Single cell transcriptome analysis using next generation sequencing.

The heterogeneity of tissues, especially in cancer research, is a central issue in transcriptome analysis. In recent years, research has primarily focused on the development of methods for single cell analysis. Single cell analysis aims at gaining (novel) insights into biological processes of healthy and diseased cells. Some of the challenges in transcriptome analysis concern low abundance of sample starting material, necessary sample amplification steps and subsequent analysis. In this study, two fundamentally different approaches to amplification were compared using next-generation sequencing analysis: I. exponential amplification using polymerase-chain-reaction (PCR) and II. linear amplification. For both approaches, protocols for single cell extraction, cell lysis, cDNA synthesis, cDNA amplification and preparation of next-generation sequencing libraries were developed. We could successfully show that transcriptome analysis of low numbers of cells is feasible with both exponential and linear amplification. Using exponential amplification, the highest amplification rates up to 106 were possible. The reproducibility of results is a strength of the linear amplification method. The analysis of next generation sequencing data in single cell samples showed detectable expression in at least 16.000 genes. The variance between samples results in a need to work with a greater amount of biological replicates. In summary it can be said that single cell transcriptome analysis with next generation sequencing is possible but improvements leading to a higher yield of transcriptome reads is required. In the near future by comparing single cancer cells with healthy ones for example, a basis for improved prognosis and diagnosis can be realised

Quantum Double-Torus

A symmetry extending the $T^2$-symmetry of the noncommutative torus $T^2_q$ is studied in the category of quantum groups. This extended symmetry is given by the quantum double-torus defined as a compact matrix quantum group consisting of the disjoint union of $T^2$ and $T^2_{q^2}$. The bicross-product structure of the polynomial Hopf algebra of the quantum double-torus is computed. The Haar measure and the complete list of unitary irreducible representations of the quantum double-torus are determined explicitly.Comment: 6 pages, no figures, amslatex, reformatted for Comptes Rendus, references added, typos and French correcte

Heat Conduction Process on Community Networks as a Recommendation Model

Using heat conduction mechanism on a social network we develop a systematic method to predict missing values as recommendations. This method can treat very large matrices that are typical of internet communities. In particular, with an innovative, exact formulation that accommodates arbitrary boundary condition, our method is easy to use in real applications. The performance is assessed by comparing with traditional recommendation methods using real data.Comment: 4 pages, 2 figure

The many facets of auditory display

In this presentation we will examine some of the ways sound can be used in a virtual world. We make the case that many different types of audio experience are available to us. A full range of audio experiences include: music, speech, real-world sounds, auditory displays, and auditory cues or messages. The technology of recreating real-world sounds through physical modeling has advanced in the past few years allowing better simulation of virtual worlds. Three-dimensional audio has further enriched our sensory experiences

Using non-speech sounds to provide navigation cues

This article describes 3 experiments that investigate the possibiity of using structured nonspeech audio messages called earcons to provide navigational cues in a menu hierarchy. A hierarchy of 27 nodes and 4 levels was created with an earcon for each node. Rules were defined for the creation of hierarchical earcons at each node. Participants had to identify their location in the hierarchy by listening to an earcon. Results of the first experiment showed that participants could identify their location with 81.5% accuracy, indicating that earcons were a powerful method of communicating hierarchy information. One proposed use for such navigation cues is in telephone-based interfaces (TBIs) where navigation is a problem. The first experiment did not address the particular problems of earcons in TBIs such as “does the lower quality of sound over the telephone lower recall rates,” “can users remember earcons over a period of time.” and “what effect does training type have on recall?” An experiment was conducted and results showed that sound quality did lower the recall of earcons. However; redesign of the earcons overcame this problem with 73% recalled correctly. Participants could still recall earcons at this level after a week had passed. Training type also affected recall. With personal training participants recalled 73% of the earcons, but with purely textual training results were significantly lower. These results show that earcons can provide good navigation cues for TBIs. The final experiment used compound, rather than hierarchical earcons to represent the hierarchy from the first experiment. Results showed that with sounds constructed in this way participants could recall 97% of the earcons. These experiments have developed our general understanding of earcons. A hierarchy three times larger than any previously created was tested, and this was also the first test of the recall of earcons over time

Phylogeny and New Intrageneric Classification of Allium (Alliaceae) Based on Nuclear Ribosomal DNA ITS Sequences

The internal transcribed spacer region (ITS) of nuclear ribosomal DNA was sequenced from 195 representative species of Allium, two species of Nothoscordum, and one species each of lpheion, Dichelostemma, and Tulbaghia. Within the Allium species the lengths of the ITS regions were in a range from 612 to 661 base pairs and pairwise genetic distances reached up to 46%. The ITS data supported the inclusion of Nectaroscordum, Caloscordum, and Milula into Allium. Subgenera Rhizirideum and Allium, as well as sects. Reticulatobulbosa and Oreiprason were non-monophyletic taxa. Based on the phylogenetic relations, a new classification of genus Allium consisting of 15 monophyletic subgenera is presented. Sections Microscordum, Anguinum, Porphyroprason, Vvedenskya, Butomissa, Cyathophora, and Reticulatobulbosa are raised to subgeneric rank. Sections Austromontana N. Friesen, Eduardia N. Friesen, Mediasia F. O. Khassanov, S. C. Yengalycheva et N. Friesen, Nigrimontana N. Friesen, Falcatifolia N. Friesen, and Condensatum N. Friesen are newly described. Series Daghestanica, Pallasia, and Scabriscapa, as well as subsects. Eremoprasum, Longivaginata, and Sikkimensia are raised to sectional rank. A taxonomic conspectus of Allium at sectional level is given

Recommendation model based on opinion diffusion

Information overload in the modern society calls for highly efficient recommendation algorithms. In this letter we present a novel diffusion based recommendation model, with users' ratings built into a transition matrix. To speed up computation we introduce a Green function method. The numerical tests on a benchmark database show that our prediction is superior to the standard recommendation methods.Comment: 5 pages, 2 figure

A toolkit of mechanism and context independent widgets

Most human-computer interfaces are designed to run on a static platform (e.g. a workstation with a monitor) in a static environment (e.g. an office). However, with mobile devices becoming ubiquitous and capable of running applications similar to those found on static devices, it is no longer valid to design static interfaces. This paper describes a user-interface architecture which allows interactors to be flexible about the way they are presented. This flexibility is defined by the different input and output mechanisms used. An interactor may use different mechanisms depending upon their suitability in the current context, user preference and the resources available for presentation using that mechanism

Antimony doping of Si layers grown by solid-phase epitaxy

We report here that layers of Si formed by solid-phase epitaxial growth (SPEG) can be doped intentionally. The sample consists initially of an upper layer of amorphous Si (~1 µm thick), a very thin intermediate layer of Sb (nominally 5 Å), and a thin lower layer of Pd (~500 Å), all electron-gun deposited on top of a single-crystal substrate (1–10 Ω cm, p type, orientation). After a heating cycle which induces epitaxial growth, electrically active Sb atoms are incorporated into the SPEG layer, as shown by the following facts: (a) the SPEG layer forms a p-n junction against the p-type substrate, (b) the Hall effect indicates strong n-type conduction of the layer, and (c) Auger electron spectra reveal the presence of Sb in the layer