Replication-based inference algorithms for hard computational problems

Inference algorithms based on evolving interactions between replicated solutions are introduced and analyzed on a prototypical NP-hard problem: the capacity of the binary Ising perceptron. The efficiency of the algorithm is examined numerically against that of the parallel tempering algorithm, showing improved performance in terms of the results obtained, computing requirements and simplicity of implementation. © 2013 American Physical Society.

Satisfaction as a predictor of future performance:a replication

Since the introduction of the Net Promoter concept there has been a vivid and ongoing debate among academics and practitioners about the performance of the Net Promoter Score (NPS) in comparison to other customer metrics, such as customer satisfaction, to predict company growth rates. We report results from a study using data from customers and firms in the Netherlands on the relationship between different satisfaction and loyalty metrics as well as the NPS with sales revenue growth, gross margins and net operating cash flows. We find that all metrics perform equally well in predicting current gross margins and current sales revenue growth and equally poor for predicting future sales growth and gross margins as well as current and future net cash flows. The NPS is neither superior nor inferior to other metrics. Taken together, our study suggests that the predictive capability of customer metrics, such as NPS, for future company growth rates is limited. © 2013 Elsevier B.V.

Compression by replication

A recently introduced inference method based on system replication and an online message passing algorithm is employed to complete a previously suggested compression scheme based on a nonlinear perceptron. The algorithm is shown to approach the information theoretical bounds for compression as the number of replicated systems increases, offering superior performance compared to basic message passing algorithms. In addition, the suggested method does not require fine-tuning of parameters or other complementing heuristic techniques, such as the introduction of inertia terms, to improve convergence rates to nontrivial results. © 2014 American Physical Society.

Data partitioning and replication management in distributed geographic information system (GIS) database

This research presents several components encompassing the scope of the objective of Data Partitioning and Replication Management in Distributed GIS Database. Modern Geographic Information Systems (GIS) databases are often large and complicated. Therefore data partitioning and replication management problems need to be addresses in development of an efficient and scalable solution. ^ Part of the research is to study the patterns of geographical raster data processing and to propose the algorithms to improve availability of such data. These algorithms and approaches are targeting granularity of geographic data objects as well as data partitioning in geographic databases to achieve high data availability and Quality of Service(QoS) considering distributed data delivery and processing. To achieve this goal a dynamic, real-time approach for mosaicking digital images of different temporal and spatial characteristics into tiles is proposed. This dynamic approach reuses digital images upon demand and generates mosaicked tiles only for the required region according to user's requirements such as resolution, temporal range, and target bands to reduce redundancy in storage and to utilize available computing and storage resources more efficiently. ^ Another part of the research pursued methods for efficient acquiring of GIS data from external heterogeneous databases and Web services as well as end-user GIS data delivery enhancements, automation and 3D virtual reality presentation. ^ There are vast numbers of computing, network, and storage resources idling or not fully utilized available on the Internet. Proposed "Crawling Distributed Operating System "(CDOS) approach employs such resources and creates benefits for the hosts that lend their CPU, network, and storage resources to be used in GIS database context. ^ The results of this dissertation demonstrate effective ways to develop a highly scalable GIS database. The approach developed in this dissertation has resulted in creation of TerraFly GIS database that is used by US government, researchers, and general public to facilitate Web access to remotely-sensed imagery and GIS vector information. ^

The functional subdivision of the visual brain : Is there a real illusion effect on action? A multi-lab replication study

Acknowledgements We thank Brian Roberts and Mike Harris for responding to our questions regarding their paper; Zoltan Dienes for advice on Bayes factors; Denise Fischer, Melanie Römer, Ioana Stanciu, Aleksandra Romanczuk, Stefano Uccelli, Nuria Martos Sánchez, and Rosa María Beño Ruiz de la Sierra for help collecting data; Eva Viviani for managing data collection in Parma. We thank Maurizio Gentilucci for letting us use his lab, and the Centro Intradipartimentale Mente e Cervello (CIMeC), University of Trento, and especially Francesco Pavani for lending us his motion tracking equipment. We thank Rachel Foster for proofreading. KKK was supported by a Ph.D. scholarship as part of a grant to VHF within the International Graduate Research Training Group on Cross-Modal Interaction in Natural and Artificial Cognitive Systems (CINACS; DFG IKG-1247) and TS by a grant (DFG – SCHE 735/3-1); both from the German Research Council.

Necessary conditions for the emergence of homochirality via autocatalytic self-replication

We analyze a recent proposal for spontaneous mirror symmetry breaking based on the coupling of first-order enantioselective autocatalysis and direct production of the enantiomers that invokes a critical role for intrinsic reaction noise. For isolated systems, the racemic state is the unique stable outcome for both stochastic and deterministic dynamics when the system is in compliance with the constraints dictated by the thermodynamics of chemical reaction processes. In open systems, the racemic outcome also results for both stochastic and deterministic dynamics when driving the auto-catalysis unidirectionally by external reagents. Nonracemic states can result in the latter only if the reverse reactions are strictly zero: these are kinetically controlled outcomes for small populations and volumes, and can be simulated by stochastic dynamics. However, the stability of the thermodynamic limit proves that the racemic outcome is the unique stable state for strictly irreversible externally driven autocatalysis. These findings contradict the suggestion that the inhibition requirement of the Frank autocatalytic model for the emergence of homochirality may be relaxed in a noise-induced mechanism.

Early Word Comprehension in Infants: Replication and Extension.

A handful of recent experimental reports have shown that infants of 6 to 9 months know the meanings of some common words. Here, we replicate and extend these findings. With a new set of items, we show that when young infants (age 6-16 months, n=49) are presented with side-by-side video clips depicting various common early words, and one clip is named in a sentence, they look at the named video at above-chance rates. We demonstrate anew that infants understand common words by 6-9 months, and that performance increases substantially around 14 months. The results imply that 6-9 month olds' failure to understand words not referring to objects (verbs, adjectives, performatives) in a similar prior study is not attributable to the use of dynamic video depictions. Thus, 6-9 month olds' experience of spoken language includes some understanding of common words for concrete objects, but relatively impoverished comprehension of other words.

Integrase mutants defective for interaction with LEDGF/p75 are impaired in chromosome tethering and HIV-1 replication

The insertion of a DNA copy of its RNA genome into a chromosome of the host cell is mediated by the viral integrase with the help of mostly uncharacterized cellular cofactors. We have recently described that the transcriptional co-activator LEDGF/p75 strongly interacts with HIV-1 integrase. Here we show that interaction of HIV-1 integrase with LEDGF/p75 is important for viral replication. Using multiple approaches including two-hybrid interaction studies, random and directed mutagenesis, we could demonstrate that HIV-1 virus harboring a single mutation that disrupts integrase-LEDGF/p75 interaction, resulted in defective HIV-1 replication. Furthermore, we found that LEDGF/p75 tethers HIV-1 integrase to chromosomes and that this interaction may be important for the integration process and the replication of HIV-1.

Black-White Wage Gap Among Restaurant Servers: A Replication, Extension, and Exploration of Consumer Racial Discrimination in Tipping

There is a rich history of social science research centering on racial inequalities that continue to be observed across various markets (e.g., labor, housing, and credit markets) and social milieus. Existing research on racial discrimination in consumer markets, however, is relatively scarce and that which has been done has disproportionately focused on consumers as the victims of race-based mistreatment. As such, we know relatively little about how consumers contribute to inequalities in their roles as perpetrators of racial discrimination. In response, in this paper we elaborate on a line of research that is only in its’ infancy stages of development and yet is ripe with opportunities to advance the literature on consumer racial discrimination and racial earnings inequities among tip dependent employees in the United States. Specifically, we analyze data derived from a large exit survey of restaurant consumers (n=378) in an attempt to replicate, extend, and further explore the recently documented effect of service providers’ race on restaurant consumers’ tipping decisions. Our results indicate that both White and Black restaurant customers discriminate against Black servers by tipping them less than their White coworkers. Importantly, we find no evidence that this Black tip penalty is the result of interracial differences in service skills possessed by Black and White servers. We conclude by delineating directions for future research in this neglected but salient area study.

Identification and Characterization of New Small Molecule Inhibitors of Picornavirus Replication

The Picornaviridae family consists of positive-strand RNA viruses that are the causative agents of a variety of diseases in humans and animals. Few drugs targeting picornaviruses are available, making the discovery of new antivirals a high priority. Here, we identified and characterized three compounds from a library of kinase inhibitors that block replication of poliovirus, coxsackievirus B3, and encephalomyocarditis virus. The antiviral effect of these compounds is not likely related to their known cellular targets because other inhibitors targeting the same pathways did not inhibit viral replication. Using an in vitro translation-replication system, we showed that these drugs inhibit different stages of the poliovirus life cycle. A4(1) inhibited the formation of a functional replication complex, while E5(1) and E7(2) affected replication after the replication complex had formed. A4(1) demonstrated partial protection from paralysis in a murine model of poliomyelitis. Poliovirus resistant to E7(2) had a single mutation in the 3A protein. This mutation was previously found to confer resistance to enviroxime-like compounds, which target either PI4KIIIβ (major enviroxime-like compounds) or OSBP (minor enviroxime-like compounds), cellular factors involved in lipid metabolism and shown to be important for replication of diverse positive-strand RNA viruses. We classified E7(2) as a minor enviroxime-like compound, because the localization of OSBP changed in the presence of this inhibitor. Interestingly, both E7(2) and major enviroxime-like compound GW5074 interfered with the viral polyprotein processing. Multiple attempts to isolate resistant mutants in the presence of A4(1) or E5(1) were unsuccessful, showing that effective broad-spectrum antivirals could be developed on the basis of these compounds. Studies with these compounds shed light on pathways shared by diverse picornaviruses that could be potential targets for the development of broad-spectrum antiviral drugs.

The emergence and evolution of optimistic expectations in schoolchildren

When we study optimism in children, we note the temporary emergence of a bias that leads them to make optimistic predictions. In this study we intend to learn more about changes that can be observed in the optimistic bias of 6- to 12-year old schoolchildren when they predict future events, and in the way they justify those predictions. A total of 77 pupils participated in this study; we evaluated each one of them individually with a Piagetian interview, asking them to formulate predictions about a series of hypothetical situations. After analyzing whether a child's prediction implied that the situation would maintain itself or would change for better or for worse, we classified the justifications they provided for their predictions. Results show that these subjects regarded positive change as more likely in the case of psychological or hybrid events than for purely biological ones, and that younger children tended to display a greater bias in favor of the likelihood of positive change. These younger children justified their predictions stating that nature or the passing of time could be responsible for the changes, without needing further intervention on the part of other agents. Older children, on the other hand, tended to provide similar kinds of explanations to justify their expectation of stasis.

MECHANISM OF UPREGULATION OF PHOSPHATIDYLCHOLINE SYNTHESIS DURING PICORNAVIRUS INFECTION AND ITS ROLE IN THE DEVELOPMENT OF VIRAL REPLICATION ORGANELLES

Picornaviruses are a group of human and animal pathogens capable of inflicting serious public health diseases and economic burdens. Treatments options through vaccines for prevention or antivirals to cure infection are not available for the vast majority of these viruses. These shortcomings, in the development of vaccines or antivirals therapeutic, are linked to the genetic diversity and to an incomplete understanding of the biology of these viruses. Despite the diverse host range, this group of positive-strand RNA viruses shares the same replication mechanisms, including the development of membranous structures (replication organelles) in the cytoplasm of infected cells. The development of these membranous structures, which serve as sites for the replication of the viral RNA genome, has been linked to the hijacking of elements of the cellular membrane metabolism pathways. Here we show that upon picornavirus infection, there is a specific activation of acyl-CoA synthetase enzymes resulting in strong import and accumulation of long chain fatty acids in the cytoplasm of infected cells. We show that the newly imported fatty acids serve as a substrate for the upregulation of phosphatidylcholine synthesis required for the structural development of replication organelles. In this work, we identified that acyl-CoA synthetase long chain 3 (ACSL3) is required for the upregulation of lipids syntheses and the replication of poliovirus. We have shown that the poliovirus protein 2A was required but not sufficient for the activation of import of long chain fatty acids in infected cells. We demonstrated that the fatty acid import is upregulated upon infection by diverse picornaviruses and that such upregulation is not dependent on activation of ER stress response or the autophagy pathways. In this work, we have demonstrated that phosphatidylcholine was required for the structural development of replication organelles. Phosphatidylcholine synthesis was dispensable for the production of infectious particles at high MOI but required at a low MOI for the protection of the replication complexes from the cellular innate immunity mechanisms.

The interpretation of scholars' interpretations of confidence intervals: criticism, replication, and extension of Hoekstra et al. (2014)

Hoekstra et al. (Psychonomic Bulletin & Review, 2014, 21:1157–1164) surveyed the interpretation of confidence intervals (CIs) by first-year students, master students, and researchers with six items expressing misinterpretations of CIs. They asked respondents to answer all items, computed the number of items endorsed, and concluded that misinterpretation of CIs is robust across groups. Their design may have produced this outcome artifactually for reasons that we describe. This paper discusses first the two interpretations of CIs and, hence, why misinterpretation cannot be inferred from endorsement of some of the items. Next, a re-analysis of Hoekstra et al.’s data reveals some puzzling differences between first-year and master students that demand further investigation. For that purpose, we designed a replication study with an extended questionnaire including two additional items that express correct interpretations of CIs (to compare endorsement of correct vs. nominally incorrect interpretations) and we asked master students to indicate which items they would have omitted had they had the option (to distinguish deliberate from uninformed endorsement caused by the forced-response format). Results showed that incognizant first-year students endorsed correct and nominally incorrect items identically, revealing that the two item types are not differentially attractive superficially; in contrast, master students were distinctively more prone to endorsing correct items when their uninformed responses were removed, although they admitted to nescience more often that might have been expected. Implications for teaching practices are discussed.

OriDB: a DNA replication origin database

Replication of eukaryotic chromosomes initiates at multiple sites called replication origins. Replication origins are best understood in the budding yeast Saccharomyces cerevisiae, where several complementary studies have mapped their locations genome-wide. We have collated these datasets, taking account of the resolution of each study, to generate a single list of distinct origin sites. OriDB provides a web-based catalogue of these confirmed and predicted S.cerevisiae DNA replication origin sites. Each proposed or confirmed origin site appears as a record in OriDB, with each record comprising seven pages. These pages provide, in text and graphical formats, the following information: genomic location and chromosome context of the origin site; time of origin replication; DNA sequence of proposed or experimentally confirmed origin elements; free energy required to open the DNA duplex (stress-induced DNA duplex destabilization or SIDD); and phylogenetic conservation of sequence elements. In addition, OriDB encourages community submission of additional information for each origin site through a User Notes facility. Origin sites are linked to several external resources, including the Saccharomyces Genome Database (SGD) and relevant publications at PubMed. Finally, a Chromosome Viewer utility allows users to interactively generate graphical representations of DNA replication data genome-wide. OriDB is available at www.oridb.org.

The hierarchic structure of fears: A cross-cultural replication with the fear survey schedule in a portuguese sample

A confirmatory attempt is made to assess the validity of a hierarchic structural model of fears. Using a sample comprising 1,980 adult volunteers in Portugal, the present study set out to delineate the multidimensional structure and hierarchic organization of a large set of feared stimuli by contrasting a higher-order model comprising general fear at the highest level against a first-order model and a unitary fear model. Following a refinement of the original model, support was found for a five-factor model on a first-order level, namely (1) Social fears, (2) Agoraphobic fears, (3) Fears of bodily injury, death and illness, (4) Fears of display to aggressive scenes, and (5) Harmless animals fears. These factors in turn loaded on a General fear factor at the second-order level. However, the firstorder model was as parsimonious as a hierarchic higher-order model. The hierarchic model supports a quantitative hierarchic approach which decomposes fear disorders into agoraphobic, social, and specific (animal and bloodinjury) fears.