Games, Mobile Processes, and Functions

Long version of a CSL'22 paperInternational audienceWe establish a tight connection between two models of the λ-calculus, namely Milner's encoding into the π-calculus (precisely, the Internal π-calculus), and operational game semantics (OGS). We first investigate the operational correspondence between the behaviours of the encoding provided by π and OGS. We do so for various LTSs: the standard LTS for π and a new 'concurrent' LTS for OGS; an 'output-prioritised' LTS for π and the standard alternating LTS for OGS. We then show that the equivalences induced on λ-terms by all these LTSs (for π and OGS) coincide. These connections allow us to transfer results and techniques between π and OGS. In particular we import up-to techniques from π onto OGS and we derive congruence and compositionality results for OGS from those of π. The study is illustrated for call-by-value; similar results hold for call-by-name

Comparison of Modules of Wild Type and Mutant Huntingtin and TP53 Protein Interaction Networks: Implications in Biological Processes and Functions

Disease-causing mutations usually change the interacting partners of mutant proteins. In this article, we propose that the biological consequences of mutation are directly related to the alteration of corresponding protein protein interaction networks (PPIN). Mutation of Huntingtin (HTT) which causes Huntington's disease (HD) and mutations to TP53 which is associated with different cancers are studied as two example cases. We construct the PPIN of wild type and mutant proteins separately and identify the structural modules of each of the networks. The functional role of these modules are then assessed by Gene Ontology (GO) enrichment analysis for biological processes (BPs). We find that a large number of significantly enriched (p<0.0001) GO terms in mutant PPIN were absent in the wild type PPIN indicating the gain of BPs due to mutation. Similarly some of the GO terms enriched in wild type PPIN cease to exist in the modules of mutant PPIN, representing the loss. GO terms common in modules of mutant and wild type networks indicate both loss and gain of BPs. We further assign relevant biological function(s) to each module by classifying the enriched GO terms associated with it. It turns out that most of these biological functions in HTT networks are already known to be altered in HD and those of TP53 networks are altered in cancers. We argue that gain of BPs, and the corresponding biological functions, are due to new interacting partners acquired by mutant proteins. The methodology we adopt here could be applied to genetic diseases where mutations alter the ability of the protein to interact with other proteins.Comment: 35 pages, 10 eps figures, (Supplementary material and Datasets are available on request

The Emerging Role of Ten-Eleven Translocation 1 in Epigenetic Responses to Environmental Exposures.

Mounting evidence from epidemiological studies and animal models has linked exposures to environmental factors to changes in epigenetic markers, especially in DNA methylation. These epigenetic changes may lead to dysregulation of molecular processes and functions and mediate the impact of environmental exposures in complex diseases. However, detailed molecular events that result in epigenetic changes following exposures remain unclear. Here, we review the emerging evidence supporting a critical role of ten-eleven translocation 1 (TET1) in mediating these processes. Targeting TET1 and its associated pathways may have therapeutic potential in alleviating negative impacts of environmental exposures, preventing and treating exposure-related diseases

Community detection of agents interacting through regional innovation policies: structures, processes and functions

The detection of communities of agents that interacted over time through regional innovation policies is analyzed through the application of three methodologies: Clique Percolation Method (CPM) by Palla et al. (2005), Infomap by Rosvall and Bergstrom (2008), and Dynamic Cluster Index analysis (DCI) by Villani et al. (2013). In a economic context of analysis centered on such a complex object as innovation, the three methodologies are applied to investigate different specific aspects of community organizations aimed at developing innovative activities. The investigation of relational structures (through CPM), of shared processes (through Infomap) and of integrated behaviors (through DCI analysis) allowed the identification of communities that reveal, respectively, meaningful characterizations in terms of agents\u2019 participations in specific waves of the policy, of agents\u2019 participations in projects operating in particular technological domains, and in terms of agents\u2019 institutional typologies. The case study regards the policy interventions implemented by region Tuscany (Italy) in 2000-2006 with the aim of supporting innovative network projects among local actors

Interaction and cross-talk between non-coding RNAs.

Non-coding RNA (ncRNA) has been shown to regulate diverse cellular processes and functions through controlling gene expression. Long non-coding RNAs (lncRNAs) act as a competing endogenous RNAs (ceRNAs) where microRNAs (miRNAs) and lncRNAs regulate each other through their biding sites. Interactions of miRNAs and lncRNAs have been reported to trigger decay of the targeted lncRNAs and have important roles in target gene regulation. These interactions form complicated and intertwined networks. Certain lncRNAs encode miRNAs and small nucleolar RNAs (snoRNAs), and may regulate expression of these small RNAs as precursors. SnoRNAs have also been reported to be precursors for PIWI-interacting RNAs (piRNAs) and thus may regulate the piRNAs as a precursor. These miRNAs and piRNAs target messenger RNAs (mRNAs) and regulate gene expression. In this review, we will present and discuss these interactions, cross-talk, and co-regulation of ncRNAs and gene regulation due to these interactions

Natural Resource Information System. Volume 1: Overall description

A prototype computer-based Natural Resource Information System was designed which could store, process, and display data of maximum usefulness to land management decision making. The system includes graphic input and display, the use of remote sensing as a data source, and it is useful at multiple management levels. A survey established current decision making processes and functions, information requirements, and data collection and processing procedures. The applications of remote sensing data and processing requirements were established. Processing software was constructed and a data base established using high-altitude imagery and map coverage of selected areas of SE Arizona. Finally a demonstration of system processing functions was conducted utilizing material from the data base

Biochar Application to Soils - A Critical Scientific Review of Effects on Soil Properties, Processes and Functions

Biochar application to soils is being considered as a means to sequester carbon (C) while concurrently improving soil functions. This report reviews the evidence for potential effects of biochar incorporation into soils on soil properties and processes with implications for agronomic and environmental functions. Further to this, while beyond the main scope of this report, an overview of the main environmental and occupational health issues associated to biochar production and handling, and the socio-economic implications is given. Extrapolation of reported results must be done with caution, owing to the relatively small number of studies reported in the primary literature, when compared to possible instigation of biochar application to soils on a national or European scale . To try and bridge the gap between small scale, controlled experiments and large scale implementation of biochar application to a range of soil types across a range of different climates, a statistical meta-analysis was undertaken. A full search of the scientific literature led to a compilation of studies used for a meta-analysis of the effects of biochar application to soils and plant productivity. Results showed a small overall, but statistically significant, positive effect of biochar application to soils on plant productivity. The greatest positive effects were seen on acidic free-draining soils with other soil types, specifically calcarosols showing no significant effect (either positive or negative). This suggests that one of the main mechanisms behind the reported positive effects of biochar application to soils on plant productivity may be a liming effect although further research is needed to confirm this hypothesis. There is currently a lack of data concerning the effects of biochar application to soils on other soil functions. This means that although these are qualitatively and comprehensively discussed in this report, a robust meta-analysis on such effects is not possible currently. Effects that are expected (both positive and negative) include nutrient leaching to ground/surface waters, soil water retention, soil water repellency, N2O and CH4 emissions, albedo and soil biological activity although insufficient data are available at present to accurately quantify any of these effects or to report a consensus on their direction (either positive or negative). Preliminary evidence has also been reported concerning a possible priming effect whereby accelerated decomposition of soil organic matter occurs upon biochar addition to soil. This has the potential to both harm crop productivity in the long term due to loss of soil organic matter, as well as releasing more CO2 into the atmosphere as increased quantities of soil organic matter is respired from the soil. This is an area which requires urgent further research and is discussed in more detail in this report.JRC.DDG.H.7-Land management and natural hazard