performance bottlenecks is crucial. In packet switching devices, since data plane functionalities need to be executed for each incoming packet and power per given bandwidth is strongly related to the amount of processing on this data, packet processing at ultra-high rate is becoming the major challenge. The main trend to address such power consumption and scalability issues is to bypass packet switches by switching traffic at lower layers. This results in the packet optical transport network approach, where packet switching provides flexible end-to-end connectivity based on tunnel encapsulation while wavelength switching, exploiting optical bypass, allows reducing electrical switch size at transit nodes. There are also opportunities consisting in simplifying packet switch functionalities or designing completely different packet switch architectures. In this paper a new Ethernet aggregation and switching solution with potentialities to simplify and scale Ethernet switch forwarding functionality is proposed. This solution, based on a burst-basis transmission compliant with the Ethernet Standard, is able to maintain flexibility and any to any connectivity deriving from the connectionless nature of Ethernet. At the same time, it provides Ethernet technology with efficient aggregation capabilities allowing to reduce processing of transit traffic. This is allowed thanks to an Ethernet burst structure conceived as a variable number of consecutive frames of the same connection preceded by a proprietary burst control frame carrying information necessary for burst data frames classification. As a result, burst control frames experience the conventional Ethernet switch packet processing while data frames are mapped on the corresponding queue/output port according to the result of control frames classification. The proposed solution also provides the possibility to recognize data frames of the same burst through a proprietary inter-frame gap inserted among them; that allows to dynamically adapt burst size to the available bandwidth at transit nodes in order to limit frame delay and jitter and to support intermediate grooming. These features make it a very competitive approach in the context of packet optical transport being able to support dynamic multi-granular switching. The proposed solution has been validated by estimating its efficiency in terms of energy consumption with respect to a commercial packet switch. The impact of burst transmission on packet delay and jitter across ring and mesh networks has been also evaluated through different sets of simulations.
Digital subcarrier optical networks and cross-connects
Authors: Hui Rongqing , Huang Wanjun , Zhang Yuanyuan , Hameed Mahmood , Razo Miguel , Tacca Marco , Fumagalli Andrea
Published: December 2019

This paper describes a rate flexible network transport solution to achieve sub-wavelength circuit provisioning between edge node pairs. Sub-wavelength circuits are obtained by concatenating spectrally efficient digital subcarrier channels along the network path, with each subcarrier frequency carrying only a fraction of the wavelength bandwidth. By reserving one or more such subcarrier frequencies along a path connecting two edge nodes, a dedicated end-to-end sub-wavelength circuit is provisioned. At an intermediate node, incoming frequencies are switched to outgoing frequencies via a cross-bar electronic circuit switch or cross-connect. By performing digital subcarrier multiplexing (DSCM) using CMOS based advanced digital signal processing (DSP) algorithms, spectral guard-bands between adjacent channels are not necessary, thus yielding good bandwidth efficiency when multiplexing multiple subcarrier channels onto the same wavelength.

Compared to current TDM based transport network solutions, e.g., OTN/SONET/SDH, the described solution offers the unique advantage of implementing two key transport functionalities in the same DSP system, which is capable of (1) performing compensation of fiber transmission impairments in the electronic domain to ensure good signal integrity, and (2) multiplexing (demultiplexing) subcarrier channels after (before) add/drop and switching circuit operations. Because of this design advantage, system complexity and fabrication of the network equipment are ameliorated, possibly leading to tangible cost and electric power consumption reductions.
Fuzzy logic optimized wireless sensor network routing protocol
Authors: Izadi Davood , Abawajy Jemal , Ghanavati Sara
Published: December 2019

Wireless sensor networks (WSNs) are used in health monitoring, tracking and security applications. Such networks transfer data from specific areas to a nominated destination. In the network, each sensor node acts as a routing element for other sensor nodes during the transmission of data. This can increase energy consumption of the sensor node. In this paper, we propose a routing protocol for improving network lifetime and performance. The proposed protocol uses type-2 fuzzy logic to minimize the effects of uncertainty produced by the environmental noise. Simulation results show that the proposed protocol performs better than a recently developed routing protocol in terms of extending network lifetime and saving energy and also reducing data packet lost.
Analyzing job completion reliability and job energy consumption for a general MapReduce infrastructure
Authors: Lin Jia-Chun , Leu Fang-Yie , Chen Ying-ping
Published: December 2019

Recently, MapReduce has been a popular distributed programming framework, which divides a job into map tasks and reduce tasks and executes these tasks in parallel over a large-scale MapReduce cluster to speed up job execution. Generally, the cluster is a master-slave infrastructure. To prevent jobs from being interrupted due to node failure, current MapReduce implementations, such as Hadoop, adopt a task-reexecution policy on the slave side, i.e., when a slave node due to failure cannot complete a task, this task will be reassigned to another available slave for reexecution. However, on the master side by default, no redundancy scheme is provided. Since this type of infrastructure has been worldwide adopted, we call it the general MapReduce infrastructure (GMI). To achieve a more reliable and energy-efficient working environment, understanding the impact of GMI on its job completion reliability (JCR) and job energy consumption (JEC) is required. In this paper, we base on a Poisson distribution to analyze GMI's JCR from a single-job perspective. After that, we accordingly derive the corresponding JEC. Through the analytical results, MapReduce managers can comprehend how GMI behaves and how their MapReduce can be improved so as to achieve a more reliable and energy-efficient MapReduce environment.
Fuzzy based scheduling technique for multiple service flows in 802.16 WiMAX
Authors: Gopalan M. , Marthandan G. , Eswaran C.
Published: December 2019

In IEEE 802.16 WiMAX, it is a challenging task to achieve quality of service (QoS) by using scheduling technique as it requires understanding the traffic features and service requirements. Also most of existing works have considered only one of the service flows among rtPS, ertPS, nrtPS, UGS and BE. In addition, the existing priority estimation methods are not so accurate. To overcome these problems, in this paper, we propose a fuzzy based scheduling technique for multiple service flows in IEEE 802.16 WiMAX networks. This technique involves two entities namely evaluator and slot allocator. When the service flow enters into the network, the evaluator distinguishes the service flow as real time or non real time and estimates its priority using fuzzy logic technique. Then the evaluator arranges the real time and non real time service flows in two sub queues and then sorts them by their priority levels. The slot allocator obtains the priority information of service flows from the evaluator to allocate slots. By simulation results, we show that the proposed approach is better in terms of the measured channel utilization and received bandwidth for real-time and non real time flows.