Pseudo-messenger RNA: Phantoms of the transcriptome

The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo-messenger RNA to be RNA molecules that resemble protein- coding mRNA, but cannot encode full-length proteins owing to disruptions of the reading frame. Using a rigorous computational pipeline, which rules out sequencing errors, we identify 10,679 pseudo - messenger RNAs ( approximately half of which are transposonassociated) among the 102,801 FANTOM3 mouse cDNAs: just over 10% of the FANTOM3 transcriptome. These comprise not only transcribed pseudogenes, but also disrupted splice variants of otherwise protein- coding genes. Some may encode truncated proteins, only a minority of which appear subject to nonsense- mediated decay. The presence of an excess of transcripts whose only disruptions are opal stop codons suggests that there are more selenoproteins than currently estimated. We also describe compensatory frameshifts, where a segment of the gene has changed frame but remains translatable. In summary, we survey a large class of non- standard but potentially functional transcripts that are likely to encode genetic information and effect biological processes in novel ways. Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level.

XPS study of the major minerals in bauxite: Gibbsite, bayerite and (pseudo-)boehmite

Synthetic corundum (Al2O3), gibbsite (Al(OH)(3)), bayerite (Al(OH)(3)), boehmite (AlO(OH)) and pseudoboehmite (AlO(OH)) have been studied by high resolution XPS. The chemical compositions based on the XPS survey scans were in good agreement with the expected composition. High resolution A12p scans showed no significant changes in binding energy, with all values between 73.9 and 74.4 eV. Only bayerite showed two transitions, associated with the presence of amorphous material in the sample. More information about the chemical and crystallographic environment was obtained from the 0 Is high resolution spectra. Here a clear distinction could be made between oxygen in the crystal structure, hydroxyl groups and adsorbed water. Oxygen in the crystal structure was characterised by a binding energy of about 530.6 eV in all minerals. Hydroxyl groups, present either in the crystal structure or on the surface, exhibited binding energies around 531.9 eV, while water on the surface showed binding energies around 533.0 eV. A distinction could be made between boehmite and pseudoboehmite based on the slightly lower ratio of oxygen to hydroxyl groups and water in pseudoboehmite. (c) 2005 Elsevier Inc. All rights reserved.

A comparison of pseudo-paper and paper prototyping methods for mobile evaluations

The research presented in this paper is part of an ongoing investigation into how best to support meaningful lab-based usability evaluations of mobile technologies. In particular, we report on a comparative study of (a) a standard paper prototype of a mobile application used to perform an early-phase seated (static) usability evaluation, and (b) a pseudo-paper prototype created from the paper prototype used to perform an early-phase,contextually-relevant, mobile usability evaluation. We draw some initial conclusions regarding whether it is worth the added effort of conducting a usability evaluation of a pseudo-paper prototype in a contextually-relevant setting during early-phase user interface development.

Real teams or pseudo teams? The changing landscape needs a better map

Commentary on focal article by Tannenbaum et al., Teams are changing: Are research and practice evolving fast enough?

A comparison of pseudo-paper and paper prototyping methods for mobile evaluations

The research presented in this paper is part of an ongoing investigation into how best to support meaningful lab-based usability evaluations of mobile technologies. In particular, we report on a comparative study of (a) a standard paper prototype of a mobile application used to perform an early-phase seated (static) usability evaluation, and (b) a pseudo-paper prototype created from the paper prototype used to perform an early-phase,contextually-relevant, mobile usability evaluation. We draw some initial conclusions regarding whether it is worth the added effort of conducting a usability evaluation of a pseudo-paper prototype in a contextually-relevant setting during early-phase user interface development.

Continuity of Pseudo-differential Operators on Bessel And Besov Spaces

We study the continuity of pseudo-differential operators on Bessel potential spaces Hs|p (Rn ), and on the corresponding Besov spaces B^(s,q)p (R ^n). The modulus of continuity ω we use is assumed to satisfy j≥0, ∑ [ω(2−j )Ω(2j )]2 < ∞ where Ω is a suitable positive function.

Identification of DNA-binding proteins by incorporating evolutionary information into pseudo amino acid composition via the top-n-gram approach

DNA-binding proteins are crucial for various cellular processes and hence have become an important target for both basic research and drug development. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to establish an automated method for rapidly and accurately identifying DNA-binding proteins based on their sequence information alone. Owing to the fact that all biological species have developed beginning from a very limited number of ancestral species, it is important to take into account the evolutionary information in developing such a high-throughput tool. In view of this, a new predictor was proposed by incorporating the evolutionary information into the general form of pseudo amino acid composition via the top-n-gram approach. It was observed by comparing the new predictor with the existing methods via both jackknife test and independent data-set test that the new predictor outperformed its counterparts. It is anticipated that the new predictor may become a useful vehicle for identifying DNA-binding proteins. It has not escaped our notice that the novel approach to extract evolutionary information into the formulation of statistical samples can be used to identify many other protein attributes as well.

Fractional Derivatives and Fractional Powers as Tools in Understanding Wentzell Boundary Value Problems for Pseudo-Differential Operators Generating Markov Processes

Mathematics Subject Classification: 26A33, 31C25, 35S99, 47D07.

Well-Posedness of the Cauchy Problem for Inhomogeneous Time-Fractional Pseudo-Differential Equations

Mathematics Subject Classification: 26A33, 45K05, 35A05, 35S10, 35S15, 33E12

Pseudo-Differential Operators in a Wave Diffraction Problem with Impedance Conditions

Mathematics Subject Classification: 35J05, 35J25, 35C15, 47H50, 47G30

Investigation of a Stolarsky type Inequality for Integrals in Pseudo-Analysis

MSC 2010: 03E72, 26E50, 28E10