Full Replication Research Articles

A routing and wavelength assignment scheme considering full optical carrier replication in multi-carrier-distributed optical mesh networks with wavelength reuse

This paper proposes a routing and wavelength assignment (RWA) scheme that considers full optical carrier replication to minimize the number of required wavelengths for wavelength-reusable multi-carrier-distributed (WRMD) mesh networks. Unlike the conventional wavelength division multiplexing networks where each node contains multiple laser diodes, the WRMD networks use a light source, called the multi-carrier light source, to ease the difficulty of controlling many light source devices. The optical carrier replication at any node of optical carrier or any end node of lightpath, called full optical carrier replication, improves the performance of the conventional schemes, which do not consider full optical carrier replication. This paper first formulates the RWA problem considering full optical carrier replication as an integer linear programming problem that minimizes the number of required wavelengths to satisfy the given lightpath setup requests. A heuristic RWA scheme is then proposed to solve the RWA problem in practical times. Simulation results show that our proposed heuristic RWA scheme for the WRMD network achieves a near-optimum number of wavelengths. In addition, it is able to reduce the number of required wavelengths for lightpath establishment, compared to the conventional scheme.

Toward General Software Level Silent Data Corruption Detection for Parallel Applications

Silent data corruption (SDC) poses a great challenge for high-performance computing (HPC) applications as we move to extreme-scale systems. Mechanisms have been proposed that are able to detect SDC in HPC applications by using the peculiarities of the data (more specifically, its “smoothness” in time and space) to make predictions. However, these data-analytic solutions are still far from fully protecting applications to a level comparable with more expensive solutions such as full replication. In this work, we propose partial replication to overcome this limitation. More specifically, we have observed that not all processes of an MPI application experience the same level of data variability at exactly the same time. Thus, we can smartly choose and replicate only those processes for which the lightweight data-analytic detectors would perform poorly. In addition, we propose a new evaluation method based on the probability that a corruption will pass unnoticed by a particular detector (instead of just reporting overall single-bit precision and recall). In our experiments, we use four applications dealing with different explosions. Our results indicate that our new approach can protect the MPI applications analyzed with 7-70 percent less overhead (depending on the application) than that of full duplication with similar detection recall.

Human Herpesvirus 8 Infects and Replicates in Langerhans Cells and Interstitial Dermal Dendritic Cells and Impairs Their Function.

ABSTRACTThe predominant types of dendritic cells (DC) in the skin and mucosa are Langerhans cells (LC) and interstitial dermal DC (iDDC). LC and iDDC process cutaneous antigens and migrate out of the skin and mucosa to the draining lymph nodes to present antigens to T and B cells. Because of the strategic location of LC and iDDC and the ability of these cells to capture and process pathogens, we hypothesized that they could be infected with human herpesvirus 8 (HHV-8) (Kaposi's sarcoma [KS]-associated herpesvirus) and have an important role in the development of KS. We have previously shown that HHV-8 enters monocyte-derived dendritic cells (MDDC) through DC-SIGN, resulting in nonproductive infection. Here we show that LC and iDDC generated from pluripotent cord blood CD34+ cell precursors support productive infection with HHV-8. Anti-DC-SIGN monoclonal antibody (MAb) inhibited HHV-8 infection of iDDC, as shown by low expression levels of viral proteins and DNA. In contrast, blocking of both langerin and the receptor protein tyrosine kinase ephrin A2 was required to inhibit HHV-8 infection of LC. Infection with HHV-8 did not alter the cell surface expression of langerin on LC but downregulated the expression of DC-SIGN on iDDC, as we previously reported for MDDC. HHV-8-infected LC and iDDC had a reduced ability to stimulate allogeneic CD4+ T cells in the mixed-lymphocyte reaction. These results indicate that HHV-8 can target both LC and iDDC for productive infection via different receptors and alter their function, supporting their potential role in HHV-8 pathogenesis and KS.IMPORTANCE Here we show that HHV-8, a DNA tumor virus that causes Kaposi's sarcoma, infects three types of dendritic cells: monocyte-derived dendritic cells, Langerhans cells, and interstitial dermal dendritic cells. We show that different receptors are used by this virus to infect these cells. DC-SIGN is a major receptor for infection of both monocyte-derived dendritic cells and interstitial dermal dendritic cells, yet the virus fully replicates only in the latter. HHV-8 uses langerin and the ephrin A2 receptor to infect Langerhans cells, which support full HHV-8 lytic replication. This infection of Langerhans cells and interstitial dermal dendritic cells results in an impaired ability to stimulate CD4+ helper T cell responses. Taken together, our data show that HHV-8 utilizes alternate receptors to differentially infect and replicate in these tissue-resident DC and support the hypothesis that these cells play an important role in HHV-8 infection and pathogenesis.

Role of Cell-Penetrating Peptides in Intracellular Delivery of Peptide Nucleic Acids Targeting Hepadnaviral Replication.

Peptide nucleic acids (PNAs) are potentially attractive antisense agents against hepatitis B virus (HBV), although poor cellular uptake limits their therapeutic application. In the duck HBV (DHBV) model, we evaluated different cell-penetrating peptides (CPPs) for delivery to hepatocytes of a PNA-targeting hepadnaviral encapsidation signal (ε). This anti-ε PNA exhibited sequence-specific inhibition of DHBV RT in a cell-free system. Investigation of the best in vivo route of delivery of PNA conjugated to (D-Arg)8 (P1) showed that intraperitoneal injection to ducklings was ineffective, whereas intravenously (i.v.) injected fluorescein-P1-PNA reached the hepatocytes. Treatment of virus carriers with i.v.-administered P1-PNA resulted in a decrease in viral DNA compared to untreated controls. Surprisingly, a similar inhibition of viral replication was observed in vivo as well as in vitro in primary hepatocyte cultures for a control 2 nt mismatched PNA conjugated to P1. By contrast, the same PNA coupled to (D-Lys)4 (P2) inhibited DHBV replication in a sequence-specific manner. Interestingly, only P1, but not P2, displayed anti-DHBV activity in the absence of PNA cargo. Hence, we provide new evidence that CPP-PNA conjugates inhibit DHBV replication following low-dose administration. Importantly, our results demonstrate the key role of CPPs used as vehicles in antiviral specificity of CPP-PNA conjugates.

Optimizing cost for geo-distributed storage systems in online social networks

Globally distributed data centers provide an opportunity to deploy geo-distributed Online Social Networks (OSNs). For so big data generated by users, how to store them among those data centers is a key issue in the geo-distributed storage system. Today's popular OSN providers store users’ data in each deployed data center, so as to guarantee access latency. However, the full replication manner brings relatively high storage cost and traffic cost, which extremely increases the economic expenditure of OSN providers. Data placement based on social graph partitioning is an efficient way to minimize cost, but it requires the information of entire social graph and cannot fully guarantee latency. Recently, accomplished by partitioning replication is proposed to optimize cost as well as guarantee latency, but it has two drawbacks: (1) the separated manners of optimization cannot efficiently reduce the cost; (2) the placement of master replicas and slave replicas influence each other, and eventually reduces the optimization effects. In this paper, we explore an integrated manner of optimizing partitioning and replication simultaneously without distinguishing replica's role. We propose a lightweight replica placement (LRP) scheme, which conducts optimizations in a distributed manner and is well adapted to dynamic scenarios. Evaluations with two datasets from Twitter and Facebook show that LRP significantly reduces the cost compared with state-of-the-art schemes.

Reproducibility of studies on text mining for citation screening in systematic reviews: Evaluation and checklist

ContextIndependent validation of published scientific results through study replication is a pre-condition for accepting the validity of such results. In computation research, full replication is often unrealistic for independent results validation, therefore, study reproduction has been justified as the minimum acceptable standard to evaluate the validity of scientific claims. The application of text mining techniques to citation screening in the context of systematic literature reviews is a relatively young and growing computational field with high relevance for software engineering, medical research and other fields. However, there is little work so far on reproduction studies in the field. ObjectiveIn this paper, we investigate the reproducibility of studies in this area based on information contained in published articles and we propose reporting guidelines that could improve reproducibility. MethodsThe study was approached in two ways. Initially we attempted to reproduce results from six studies, which were based on the same raw dataset. Then, based on this experience, we identified steps considered essential to successful reproduction of text mining experiments and characterized them to measure how reproducible is a study given the information provided on these steps. 33 articles were systematically assessed for reproducibility using this approach. ResultsOur work revealed that it is currently difficult if not impossible to independently reproduce the results published in any of the studies investigated. The lack of information about the datasets used limits reproducibility of about 80% of the studies assessed. Also, information about the machine learning algorithms is inadequate in about 27% of the papers. On the plus side, the third party software tools used are mostly free and available. ConclusionsThe reproducibility potential of most of the studies can be significantly improved if more attention is paid to information provided on the datasets used, how they were partitioned and utilized, and how any randomization was controlled. We introduce a checklist of information that needs to be provided in order to ensure that a published study can be reproduced.

Bayesian D-optimal screening experiments with partial replication

Screening designs are frequently used in the initial stages of experimentation with the goal of identifying important main effects as well as to gain insight on potentially important two-factor interactions. Commonly utilized experimental designs for screening are unreplicated and as such, provide no unbiased estimate of experimental error. However, if statistical inference is to be performed as part of the experimental analysis, one view is that inferential procedures should be performed using a model independent error estimate instead of the residual mean square from the fitted model. As full replication of an experiment may be quite costly, partial replication offers an alternative. Gilmour and Trinca (2012) introduce criteria for constructing optimal designs for statistical inference (and hence, provide for optimal selection of replicate design points). An extension of their work is introduced by modifying the popular Bayesian D-optimality criterion to construct partially replicated screening designs with less dependence on an assumed model. Designs are compared using various criteria and a simulation study is conducted to investigate design performance with respect to power and false discovery rates.

Causal consistency algorithms for partially replicated and fully replicated systems

Data replication is commonly used for fault-tolerance in reliable distributed systems. In large-scale systems, it additionally provides low latency. Recently, causal consistency in such systems has received much attention. However, existing works assume the data is fully replicated. This greatly simplifies the design of the algorithms to implement causal consistency. In this paper, we propose that it can be advantageous to have partial replication of data, and we propose two algorithms for achieving causal consistency in such systems where the data is only partially replicated. This work provides the first evidence that explores causal consistency for partially replicated distributed systems. We also give a special case algorithm for causal consistency in the full-replication case. We give simulation results to show the performance of our algorithms, and to present the advantage of partial replication over full replication.

Nuclear localization and secretion competence are conserved among henipavirus matrix proteins.

Viruses of the genus Henipavirus of the family Paramyxoviridae are zoonotic pathogens, which have emerged in Southeast Asia, Australia and Africa. Nipah virus (NiV) and Hendra virus are highly virulent pathogens transmitted from bats to animals and humans, while the henipavirus Cedar virus seems to be non-pathogenic in infection studies. The full replication cycle of the Paramyxoviridae occurs in the host cell's cytoplasm, where viral assembly is orchestrated by the matrix (M) protein. Unexpectedly, the NiV-M protein traffics through the nucleus as an essential step to engage the plasma membrane in preparation for viral budding/release. Comparative studies were performed to assess whether M protein nuclear localization is a common feature of the henipaviruses, including the recently sequenced (although not yet isolated) Ghanaian bat henipavirus (Kumasi virus, GH-M74a virus) and Mojiang virus. Live-cell confocal microscopy revealed that nuclear translocation of GFP-fused M protein is conserved between henipaviruses in both human- and bat-derived cell lines. However, the efficiency of M protein nuclear localization and virus-like particle budding competency varied. Additionally, Cedar virus-, Kumasi virus- and Mojiang virus-M proteins were mutated in a bipartite nuclear localization signal, indicating that a key lysine residue is essential for nuclear import, export and induction of budding events, as previously reported for NiV-M. The results of this study suggest that the M proteins of henipaviruses may utilize a similar nucleocytoplasmic trafficking pathway as an essential step during viral replication in both humans and bats.

PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription

Transcription complexes that assemble at the HIV-1 promoter efficiently initiate transcription but generate paused RNA polymerase II downstream from the start site. The virally encoded Tat protein hijacks positive transcription elongation factor b (P-TEFb) to phosphorylate and activate this paused polymerase. In addition, Tat undergoes a series of reversible post-translational modifications that regulate distinct steps of the transcription cycle. To identify additional functionally important Tat cofactors, we performed RNAi knockdowns of sixteen previously identified Tat interactors and found that a novel E3 ligase, PJA2, ubiquitinates Tat in a non-degradative manner and specifically regulates the step of HIV transcription elongation. Interestingly, several different lysine residues in Tat can function as ubiquitin acceptor sites, and variable combinations of these lysines support both full transcriptional activity and viral replication. Further, the polyubiquitin chain conjugated to Tat by PJA2 can itself be assembled through variable ubiquitin lysine linkages. Importantly, proper ubiquitin chain assembly by PJA2 requires that Tat first binds its P-TEFb cofactor. These results highlight that both the Tat substrate and ubiquitin modification have plastic site usage, and this plasticity is likely another way in which the virus exploits the host molecular machinery to expand its limited genetic repertoire.

Would You Deliver an Electric Shock in 2015? Obedience in the Experimental Paradigm Developed by Stanley Milgram in the 50 Years Following the Original Studies

In spite of the over 50 years which have passed since the original experiments conducted by Stanley Milgram on obedience, these experiments are still considered a turning point in our thinking about the role of the situation in human behavior. While ethical considerations prevent a full replication of the experiments from being prepared, a certain picture of the level of obedience of participants can be drawn using the procedure proposed by Burger. In our experiment, we have expanded it by controlling for the sex of participants and of the learner. The results achieved show a level of participants’ obedience toward instructions similarly high to that of the original Milgram studies. Results regarding the influence of the sex of participants and of the “learner,” as well as of personality characteristics, do not allow us to unequivocally accept or reject the hypotheses offered.

ReplicationWiki: Improving Transparency in Social Sciences Research

In empirical social sciences research, only a small minority of study material is publicly available, therefore allowing full replication. The number of replication studies published in academic journals is even smaller. Our wiki documents the results of more than 300 replications, so far mainly in economics. It includes a database of more than 2,600 empirical studies. For each study we provide information about the availability of material for replication. This helps instructors to identify practical examples for courses focusing on empirical methods or on particular topics. Furthermore, it gives researchers better access to information on previous studies they can build on or compare their work with. We provide an overview of journals and their policies regarding data availability and publication of replications. The project has attracted interest from various fields and is open for expansion.

Replication of micro-sized pillars in polypropylene using the extrusion coating process

A recent advancement in nano-pattern replication using roll-to-roll extrusion coating (R2R-EC) shows potential for many biomimetic applications. For further development of the technique a study of the micro-replication regime is carried out. In this study a full and partial replication in polypropylene (PP) of micro-sized pillars has been demonstrated using the extrusion coating process. The replication fidelity of the pillars is investigated in a systematic variation of different process parameters: the line-speed of the rolls, the extruder output, the cooling roll temperature and the pressure on the cooling roll. The parameter making biggest impact on the replication is the temperature of the cooling roll.The micro-sized pillars show replication behavior opposite to what was found previously for the nano-patterns. The larger structures take the time to fill in and replicate best at the lower speeds. In this article a direct comparison of the speed at the same coating thickness is conducted.

Insights on the Activeness of Index Weighting Schemes

The contribution of this study is twofold. First of all, we categorize index weighting schemes along the dimension of active share and show that our division of index weighting schemes into three categories -- namely enhanced, full replication and sampling approaches -- corresponds to the grouping of actual mutual funds, as shown by Cremers and Petajisto (2009). In the second part, we analyze the role of the general market environment, by means of five cross-sectional (dispersion) measures, on the degree of strategies active weight tilt. We identify clear differences regarding the sensitivity towards all of the considered metrics and, thereon confirm the necessity of a separation of weighting schemes -- commonly cataloged under the umbrella term of ‘indexing’ -- given their stark differences in investment patterns.

Reproducible and Replicable Computational Fluid Dynamics: It’s Harder Than You Think

Completing a full replication study of the authors’ previously published findings on bluff-body aerodynamics was harder than they thought, despite them having good reproducible-research practices, such as sharing their code and data openly. Here’s what they learned from three years, four computational fluid dynamics codes, and hundreds of runs.

A new-generation 3D ozone FACE (Free Air Controlled Exposure)

To artificially simulate the impacts of ground-level ozone (O3) on vegetation, ozone FACE (Free Air Controlled Exposure) systems are increasingly recommended. We describe here a new-generation, three-dimensional ozone FACE, with O3 diffusion through laser-generated micro-holes, pre-mixing of air and O3, O3 generator with integral oxygen generator, continuous (day/night) exposure and full replication. Based on three O3 levels and assumptions on the pre-industrial O3 levels, we describe principles to calculate relative yield/biomass and estimate impacts even at lower-than-ambient O3 levels. The case study is called FO3X, and is at present the only ozone FACE in Mediterranean climate and one of the very few ozone FACEs investigating more than one stressor at a time. The results presented here will give further impulse to the research on O3 impacts on vegetation all over the world.

Inactivation of Cytomegalovirus in Breast Milk Using Ultraviolet-C Irradiation: Opportunities for a New Treatment Option in Breast Milk Banking.

Pasteurized donor human milk is provided by milk banks to very preterm babies where their maternal supply is insufficient or unavailable. Donor milk is currently processed by Holder pasteurization, producing a microbiologically safe product but significantly reducing immunoprotective components. Ultraviolet-C (UV-C) irradiation at 254 nm is being investigated as an alternative treatment method and has been shown to preserve components such as lactoferrin, lysozyme and secretory IgA considerably better than Holder pasteurization. We describe the inactivation of cytomegalovirus, a virus commonly excreted into breast milk, using UV-C irradiation. Full replication was ablated by various treatment doses. However, evidence of viral immediate early proteins within the cells was never completely eliminated indicating that some viral gene transcription was still occurring. In conclusion, UV-C may be a safe alternative to pasteurisation for the treatment of human donor milk that preserves the bioactivity. However, our data suggests that CMV inactivation will have to be carefully evaluated for each device designed to treat breast milk using UV-C irradiation.

The Measurement of Tracking Errors of Gold ETFS: Evidence from China

This paper presents the first study on the measurement of tracking errorsusing daily figures for gold exchange-traded funds (ETFs) in China. Threemethods are employed to measure tracking errors: 1) calculating theabsolute error measure, 2) calculating the differences between thestandard deviation of the benchmark index and the ETF, and 3) aregression analysis of empirical returns. In general, the results suggest thatthe tracking errors of these ETFs in China are lower than those of equitybasedETFs in Hong Kong, the US, and Australia. This study further appliedtwo optimised replication portfolios (50-10-10-30 and 90-2-3-5) for a totalof three types of simulation portfolio. The overall results suggest that theperformances of the optimised replication portfolios were better than theperformance of the full replication portfolio. Our results provide valuableinsight for both institutional and retail investors and the opportunity forexposure to a wide range of commodity ETFs in China.

Opposing Roles of Double-Stranded RNA Effector Pathways and Viral Defense Proteins Revealed with CRISPR-Cas9 Knockout Cell Lines and Vaccinia Virus Mutants

Vaccinia virus (VACV) decapping enzymes and cellular exoribonuclease Xrn1 catalyze successive steps in mRNA degradation and prevent double-stranded RNA (dsRNA) accumulation, whereas the viral E3 protein can bind dsRNA. We showed that dsRNA and E3 colocalized within cytoplasmic viral factories in cells infected with a decapping enzyme mutant as well as with wild-type VACV and that they coprecipitated with antibody. An E3 deletion mutant induced protein kinase R (PKR) and eukaryotic translation initiation factor alpha (eIF2α) phosphorylation earlier and more strongly than a decapping enzyme mutant even though less dsRNA was made, leading to more profound effects on viral gene expression. Human HAP1 and A549 cells were genetically modified by clustered regularly interspaced short palindromic repeat-Cas9 (CRISPR-Cas9) to determine whether the same pathways restrict E3 and decapping mutants. The E3 mutant replicated in PKR knockout (KO) HAP1 cells in which RNase L is intrinsically inactive but only with a double knockout (DKO) of PKR and RNase L in A549 cells, indicating that both pathways decreased replication equivalently and that no additional dsRNA pathway was crucial. In contrast, replication of the decapping enzyme mutant increased significantly (though less than that of wild-type virus) in DKO A549 cells but not in DKO HAP1 cells where a smaller increase in viral protein synthesis occurred. Xrn1 KO A549 cells were viable but nonpermissive for VACV; however, wild-type and mutant viruses replicated in triple-KO cells in which RNase L and PKR were also inactivated. Since KO of PKR and RNase L was sufficient to enable VACV replication in the absence of E3 or Xrn1, the poor replication of the decapping mutant, particularly in HAP1 DKO, cells indicated additional translational defects. Viruses have evolved ways of preventing or counteracting the cascade of antiviral responses that double-stranded RNA (dsRNA) triggers in host cells. We showed that the dsRNA produced in excess in cells infected with a vaccinia virus (VACV) decapping enzyme mutant and by wild-type virus colocalized with the viral E3 protein in cytoplasmic viral factories. Novel human cell lines defective in either or both protein kinase R and RNase L dsRNA effector pathways and/or the cellular 5' exonuclease Xrn1 were prepared by CRISPR-Cas9 gene editing. Inactivation of both pathways was necessary and sufficient to allow full replication of the E3 mutant and reverse the defect cause by inactivation of Xrn1, whereas the decapping enzyme mutant still exhibited defects in gene expression. The study provided new insights into functions of the VACV proteins, and the well-characterized panel of CRISPR-Cas9-modified human cell lines should have broad applicability for studying innate dsRNA pathways.

Microstructural and Corrosion Properties of Atmospheric Plasma Sprayed Alumina Coatings on AZ31B Magnesium Alloy Under Sodium Chloride Environment

AbstractThe corrosion deterioration process of plasma sprayed alumina coatings on AZ31B magnesium alloy was investigated using immersion corrosion test in NaCl solution at different chloride ion concentrations, pH value and immersion time. The experiments were conducted based on a three factor, five level, central composite rotatable design matrix with full replications technique. Response surface methodology was used to develop the relationship. The developed relationship can be effectively used to predict the corrosion rate of plasma sprayed alumina coatings on AZ31B magnesium alloy at 95 % confidence level. The results showed that the corrosion deterioration of alumina coated magnesium alloy in NaCl solutions was significantly influenced by chloride ion concentration and pH value. The alumina coatings were found to be highly susceptible to localized damage, and could not provide an effective corrosion protection to Mg alloy substrate in solutions containing acidic environments (pH3), higher chloride concentrations and immersion time.