Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Background Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system. Results In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function. Conclusions We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.

Influence of the feeding mechanism on deposits of square particles

In a previous paper [Hidalgo et al., Phys. Rev. Lett. 103, 118001 (2009)] it was shown that square particles deposited in a silo tend to align with a diagonal parallel to the gravity, giving rise to a deposit with very particular properties. Here we explore, both experimentally and numerically, the effect on these properties of the filling mechanism. In particular, we modify the volume fraction of the initial configuration from which the grains are deposited. Starting from a very dilute case, increasing the volume fraction results in an enhancement of the disorder in the final deposit characterized by a decrease of the final packing fraction and a reduction of the number of particles oriented with their diagonal in the direction of gravity. However, for very high initial volume fractions, the final packing fraction increases again. This result implies that two deposits with the same final packing fraction can be obtained from very different initial conditions. The structural properties of such deposits are analyzed, revealing that, although the final volume fraction is the same, their micromechanical properties notably differ.

Tailoring the surface density of silicon nanocrystals embedded in SiOx single layers

In this article, we explore the possibility of modifying the silicon nanocrystal areal density in SiOx single layers, while keeping constant their size. For this purpose, a set of SiOx monolayers with controlled thickness between two thick SiO2 layers has been fabricated, for four different compositions (x=1, 1.25, 1.5, or 1.75). The structural properties of the SiO x single layers have been analyzed by transmission electron microscopy (TEM) in planar view geometry. Energy-filtered TEM images revealed an almost constant Si-cluster size and a slight increase in the cluster areal density as the silicon content increases in the layers, while high resolution TEM images show that the size of the Si crystalline precipitates largely decreases as the SiO x stoichiometry approaches that of SiO2. The crystalline fraction was evaluated by combining the results from both techniques, finding a crystallinity reduction from 75% to 40%, for x = 1 and 1.75, respectively. Complementary photoluminescence measurements corroborate the precipitation of Si-nanocrystals with excellent emission properties for layers with the largest amount of excess silicon. The integrated emission from the nanoaggregates perfectly scales with their crystalline state, with no detectable emission for crystalline fractions below 40%. The combination of the structural and luminescence observations suggests that small Si precipitates are submitted to a higher compressive local stress applied by the SiO2 matrix that could inhibit the phase separation and, in turn, promotes the creation of nonradiative paths.

Structure of a-Si:H/a-Si1-xCx:H multilayers deposited in a reactor with automated substrate holder

This paper deals with the structural properties of a-Si:H/a-Si1-xCx: H multilayers deposited by glow-discharge decomposition of SiH4 and SiH4 and CH4 mixtures. The main feature of the rf plasma reactor is an automated substrate holder. The plasma stabilization time and its influence on the multilayer obtained is discussed. A series of a-Si:H/a-Si1-xCx: H multilayers has been deposited and characterized by secondary ion mass spectrometry (SIMS), X-ray diffraction (XRD) and transmission electron microscopy (TEM). No asymmetry between the two types of interface has been observed. The results show that the multilayers present a very good periodicity and low roughness. The difficulty of determining the abruptness of the multilayer at the nanometer scale is discussed.

Structural and functional properties of genes involved in human cancer

Background: One of the main goals of cancer genetics is to identify the causative elements at the molecular level leading to cancer.Results: We have conducted an analysis of a set of genes known to be involved in cancer in order to unveil their unique features that can assist towards the identification of new candidate cancer genes. Conclusion: We have detected key patterns in this group of genes in terms of the molecular function or the biological process in which they are involved as well as sequence properties. Based on these features we have developed an accurate Bayesian classification model with which human genes have been scored for their likelihood of involvement in cancer.

Structural and optical properties of dilute InAsN grown by molecular beam epitaxy

We perform a structural and optical characterization of InAs1¿xNx epilayers grown by molecular beam epitaxy on InAs substrates x 2.2% . High-resolution x-ray diffraction HRXRD is used to obtain information about the crystal quality and the strain state of the samples and to determine the N content of the films. The composition of two of the samples investigated is also obtained with time-of-flight secondary ion mass spectroscopy ToF-SIMS measurements. The combined analysis of the HRXRD and ToF-SIMS data suggests that the lattice parameter of InAsN might significantly deviate from Vegard"s law. Raman scattering and far-infrared reflectivity measurements have been carried out to investigate the incorporation of N into the InAsN alloy. N-related local vibrational modes are detected in the samples with higher N content. The origin of the observed features is discussed. We study the compositional dependence of the room-temperature band gap energy of the InAsN alloy. For this purpose, photoluminescence and optical absorption measurements are presented. The results are analyzed in terms of the band-anticrossing BAC model. We find that the room-temperature coupling parameter for InAsN within the BAC model is CNM=2.0 0.1 eV.

Collective dynamic properties in simple crystals: Influence of the structural disorder

Collective dynamic properties in Lennard-Jones crystals are investigated by molecular dynamics simulation. The study is focused on properties such as the dynamic structure factors, the longitudinal and transverse currents and the density of states. The influence on these properties of the structural disorder is analyzed by comparing the results for one-component crystals with those for liquids and supercooled liquids at analogous conditions. The effects of species-disorder on the collective properties of binary crystals are also discussed.

Silicon quantum dots embedded in a SiO2 matrix: From structural study to carrier transport properties

We study the details of electronic transport related to the atomistic structure of silicon quantum dots embedded in a silicon dioxide matrix using ab initio calculations of the density of states. Several structural and composition features of quantum dots (QDs), such as diameter and amorphization level, are studied and correlated with transport under transfer Hamiltonian formalism. The current is strongly dependent on the QD density of states and on the conduction gap, both dependent on the dot diameter. In particular, as size increases, the available states inside the QD increase, while the QD band gap decreases due to relaxation of quantum confinement. Both effects contribute to increasing the current with the dot size. Besides, valence band offset between the band edges of the QD and the silica, and conduction band offset in a minor grade, increases with the QD diameter up to the theoretical value corresponding to planar heterostructures, thus decreasing the tunneling transmission probability and hence the total current. We discuss the influence of these parameters on electron and hole transport, evidencing a correlation between the electron (hole) barrier value and the electron (hole) current, and obtaining a general enhancement of the electron (hole) transport for larger (smaller) QD. Finally, we show that crystalline and amorphous structures exhibit enhanced probability of hole and electron current, respectively.

Ferromagnetic shape memory alloys: structural and thermal properties

The most extensively studied Heusler alloys are those based on the Ni-Mn-Ga system. However, to overcome the high cost of Gallium and the usually low martensitic transformation temperature, the search for Ga-free alloys has been recently attempted, particularly, by introducing In, Sn or Sb. In this work, two alloys (Mn50Ni35.5In14.5 and Ni50Mn35In15) have been obtained by melt spinning. We outline their structural and thermal behaviour. Mn50Ni35.5In14.5 alloy has the transformation above room temperature whereas Ni50Mn35In15 does not have this transformation in the temperature range here analyzed

Structural and optical properties of high quality zinc-blende/wurtzite GaAs nanowire heterostructures

The structural and optical properties of three different kinds of GaAs nanowires with 100% zinc-blende structure and with an average of 30% and 70% wurtzite are presented. A variety of shorter and longer segments of zinc-blende or wurtzite crystal phases are observed by transmission electron microscopy in the nanowires. Sharp photoluminescence lines are observed with emission energies tuned from 1.515 eV down to 1.43 eV when the percentage of wurtzite is increased. The downward shift of the emission peaks can be understood by carrier confinement at the interfaces, in quantum wells and in random short period superlattices existent in these nanowires, assuming a staggered band offset between wurtzite and zinc-blende GaAs. The latter is confirmed also by time-resolved measurements. The extremely local nature of these optical transitions is evidenced also by cathodoluminescence measurements. Raman spectroscopy on single wires shows different strain conditions, depending on the wurtzite content which affects also the band alignments. Finally, the occurrence of the two crystallographic phases is discussed in thermodynamic terms.

Further evidence on the statistical properties of real GNP

The well-known lack of power of unit root tests has often been attributed to the shortlength of macroeconomic variables and also to DGP s that depart from the I(1)-I(0)alternatives. This paper shows that by using long spans of annual real GNP and GNPper capita (133 years) high power can be achieved, leading to the rejection of both theunit root and the trend-stationary hypothesis. This suggests that possibly neither modelprovides a good characterization of these data. Next, more flexible representations areconsidered, namely, processes containing structural breaks (SB) and fractional ordersof integration (FI). Economic justification for the presence of these features in GNP isprovided. It is shown that the latter models (FI and SB) are in general preferred to theARIMA (I(1) or I(0)) ones. As a novelty in this literature, new techniques are appliedto discriminate between FI and SB models. It turns out that the FI specification ispreferred, implying that GNP and GNP per capita are non-stationary, highly persistentbut mean-reverting series. Finally, it is shown that the results are robust when breaksin the deterministic component are allowed for in the FI model. Some macroeconomicimplications of these findings are also discussed.

Is the observed persistence spurious? A test for fractional integration versus short memory and structural breaks

Although it is commonly accepted that most macroeconomic variables are nonstationary, it is often difficult to identify the source of the non-stationarity. In particular, it is well-known that integrated and short memory models containing trending components that may display sudden changes in their parameters share some statistical properties that make their identification a hard task. The goal of this paper is to extend the classical testing framework for I(1) versus I(0)+ breaks by considering a a more general class of models under the null hypothesis: non-stationary fractionally integrated (FI) processes. A similar identification problem holds in this broader setting which is shown to be a relevant issue from both a statistical and an economic perspective. The proposed test is developed in the time domain and is very simple to compute. The asymptotic properties of the new technique are derived and it is shown by simulation that it is very well-behaved in finite samples. To illustrate the usefulness of the proposed technique, an application using inflation data is also provided.

What is what?: A simple time-domain test of long-memory vs. structural breaks

This paper proposes a new time-domain test of a process being I(d), 0 < d = 1, under the null, against the alternative of being I(0) with deterministic components subject to structural breaks at known or unknown dates, with the goal of disentangling the existing identification issue between long-memory and structural breaks. Denoting by AB(t) the different types of structural breaks in the deterministic components of a time series considered by Perron (1989), the test statistic proposed here is based on the t-ratio (or the infimum of a sequence of t-ratios) of the estimated coefficient on yt-1 in an OLS regression of ?dyt on a simple transformation of the above-mentioned deterministic components and yt-1, possibly augmented by a suitable number of lags of ?dyt to account for serial correlation in the error terms. The case where d = 1 coincides with the Perron (1989) or the Zivot and Andrews (1992) approaches if the break date is known or unknown, respectively. The statistic is labelled as the SB-FDF (Structural Break-Fractional Dickey- Fuller) test, since it is based on the same principles as the well-known Dickey-Fuller unit root test. Both its asymptotic behavior and finite sample properties are analyzed, and two empirical applications are provided.