Transcriptional changes in trichothiodystrophy cells

Mutations in three of the genes encoding the XPB, XPD and TTDA components of transcription factor TFIIH can result in the clinical phenotype of trichothiodystrophy (TTD). Different mutations in XPB and XPD can instead cause xeroderma pigmentosum (XP). The completely different features of these disorders have been attributed to TTD being a transcription syndrome. In order to detect transcriptional differences between TTD and XP cells from the XP-D complementation group, we have compared gene expression profiles in cultured fibroblasts from normal, XP and TTD donors. Although we detected transcriptional differences between individual cell strains, using an algorithm of moderate stringency, we did not identify any genes whose expression was reproducibly different in proliferating fibroblasts from each type of donor. Following UV-irradiation, many genes were up- and down-regulated in all three cell types. The microarray analysis indicated some apparent differences between the different donor types, but on more detailed inspection, these turned out to be false positives. We conclude that there are minimal differences in gene expression in proliferating fibroblasts from TTD, XP-D and normal donors

Superparamagnetic behaviour of antiferromagnetic DyPO4 nanoparticles

We report on the low-temperature magnetic ac-susceptibility of antiferromagnetic DyPO4 nanoparticles with a very high surface to volume ratio. The results are interpreted in terms of superparamagnetic relaxation of the Neel vector arising from a relatively large number approx 0.2 Na of uncompensated spins probably existing on the surface of the nanoparticles. The activation energy of the relaxation process is found to be Ea / kB = (2.6+-0.1) K within a model taking into account the magnetic interaction between nanoparticles.Comment: 3 pages, 1 figure, Espcrc2, ICM0

Live and Dead Nodes

In this paper, we explore the consequences of a distinction between `live' and `dead' network nodes; `live' nodes are able to acquire new links whereas `dead' nodes are static. We develop an analytically soluble growing network model incorporating this distinction and show that it can provide a quantitative description of the empirical network composed of citations and references (in- and out-links) between papers (nodes) in the SPIRES database of scientific papers in high energy physics. We also demonstrate that the death mechanism alone can result in power law degree distributions for the resulting network.Comment: 12 pages, 3 figures. To be published in Computational and Mathematical Organization Theor

A vocabulary-independent generation framework for DBpedia and beyond

The dbpedia Extraction Framework, the generation framework behind one of the Linked Open Data cloud’s central hubs, has limitations which lead to quality issues with the dbpedia dataset. Therefore, we provide a new take on its Extraction Framework that allows for a sustainable and general-purpose Linked Data generation framework by adapting a semantic-driven approach. The proposed approach decouples, in a declarative manner, the extraction, transformation, and mapping rules execution. This way, among others, interchanging different schema annotations is supported, instead of being coupled to a certain ontology as it is now, because the dbpedia Extraction Framework allows only generating a certain dataset with a single semantic representation. In this paper, we shed more light to the added value that this aspect brings. We provide an extracted dbpedia dataset using a different vocabulary, and give users the opportunity to generate a new dbpedia dataset using a custom combination of vocabularies

Neutrino induced hard exclusive D_s production

Motivated by the possibility to use high intensity neutrino beams for neutrino-nucleon scattering experiments we analyze charged current induced exclusive meson production within the framework of generalized parton distributions. The cross section for hard exclusive D_s production is estimated in this formalism to leading order in QCD. The integrated cross section proves to be sizable. It is shown that the considered process is well suited to provide novel information on the gluon structure of nucleons, which is contained in the generalized gluon parton distribution.Comment: 7 pages; modified plots in Fig. 3; accepted for publication in Phys. Lett.

Investigating plywood behaviour in outdoor conditions

Moisture behaviour of plywood is investigated in combination with detailed structural analysis. In the lab, neutron radiography and X-ray computed tomography (X-ray CT) were used to map the moisture distribution and internal structure of plywood respectively. In an outdoor natural weathering test, the average moisture content (MC) and moisture distribution of plywood were monitored using a continuous moisture measurement set-up and an adapted electrical method, respectively. The structural changes of the specimens during weathering were recorded by using X-ray CT. Based on the interrelationship of moisture behaviour and structure, suggestions are given for improving the water resistance of plywood by optimising structure

Assessing and refining mappings to RDF to improve dataset quality

RDF dataset quality assessment is currently performed primarily after data is published. However, there is neither a systematic way to incorporate its results into the dataset nor the assessment into the publishing workflow. Adjustments are manually -but rarely- applied. Nevertheless, the root of the violations which often derive from the mappings that specify how the RDF dataset will be generated, is not identified. We suggest an incremental, iterative and uniform validation workflow for RDF datasets stemming originally from (semi-) structured data (e.g., CSV, XML, JSON). In this work, we focus on assessing and improving their mappings. We incorporate (i) a test-driven approach for assessing the mappings instead of the RDF dataset itself, as mappings reflect how the dataset will be formed when generated; and (ii) perform semi-automatic mapping refinements based on the results of the quality assessment. The proposed workflow is applied to diverse cases, e.g., large, crowdsourced datasets such as DBpedia, or newly generated, such as iLastic. Our evaluation indicates the efficiency of our workflow, as it significantly improves the overall quality of an RDF dataset in the observed cases

The population genetics of clonal and partially clonal diploids.

The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci)

Life, Death and Preferential Attachment

Scientific communities are characterized by strong stratification. The highly skewed frequency distribution of citations of published scientific papers suggests a relatively small number of active, cited papers embedded in a sea of inactive and uncited papers. We propose an analytically soluble model which allows for the death of nodes. This model provides an excellent description of the citation distributions for live and dead papers in the SPIRES database. Further, this model suggests a novel and general mechanism for the generation of power law distributions in networks whenever the fraction of active nodes is small.Comment: 5 pages, 2 figure