A Number-Theoretic Error-Correcting Code

In this paper we describe a new error-correcting code (ECC) inspired by the Naccache-Stern cryptosystem. While by far less efficient than Turbo codes, the proposed ECC happens to be more efficient than some established ECCs for certain sets of parameters. The new ECC adds an appendix to the message. The appendix is the modular product of small primes representing the message bits. The receiver recomputes the product and detects transmission errors using modular division and lattice reduction

Epstein-Barr virus-specific methylation of human genes in gastric cancer cells

<p>Abstract</p> <p>Background</p> <p>Epstein-Barr Virus (EBV) is found in 10% of all gastric adenocarcinomas but its role in tumor development and maintenance remains unclear. The objective of this study was to examine EBV-mediated dysregulation of cellular factors implicated in gastric carcinogenesis.</p> <p>Methods</p> <p>Gene expression patterns were examined in EBV-negative and EBV-positive AGS gastric epithelial cells using a low density microarray, reverse transcription PCR, histochemical stains, and methylation-specific DNA sequencing. Expression of PTGS2 (COX2) was measured in AGS cells and in primary gastric adenocarcinoma tissues.</p> <p>Results</p> <p>In array studies, nearly half of the 96 human genes tested, representing 15 different cancer-related signal transduction pathways, were dysregulated after EBV infection. Reverse transcription PCR confirmed significant impact on factors having diverse functions such as cell cycle regulation (<it>IGFBP3</it>, <it>CDKN2A, CCND1, HSP70, ID2, ID4)</it>, DNA repair <it>(BRCA1, TFF1</it>), cell adhesion (<it>ICAM1</it>), inflammation (<it>COX2</it>), and angiogenesis (<it>HIF1A</it>). Demethylation using 5-aza-2'-deoxycytidine reversed the EBV-mediated dysregulation for all 11 genes listed here. For some promoter sequences, CpG island methylation and demethylation occurred in an EBV-specific pattern as shown by bisulfite DNA sequencing. Immunohistochemistry was less sensitive than was western blot for detecting downregulation of COX2 upon EBV infection. Virus-related dysregulation of COX2 levels <it>in vitro </it>was not recapitulated <it>in vivo </it>among naturally infected gastric cancer tissues.</p> <p>Conclusions</p> <p>EBV alters human gene expression in ways that could contribute to the unique pathobiology of virus-associated cancer. Furthermore, the frequency and reversability of methylation-related transcriptional alterations suggest that demethylating agents have therapeutic potential for managing EBV-related carcinoma.</p

Information inequalities and Generalized Graph Entropies

In this article, we discuss the problem of establishing relations between information measures assessed for network structures. Two types of entropy based measures namely, the Shannon entropy and its generalization, the R\'{e}nyi entropy have been considered for this study. Our main results involve establishing formal relationship, in the form of implicit inequalities, between these two kinds of measures when defined for graphs. Further, we also state and prove inequalities connecting the classical partition-based graph entropies and the functional-based entropy measures. In addition, several explicit inequalities are derived for special classes of graphs.Comment: A preliminary version. To be submitted to a journa

Perspectives of people in Mali toward genetically-modified mosquitoes for malaria control

Background: Genetically-modified (GM) mosquitoes have been proposed as part of an integrated vector control strategy for malaria control. Public acceptance is essential prior to field trials, particularly since mosquitoes are a vector of human disease and genetically modified organisms (GMOs) face strong scepticism in developed and developing nations. Despite this, in sub-Saharan Africa, where the GM mosquito effort is primarily directed, very little data is available on perspectives to GMOs. Here, results are presented of a qualitative survey of public attitudes to GM mosquitoes for malaria control in rural and urban areas of Mali, West Africa between the months of October 2008 and June 2009. Methods: The sample consisted of 80 individuals - 30 living in rural communities, 30 living in urban suburbs of Bamako, and 20 Western-trained and traditional health professionals working in Bamako and Bandiagara. Questions were asked about the cause of malaria, heredity and selective breeding. This led to questions about genetic alterations, and acceptable conditions for a release of pest-resistant GM corn and malaria-refractory GM mosquitoes. Finally, participants were asked about the decision-making process in their community. Interviews were transcribed and responses were categorized according to general themes. Results: Most participants cited mosquitoes as one of several causes of malaria. The concept of the gene was not widely understood; however selective breeding was understood, allowing limited communication of the concept of genetic modification. Participants were open to a release of pest-resistant GM corn, often wanting to conduct a trial themselves. The concept of a trial was reapplied to GM mosquitoes, although less frequently. Participants wanted to see evidence that GM mosquitoes can reduce malaria prevalence without negative consequences for human health and the environment. For several participants, a mosquito control programme was preferred; however a transgenic release that satisfied certain requirements was usually acceptable. Conclusions: Although there were some dissenters, the majority of participants were pragmatic towards a release of GM mosquitoes. An array of social and cultural issues associated with malaria, mosquitoes and genetic engineering became apparent. If these can be successfully addressed, then social acceptance among the populations surveyed seems promising

Tuning of Human Modulation Filters Is Carrier-Frequency Dependent

Licensed under the Creative Commons Attribution License

Comparative Network Analysis of Preterm vs. Full-Term Infant-Mother Interactions

Several studies have reported that interactions of mothers with preterm infants show differential characteristics compared to that of mothers with full-term infants. Interaction of preterm dyads is often reported as less harmonious. However, observations and explanations concerning the underlying mechanisms are inconsistent. In this work 30 preterm and 42 full-term mother-infant dyads were observed at one year of age. Free play interactions were videotaped and coded using a micro-analytic coding system. The video records were coded at one second resolution and studied by a novel approach using network analysis tools. The advantage of our approach is that it reveals the patterns of behavioral transitions in the interactions. We found that the most frequent behavioral transitions are the same in the two groups. However, we have identified several high and lower frequency transitions which occur significantly more often in the preterm or full-term group. Our analysis also suggests that the variability of behavioral transitions is significantly higher in the preterm group. This higher variability is mostly resulted from the diversity of transitions involving non-harmonious behaviors. We have identified a maladaptive pattern in the maternal behavior in the preterm group, involving intrusiveness and disengagement. Application of the approach reported in this paper to longitudinal data could elucidate whether these maladaptive maternal behavioral changes place the infant at risk for later emotional, cognitive and behavioral disturbance

Genome Sizes and the Benford Distribution

BACKGROUND: Data on the number of Open Reading Frames (ORFs) coded by genomes from the 3 domains of Life show the presence of some notable general features. These include essential differences between the Prokaryotes and Eukaryotes, with the number of ORFs growing linearly with total genome size for the former, but only logarithmically for the latter. RESULTS: Simply by assuming that the (protein) coding and non-coding fractions of the genome must have different dynamics and that the non-coding fraction must be particularly versatile and therefore be controlled by a variety of (unspecified) probability distribution functions (pdf's), we are able to predict that the number of ORFs for Eukaryotes follows a Benford distribution and must therefore have a specific logarithmic form. Using the data for the 1000+ genomes available to us in early 2010, we find that the Benford distribution provides excellent fits to the data over several orders of magnitude. CONCLUSIONS: In its linear regime the Benford distribution produces excellent fits to the Prokaryote data, while the full non-linear form of the distribution similarly provides an excellent fit to the Eukaryote data. Furthermore, in their region of overlap the salient features are statistically congruent. This allows us to interpret the difference between Prokaryotes and Eukaryotes as the manifestation of the increased demand in the biological functions required for the larger Eukaryotes, to estimate some minimal genome sizes, and to predict a maximal Prokaryote genome size on the order of 8-12 megabasepairs. These results naturally allow a mathematical interpretation in terms of maximal entropy and, therefore, most efficient information transmission

A Novel Estimator for the Rate of Information Transfer by Continuous Signals

The information transfer rate provides an objective and rigorous way to quantify how much information is being transmitted through a communications channel whose input and output consist of time-varying signals. However, current estimators of information content in continuous signals are typically based on assumptions about the system's linearity and signal statistics, or they require prohibitive amounts of data. Here we present a novel information rate estimator without these limitations that is also optimized for computational efficiency. We validate the method with a simulated Gaussian information channel and demonstrate its performance with two example applications. Information transfer between the input and output signals of a nonlinear system is analyzed using a sensory receptor neuron as the model system. Then, a climate data set is analyzed to demonstrate that the method can be applied to a system based on two outputs generated by interrelated random processes. These analyses also demonstrate that the new method offers consistent performance in situations where classical methods fail. In addition to these examples, the method is applicable to a wide range of continuous time series commonly observed in the natural sciences, economics and engineering

Chess databases as a research vehicle in psychology : modeling large data

The game of chess has often been used for psychological investigations, particularly in cognitive science. The clear-cut rules and well-defined environment of chess provide a model for investigations of basic cognitive processes, such as perception, memory, and problem solving, while the precise rating system for the measurement of skill has enabled investigations of individual differences and expertise-related effects. In the present study, we focus on another appealing feature of chess—namely, the large archive databases associated with the game. The German national chess database presented in this study represents a fruitful ground for the investigation of multiple longitudinal research questions, since it collects the data of over 130,000 players and spans over 25 years. The German chess database collects the data of all players, including hobby players, and all tournaments played. This results in a rich and complete collection of the skill, age, and activity of the whole population of chess players in Germany. The database therefore complements the commonly used expertise approach in cognitive science by opening up new possibilities for the investigation of multiple factors that underlie expertise and skill acquisition. Since large datasets are not common in psychology, their introduction also raises the question of optimal and efficient statistical analysis. We offer the database for download and illustrate how it can be used by providing concrete examples and a step-by-step tutorial using different statistical analyses on a range of topics, including skill development over the lifetime, birth cohort effects, effects of activity and inactivity on skill, and gender differences