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

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

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

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

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

QUANTIZATION OF A CLASS OF PIECEWISE AFFINE TRANSFORMATIONS ON THE TORUS

We present a unified framework for the quantization of a family of discrete dynamical systems of varying degrees of "chaoticity". The systems to be quantized are piecewise affine maps on the two-torus, viewed as phase space, and include the automorphisms, translations and skew translations. We then treat some discontinuous transformations such as the Baker map and the sawtooth-like maps. Our approach extends some ideas from geometric quantization and it is both conceptually and calculationally simple.Comment: no. 28 pages in AMSTE

Painting the ideal home: using art to express visions of technologically supported independent living for older people in North East England

This paper describes the investigation of the development of future technological products to support older people in everyday living through the agency of a community art group. Recent research has identified a number of challenges facing designers seeking to use traditional participatory design approaches to gather technology requirements data from older people. Here, a project is described that sought to get a group of older people to think creatively about their needs and desires for technological support through the medium of paint. The artistic expression technique described in this article allowed the identification of issues that had also been found by previous research that used a range of different techniques. This indicates that the approach shows promise, as it allows information to be gathered in an environment that is comfortable and familiar using methods already known by the participants and which they find enjoyable. It provides a complement (or possible alternative) to standard protocols and has the potential benefit of extracting even richer information as the primary task for participants is enjoyable in its own right and is not associated with an interrogative process. Furthermore, it is argued that some of the key risks of traditional approaches are lessened or removed by the naturalistic setting of this approach

Oligocene niche shift, Miocene diversification – cold tolerance and accelerated speciation rates in the St. John’s Worts (Hypericum, Hypericaceae)

Background: Our aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus Hypericum is one of these. Results: To investigate the effect of macroecological niche shifts on evolutionary success we combine historical biogeography with analyses of diversification dynamics and climatic niche shifts in a phylogenetic framework. Hypericum evolved cold tolerance c. 30 million years ago, and successfully colonized all ice-free continents, where today ~500 species exist. The other members of Hypericaceae stayed in their tropical habitats and evolved into ~120 species. We identified a 15–20 million year lag between the initial change in temperature preference in Hypericum and subsequent diversification rate shifts in the Miocene. Conclusions: Contrary to the dramatic niche shift early in the evolution of Hypericum most extant species occur in temperate climates including high elevations in the tropics. These cold/temperate niches are a distinctive characteristic of Hypericum. We conclude that the initial release from an evolutionary constraint (from tropical to temperate climates) is an important novelty in Hypericum. However, the initial shift in the adaptive landscape into colder climates appears to be a precondition, and may not be directly related to increased diversification rates. Instead, subsequent events of mountain formation and further climate cooling may better explain distribution patterns and species-richness in Hypericum. These findings exemplify important macroevolutionary patterns of plant diversification during large-scale global climate change