ALBERT

Description: Seismic refraction, profiles in Yunnan Province, southwestern China, define the crustal structure in an area of active tectonics on the southern end of the Himalaya-Burma arc. The crustal thickness ranges from 38 to 46 kilometers, and the relatively low mean crustal velocity indicates a crustal composition compatible with normal continental crust and consisting mainly of meta-sedimentary and silicic intrusive rocks, with little mafic or ultramafic component. This composition suggests a crustal evolution involving sedimentary processes on the flank of the Yangtze platform rather than the accretion of oceanic island arcs, as has been proposed. An anomalously low upper-mantle velocity observed on one profile but not on another at right angles to it may indicate active tectonic processes in the mantle or seismic anisotropy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kan, R J -- Hu, H X -- Zeng, R S -- Mooney, W D -- McEvilly, T V -- New York, N.Y. -- Science. 1986 Oct 24;234(4775):433-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17792016" target="_blank"〉PubMed〈/a〉

Description: The radiation pressure acceleration of protons in the interaction of Gaussian laser pulses and surface modulated targets is examined by multi-dimensional particle-in-cell simulations. It is shown that strong longitudinal quasi-static magnetic field is generated on the modulated surface of the target, which significantly enhances the transverse diffusion of electrons. This is beneficial for suppressing the transverse Rayleigh-Taylor instability. Finally, the surface of the accelerated proton beams becomes smoother than that in the case of the planar target, and a final mono-energetic proton beam is obtained by using the surface modulated target.

Description: Motivation: The identification of microRNA (miRNA) target sites is fundamentally important for studying gene regulation. There are dozens of computational methods available for miRNA target site prediction. Despite their existence, we still cannot reliably identify miRNA target sites, partially due to our limited understanding of the characteristics of miRNA target sites. The recently published CLASH (crosslinking ligation and sequencing of hybrids) data provide an unprecedented opportunity to study the characteristics of miRNA target sites and improve miRNA target site prediction methods. Results: Applying four different machine learning approaches to the CLASH data, we identified seven new features of miRNA target sites. Combining these new features with those commonly used by existing miRNA target prediction algorithms, we developed an approach called TarPmiR for miRNA target site prediction. Testing on two human and one mouse non-CLASH datasets, we showed that TarPmiR predicted more than 74.2% of true miRNA target sites in each dataset. Compared with three existing approaches, we demonstrated that TarPmiR is superior to these existing approaches in terms of better recall and better precision. Availability and Implementation: The TarPmiR software is freely available at http://hulab.ucf.edu/research/projects/miRNA/TarPmiR/ . Contacts: haihu@cs.ucf.edu or xiaoman@mail.ucf.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: MicroRNAs (miRNAs) play critical roles in gene regulation. Although it is well known that multiple miRNAs may work as miRNA modules to synergistically regulate common target mRNAs, the understanding of miRNA modules is still in its infancy. Results: We employed the recently generated high throughput experimental data to study miRNA modules. We predicted 181 miRNA modules and 306 potential miRNA modules. We observed that the target sites of these predicted modules were in general weaker compared with those not bound by miRNA modules. We also discovered that miRNAs in predicted modules preferred to bind unconventional target sites rather than canonical sites. Surprisingly, contrary to a previous study, we found that most adjacent miRNA target sites from the same miRNA modules were not within the range of 10–130 nucleotides. Interestingly, the distance of target sites bound by miRNAs in the same modules was shorter when miRNA modules bound unconventional instead of canonical sites. Our study shed new light on miRNA binding and miRNA target sites, which will likely advance our understanding of miRNA regulation. Availability and implementation: The software miRModule can be freely downloaded at http://hulab.ucf.edu/research/projects/miRNA/miRModule . Supplementary information: Supplementary data are available at Bioinformatics online. Contact: haihu@cs.ucf.edu or xiaoman@mail.ucf.edu .

Description: Earthquake taking place in a fluid-saturated porous medium can generate electromagnetic (EM) waves because of the electrokinetic effect. These generated EM waves arrive at a distant observatory much earlier than the seismic waves because their velocities are much faster than those of the seismic waves. They may explain the early EM signals which have been detected before the detection of the seismic waves after the occurrences of earthquakes. In this study, we attempt to analyse such a kind of early EM signals induced by an earthquake because of the electrokinetic effect. The earthquake is assumed to be a fault slip and is modelled by a moment tensor point source. With Pride's equations quantifying the coupling between seismic and EM waves, we first present a real-axis integration (RAI) algorithm to calculate the seismoelectric wavefields in a layered porous formation. Although full waveforms can be calculated by such a RAI technique, individual waves cannot be easily separated from the full waveforms. The need to compute the individual waves is eminent for the purpose of investigating the early EM waves, because these EM waves are usually several orders weaker than and are masked by the EM signals accompanying the seismic waves in the full waveforms. Therefore, we further develop a branch-cut integration (BCI) algorithm, by transforming the original wavenumber integral along the real axis in the complex wavenumber plane for the RAI technique to a sum of integrals along the vertical branch cuts and the residues of the poles. For performing the integrations along the vertical branch cuts, determination of the Riemann sheets are explained and displayed. Finally, the seismoelectric wavefields are represented in forms allowing calculating individual waves.

Description: We validate the branch-cut integration (BCI) technique presented in the companion paper. The numerical result shows that the early electromagnetic (EM) signal calculated by the BCI method is in good agreement with that in the full waveform calculated by the real-axis integration method. We further find that to calculate the early EM signal only the integrals along the vertical branch cuts that are around the k 0 and k em branch points are needed, whereas neither the integrals along the vertical branch cuts around the Pf ( P ), S and Ps branch points nor the residues of the poles are necessary. We conduct numerical experiments to analyse the early EM signal generated by an earthquake in a porous half-space, including its component analysis, sensitivities to the conductivity, viscosity and recording depth, and radiation pattern. The component analysis shows that the total early EM ( em Total ) signal is not a single wave but a combination of three kinds of EM waves, namely, the direct em d wave radiated from the source, the reflected em r waves converted from the em d wave, the direct P and S waves at the free surface and the critically refracted EM 0 waves which are also converted from the em d wave, the direct P and S waves at the free surface. Three pulses, namely, the em d -, P - and S -converted pulses are identified in the em Total signal according to their different arrival times. The em d -converted pulse arrives immediately after the occurrence of the earthquake and it is a combination of the em d wave, the em r and EM 0 waves converted from the em d wave at the free surface. The P -converted ( S -converted, respectively) pulse owns an arrival time approximately equal to that spent by the P wave ( S wave, respectively) travelling from the hypocentre to the epicentre, and it is a combination of the em r and EM 0 waves converted from the P wave ( S wave, respectively) at the free surface. The P -converted pulse is usually weaker than the S - and em d -converted pulses in the electrogram and is always invisible in the magnetogram. Our simulation of an M 6 earthquake shows that the electric field of the early EM signal at a receiver with an epicentral distance of 100 km is on the order of 0.1 μVm –1 for a low conductivity on the order of 10 – 5 S m – 1 , whereas it is on the order of 0.0001μVm –1 for a high conductivity on the order of 10 – 2 S m – 1 . The magnetic field of the early EM signal keeps on the order of 0.1 pT for either a low or high conductivity. The insensitivity of the magnetic field to the conductivity indicates that the early EM signal will be easier to be observed in the magnetic field than in the electric field in a highly conductive medium. Our numerical experiment also reveals that the amplitude of the early EM signal is almost inversely proportional to the viscosity of the pore fluid, implying that the earthquake will generate stronger EM signal in a low-viscosity region than in a high-viscosity one. Receiver depth has little impact on the amplitude of the early EM signal in record, indicating that we can place EM monitoring instrument at a certain depth where the noise can be well suppressed. The radiation pattern of the early EM signal is analysed, and it shows the spatial distribution of the early EM signal direction-dependent.

Description: Oncolytic virotherapy is a growing treatment modality that uses replicating viruses as selective antineoplastic agents. Safety and efficacy considerations dictate that an ideal oncolytic agent would discriminate between normal and cancer cells on the basis of common genetic abnormalities in human cancers. Here, we identify a naturally occurring alphavirus (M1)...

Description: Comprehensive motif discovery under experimental conditions is critical for the global understanding of gene regulation. To generate a nearly complete list of human DNA motifs under given conditions, we employed a novel approach to de novo discover significant co-occurring DNA motifs in 349 human DNase I hypersensitive site datasets. We predicted 845 to 1325 motifs in each dataset, for a total of 2684 non-redundant motifs. These 2684 motifs contained 54.02 to 75.95% of the known motifs in seven large collections including TRANSFAC. In each dataset, we also discovered 43 663 to 2 013 288 motif modules, groups of motifs with their binding sites co-occurring in a significant number of short DNA regions. Compared with known interacting transcription factors in eight resources, the predicted motif modules on average included 84.23% of known interacting motifs. We further showed new features of the predicted motifs, such as motifs enriched in proximal regions rarely overlapped with motifs enriched in distal regions, motifs enriched in 5' distal regions were often enriched in 3' distal regions, etc. Finally, we observed that the 2684 predicted motifs classified the cell or tissue types of the datasets with an accuracy of 81.29%. The resources generated in this study are available at http://server.cs.ucf.edu/predrem/ .