ExprAlign - the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles

<p>Abstract</p> <p>Background</p> <p>Sequence identification of ESTs from non-model species offers distinct challenges particularly when these species have duplicated genomes and when they are phylogenetically distant from sequenced model organisms. For the common carp, an environmental model of aquacultural interest, large numbers of ESTs remained unidentified using BLAST sequence alignment. We have used the expression profiles from large-scale microarray experiments to suggest gene identities.</p> <p>Results</p> <p>Expression profiles from ~700 cDNA microarrays describing responses of 7 major tissues to multiple environmental stressors were used to define a co-expression landscape. This was based on the Pearsons correlation coefficient relating each gene with all other genes, from which a network description provided clusters of highly correlated genes as 'mountains'. We show that these contain genes with known identities and genes with unknown identities, and that the correlation constitutes evidence of identity in the latter. This procedure has suggested identities to 522 of 2701 unknown carp ESTs sequences. We also discriminate several common carp genes and gene isoforms that were not discriminated by BLAST sequence alignment alone. Precision in identification was substantially improved by use of data from multiple tissues and treatments.</p> <p>Conclusion</p> <p>The detailed analysis of co-expression landscapes is a sensitive technique for suggesting an identity for the large number of BLAST unidentified cDNAs generated in EST projects. It is capable of detecting even subtle changes in expression profiles, and thereby of distinguishing genes with a common BLAST identity into different identities. It benefits from the use of multiple treatments or contrasts, and from the large-scale microarray data.</p

Slowing rates of regional exhumation in the western Himalaya: fission track evidence from the Indus Fan

Weuse apatite fission track ages from sediments recovered by the International Ocean Discovery Program in the Laxmi Basin, Arabian Sea, to constrain exhumation rates in the western Himalaya and Karakoram since 15.5 Ma. With the exception of a Triassic population in the youngest 0.93 Ma samples supplied from western Peninsular India, apatite fission track ages are overwhelmingly Cenozoic, largely <25 Ma, consistent with both a Himalaya–Karakoram source and rapid erosion. Comparison of the minimum cooling age of each sample with depositional age (lag time) indicates an acceleration in exhumation between 7.8 and 7.0 Ma, with lag times shortening from ∼6.0 Myr at 8.5–7.8 Ma to being within error of zero between 7.0 and 5.7 Ma. Sediment supply at 7.0–5.7 Mawas largely from the Karakoram, and to a lesser extent the Himalaya, based on U–Pb zircon ages from the same samples. This time coincides with a period of drying in the Himalayan foreland caused by weaker summermonsoons andWesterly winds. It also correlates with a shift of erosion away from the Karakoram, Kohistan and the Tethyan Himalaya towards more erosion of the Lesser and Greater Himalaya and Nanga Parbat, as shown by zircon U–Pb provenance data, and especially after 5.7 Ma based on Nd isotope data. Samples younger than 5.7 Ma have lag times of ∼4.5 Myr, similar to Holocene Indus delta sediments

Excitation function of nucleon and pion elliptic flow in relativistic heavy-ion collisions

Within a relativistic transport (ART) model for heavy-ion collisions, we show that the recently observed characteristic change from out-of-plane to in-plane elliptic flow of protons in mid-central Au+Au collisions as the incident energy increases is consistent with the calculated results using a stiff nuclear equation of state (K=380 MeV). We have also studied the elliptic flow of pions and the transverse momentum dependence of both the nucleon and pion elliptic flow in order to gain further insight about the collision dynamics.Comment: 8 pages, 2 figure

Phonon anharmonicity and negative thermal expansion in SnSe

The anharmonic phonon properties of SnSe in the Pnma phase were investigated with a combination of experiments and first-principles simulations. Using inelastic neutron scattering (INS) and nuclear resonant inelastic X-ray scattering (NRIXS), we have measured the phonon dispersions and density of states (DOS) and their temperature dependence, which revealed a strong, inhomogeneous shift and broadening of the spectrum on warming. First-principles simulations were performed to rationalize these measurements, and to explain the previously reported anisotropic thermal expansion, in particular the negative thermal expansion within the Sn-Se bilayers. Including the anisotropic strain dependence of the phonon free energy, in addition to the electronic ground state energy, is essential to reproduce the negative thermal expansion. From the phonon DOS obtained with INS and additional calorimetry measurements, we quantify the harmonic, dilational, and anharmonic components of the phonon entropy, heat capacity, and free energy. The origin of the anharmonic phonon thermodynamics is linked to the electronic structure.Comment: 14 pages, 12 figure

Consensus of the Second-order Multi-agent Systems under Asynchronous Switching with a Controller Fault

© 2019, Institute of Control, Robotics and Systems and The Korean Institute of Electrical Engineers and Springer-Verlag GmbH Germany, part of Springer Nature. Asynchronous switching differing from asynchronous consensus may hinder the system to reach a consensus. This receives very limited attention, especially when the multi-agent systems have a controller fault. In order to analyze the consensus in this situation, this paper studies the consensus of the second-order multi-agent systems under asynchronous switching with a controller fault. We convert the consensus problems under asynchronous switching into stability problems and obtain important results for consensus with the aid of linear matrix inequalities. An example is given to illustrate the effect of asynchronous switching on the consensus, and to validate the analytical results in this paper

Monodisperse core/shell and other complex structured nanocrystals and methods of preparing the same

Provides new compositions containing nearly monodisperse colloidal core/shell semiconductor nanocrystals with high photoluminescence quantum yields (PL QY), as well as other complex structured semiconductor nanocrystals. This invention also provides new synthetic methods for preparing these nanocrystals, and new devices comprising these compositions. In addition to core/shell semiconductor nanocrystals, this patent also provides complex semiconductor nanostructures, quantum shells, quantum wells, doped nanocrystals, and other multiple-shelled semiconductor nanocrystals

Model Checking Strategies from Synthesis Over Finite Traces

The innovations in reactive synthesis from {\em Linear Temporal Logics over finite traces} (LTLf) will be amplified by the ability to verify the correctness of the strategies generated by LTLf synthesis tools. This motivates our work on {\em LTLf model checking}. LTLf model checking, however, is not straightforward. The strategies generated by LTLf synthesis may be represented using {\em terminating} transducers or {\em non-terminating} transducers where executions are of finite-but-unbounded length or infinite length, respectively. For synthesis, there is no evidence that one type of transducer is better than the other since they both demonstrate the same complexity and similar algorithms. In this work, we show that for model checking, the two types of transducers are fundamentally different. Our central result is that LTLf model checking of non-terminating transducers is \emph{exponentially harder} than that of terminating transducers. We show that the problems are EXPSPACE-complete and PSPACE-complete, respectively. Hence, considering the feasibility of verification, LTLf synthesis tools should synthesize terminating transducers. This is, to the best of our knowledge, the \emph{first} evidence to use one transducer over the other in LTLf synthesis.Comment: Accepted by ATVA 2