Optimized network structure and routing metric in wireless multihop ad hoc communication

Inspired by the Statistical Physics of complex networks, wireless multihop ad hoc communication networks are considered in abstracted form. Since such engineered networks are able to modify their structure via topology control, we search for optimized network structures, which maximize the end-to-end throughput performance. A modified version of betweenness centrality is introduced and shown to be very relevant for the respective modeling. The calculated optimized network structures lead to a significant increase of the end-to-end throughput. The discussion of the resulting structural properties reveals that it will be almost impossible to construct these optimized topologies in a technologically efficient distributive manner. However, the modified betweenness centrality also allows to propose a new routing metric for the end-to-end communication traffic. This approach leads to an even larger increase of throughput capacity and is easily implementable in a technologically relevant manner.Comment: 25 pages, v2: fixed one small typo in the 'authors' fiel

SemanticSBML: a tool for annotating, checking, and merging of biochemical models in SBML format

Semantic annotations in SBML (systems biology markup language) enable computer programs to check and process biochemical models based on their biochemical meaning. Annotations are an important prerequisite for model merging, which would be a major step towards the construction of large-scale cell models. The software tool semanticSBML allows users to check and edit MIRIAM annotations and SBO terms, the most common forms of annotation in SBML models. It uses a large collection of biochemical names and database identifiers to support modellers in finding the right annotations. Annotated SBML models can also be built from lists of chemical reactions. In model merging, semanticSBML suggests a preliminary merged model based on MIRIAM annotations in the original models. This model provides a starting point for manually aligning the elements of all input models. To resolve conflicting element properties, conflicts are highlighted and categorised. The user can navigate through the models, change the matching of model elements, check the conflicts between them and decide how they should be resolved. Alternatively, the software can resolve all conflicts automatically, selecting each time the attribute value from the input model with highest priority.
URL: "http://www.semanticsbml.org/":http://www.semanticsbml.org

Continuum percolation of wireless ad hoc communication networks

Wireless multi-hop ad hoc communication networks represent an infrastructure-less and self-organized generalization of todays wireless cellular networks. Connectivity within such a network is an important issue. Continuum percolation and technology-driven mutations thereof allow to address this issue in the static limit and to construct a simple distributed protocol, guaranteeing strong connectivity almost surely and independently of various typical uncorrelated and correlated random spatial patterns of participating ad hoc nodes.Comment: 30 pages, to be published in Physica

Impact of network structure on the capacity of wireless multihop ad hoc communication

As a representative of a complex technological system, so-called wireless multihop ad hoc communication networks are discussed. They represent an infrastructure-less generalization of todays wireless cellular phone networks. Lacking a central control authority, the ad hoc nodes have to coordinate themselves such that the overall network performs in an optimal way. A performance indicator is the end-to-end throughput capacity. Various models, generating differing ad hoc network structure via differing transmission power assignments, are constructed and characterized. They serve as input for a generic data traffic simulation as well as some semi-analytic estimations. The latter reveal that due to the most-critical-node effect the end-to-end throughput capacity sensitively depends on the underlying network structure, resulting in differing scaling laws with respect to network size.Comment: 30 pages, to be published in Physica

Total spectrum of photon emission by an ultra-relativistic positron channeling in a periodically bent crystal

We present the results of numerical calculations of the channelling and undulator radiation generated by an ultra-relativistic positron channelling along a crystal plane, which is periodically bent. The bending might be due either to the propagation of a transverse acoustic wave through the crystal, or due to the static strain as it occurs in superlattices. The periodically bent crystal serves as an undulator. We investigate the dependence of the intensities of both the ordinary channelling and the undulator radiations on the parameters of the periodically bent channel with simultaneous account for the dechannelling effect of the positrons. We demonstrate that there is a range of parameters in which the undulator radiation dominates over the channelling one and the characteristic frequencies of both types of radiation are well separated. This result is important, because the undulator radiation can be used to create a tunable source of X-ray and gamma-radiation.Comment: published in J. Phys. G: Nucl. Part. Phys. 26 (2000) L87-L95, http://www.iop.org ; 12 pages, 4 figures, LaTe

Retrieval, alignment, and clustering of computational models based on semantic annotations

As the number of computational systems biology models increases, new methods are needed to explore their content and build connections with experimental data. In this Perspective article, the authors propose a flexible semantic framework that can help achieve these aims

GeneChip analyses point to novel pathogenetic mechanisms in mantle cell lymphoma

The translocation t(11;14)(q13;q32) is the genetic hallmark of mantle cell lymphoma (MCL) but is not sufficient for inducing lymphomagenesis. Here we performed genome-wide 100K GeneChip Mapping in 26 t(11;14)-positive MCL and six MCL cell lines. Partial uniparental disomy (pUPD) was shown to be a recurrent chromosomal event not only in MCL cell lines but also in primary MCL. Remarkably, pUPD affected recurrent targets of deletion like 11q, 13q and 17p. Moreover, we identified 12 novel regions of recurrent gain and loss as well as 12 high-level amplifications and eight homozygously deleted regions hitherto undescribed in MCL. Interestingly, GeneChip analyses identified different genes, encoding proteins involved in microtubule dynamics, such as MAP2, MAP6 and TP53, as targets for chromosomal aberration in MCL. Further investigation, including mutation analyses, fluorescence in situ hybridisation as well as epigenetic and expression studies, revealed additional aberrations frequently affecting these genes. In total, 19 of 20 MCL cases, which were subjected to genetic and epigenetic analyses, and five of six MCL cell lines harboured at least one aberration in MAP2, MAP6 or TP53. These findings provide evidence that alterations of microtubule dynamics might be one of the critical events in MCL lymphomagenesis contributing to chromosomal instability

Testing for pharmacogenomic predictors of ppRNFL thinning in individuals exposed to vigabatrin

BACKGROUND: The anti-seizure medication vigabatrin (VGB) is effective for controlling seizures, especially infantile spasms. However, use is limited by VGB-associated visual field loss (VAVFL). The mechanisms by which VGB causes VAVFL remains unknown. Average peripapillary retinal nerve fibre layer (ppRNFL) thickness correlates with the degree of visual field loss (measured by mean radial degrees). Duration of VGB exposure, maximum daily VGB dose, and male sex are associated with ppRNFL thinning. Here we test the hypothesis that common genetic variation is a predictor of ppRNFL thinning in VGB exposed individuals. Identifying pharmacogenomic predictors of ppRNFL thinning in VGB exposed individuals could potentially enable safe prescribing of VGB and broader use of a highly effective drug. METHODS: Optical coherence topography (OCT) and GWAS data were processed from VGB-exposed individuals (n = 71) recruited through the EpiPGX Consortium. We conducted quantitative GWAS analyses for the following OCT measurements: (1) average ppRNFL, (2) inferior quadrant, (3) nasal quadrant, (4) superior quadrant, (5) temporal quadrant, (6) inferior nasal sector, (7) nasal inferior sector, (8) superior nasal sector, and (9) nasal superior sector. Using the summary statistics from the GWAS analyses we conducted gene-based testing using VEGAS2. We conducted nine different PRS analyses using the OCT measurements. To determine if VGB-exposed individuals were predisposed to having a thinner RNFL, we calculated their polygenic burden for retinal thickness. PRS alleles for retinal thickness were calculated using published summary statistics from a large-scale GWAS of inner retinal morphology using the OCT images of UK Biobank participants. RESULTS: The GWAS analyses did not identify a significant association after correction for multiple testing. Similarly, the gene-based and PRS analyses did not reveal a significant association that survived multiple testing. CONCLUSION: We set out to identify common genetic predictors for VGB induced ppRNFL thinning. Results suggest that large-effect common genetic predictors are unlikely to exist for ppRNFL thinning (as a marker of VAVFL). Sample size was a limitation of this study. However, further recruitment is a challenge as VGB is rarely used today because of this adverse reaction. Rare variants may be predictors of this adverse drug reaction and were not studied here

A pharmacogenomic assessment of psychiatric adverse drug reactions to levetiracetam

OBJECTIVE: Levetiracetam (LEV) is an effective anti-seizure medicine, but 10-20% of people treated with LEV report psychiatric side-effects and up to 1% may have psychotic episodes. Pharmacogenomic predictors of these adverse drug reactions (ADRs) have yet to be identified. We sought to determine the contribution of both common and rare genetic variation to psychiatric and behavioural ADRs associated with LEV. METHODS: This case-control study compared cases of LEV-associated behavioural disorder (n=149) or psychotic reaction (n=37) to LEV-exposed people with no history of psychiatric ADRs (n=920). All samples were of European ancestry. We performed GWAS analysis comparing those with LEV ADRs to controls. We estimated the polygenic risk scores (PRS) for schizophrenia and compared cases with LEV-associated psychotic reaction to controls. Rare variant burden analysis was performed using exome sequence data of cases with psychotic reactions (n=18) and controls (n=122). RESULTS: Univariate GWAS found no significant associations with either LEV-ADR. PRS analysis showed that cases of LEV-associated psychotic reaction had an increased PRS for schizophrenia relative to controls (p = 0.0097, estimate = 0.4886). The rare-variant analysis found no evidence of an increased burden of rare genetic variants in people who had experienced LEV-associated psychotic reaction relative to controls. SIGNIFICANCE: The polygenic burden for schizophrenia is a risk factor for LEV-associated psychotic reaction. To assess the clinical utility of PRS as a predictor, it should be tested in an independent and ideally prospective cohort. Larger sample sizes are required for the identification of significant univariate common genetic signals or rare genetic signals associated with psychiatric LEV-ADRs

Propagating semantic information in biochemical network models

<p>Abstract</p> <p>Background</p> <p>To enable automatic searches, alignments, and model combination, the elements of systems biology models need to be compared and matched across models. Elements can be identified by machine-readable biological annotations, but assigning such annotations and matching non-annotated elements is tedious work and calls for automation.</p> <p>Results</p> <p>A new method called "semantic propagation" allows the comparison of model elements based not only on their own annotations, but also on annotations of surrounding elements in the network. One may either propagate feature vectors, describing the annotations of individual elements, or quantitative similarities between elements from different models. Based on semantic propagation, we align partially annotated models and find annotations for non-annotated model elements.</p> <p>Conclusions</p> <p>Semantic propagation and model alignment are included in the open-source library semanticSBML, available on sourceforge. Online services for model alignment and for annotation prediction can be used at <url>http://www.semanticsbml.org</url>.</p