Electron density effects in the modulation spectroscopy of strained and lattice-matched InGaAs/InAlAs/InP high-electron-mobility transistor structures

The effects of the channel electron density on the interband optical transitions of strained (x=0.6 and 0.65) and lattice-matched (x=0.53) InxGa1–xAs/In0.52Al0.48As/InP high-electron-mobility transistor structures have been investigated by phototransmittance at room temperature. Analysis of the ground and first excited transitions for low and high densities, respectively, enabled a separate estimation of the electron densities occupying each one of the first two subbands. It was found necessary to include the modulation of the phase-space filling in the analysis of the spectra, especially for the samples with a high electron density, in which case this modulation mechanism becomes dominant

A Cosine Similarity-Based Method to Infer Variability of Chromatin Accessibility at the Single-Cell Level

Cellular identity between generations of developing cells is propagated through the epigenome particularly via the accessible parts of the chromatin. It is now possible to measure chromatin accessibility at single-cell resolution using single-cell assay for transposase accessible chromatin (scATAC-seq), which can reveal the regulatory variation behind the phenotypic variation. However, single-cell chromatin accessibility data are sparse, binary, and high dimensional, leading to unique computational challenges. To overcome these difficulties, we developed PRISM, a computational workflow that quantifies cell-to-cell chromatin accessibility variation while controlling for technical biases. PRISM is a novel multidimensional scaling-based method using angular cosine distance metrics coupled with distance from the spatial centroid. PRISM takes differences in accessibility at each genomic region between single cells into account. Using data generated in our lab and publicly available, we showed that PRISM outperforms an existing algorithm, which relies on the aggregate of signal across a set of genomic regions. PRISM showed robustness to noise in cells with low coverage for measuring chromatin accessibility. Our approach revealed the previously undetected accessibility variation where accessible sites differ between cells but the total number of accessible sites is constant. We also showed that PRISM, but not an existing algorithm, can find suppressed heterogeneity of accessibility at CTCF binding sites. Our updated approach uncovers new biological results with profound implications on the cellular heterogeneity of chromatin architecture

Observations of a pulse driven cool polar jet by SDO/AIA

Context. We observe a solar jet at north polar coronal hole (NPCH) using SDO AIA 304 {\deg}A image data on 3 August 2010. The jet rises obliquely above the solar limb and then retraces its propagation path to fall back. Aims. We numerically model this observed solar jet by implementing a realistic (VAL-C) model of solar temperature. Methods. We solve two-dimensional ideal magnetohydrodynamic equations numerically to simulate the observed solar jet. We consider a localized velocity pulse that is essentially parallel to the background magnetic field lines and initially launched at the top of the solar photosphere. The pulse steepens into a shock at higher altitudes, which triggers plasma perturbations that exhibit the observed features of the jet. The typical direction of the pulse also clearly exhibits the leading front of the moving jet. Results. Our numerical simulations reveal that a large amplitude initial velocity pulse launched at the top of the solar photosphere produces in general the observed properties of the jet, e.g., upward and backward average velocities, height, width, life-time, and ballistic nature. Conclusions. The close matching between the jet observations and numerical simulations provides first strong evidence for the formation of this jet by a single velocity pulse. The strong velocity pulse is most likely generated by the low- atmospheric reconnection in the polar region which results in triggering of the jet. The downflowing material of the jet most likely vanishes in the next upcoming velocity pulses from lower solar atmosphere, and therefore distinctly launched a single jet upward in the solar atmosphere is observed.Comment: 8 pages, 4 figures, A&

The three-dimensional structure of sunspots II. The moat flow at two different heights

Many sunspots are surrounded by a radial outflow called the moat flow. We investigate the moat flow at two different heights of the solar atmosphere for a sunspot whose magnetic properties were reported in the first paper of this series. We use two simultaneous time series taken with the Transition Region And Coronal Explorer (TRACE) in white light and in the UV at 170 nm. The field-of-view is centered on the small sunspot NOAA 10886 located near disk center. Horizontal velocities are derived by applying two different local correlation tracking techniques. Outflows are found everywhere in the moat. In the inner moat, the velocities from the UV series are larger than those from white light, whereas in the outer part of the moat we find the converse result. The results imply that the white light velocities represent a general outflow of the quiet sun plasma in the moat, while UV velocities are dominated by small bright points that move faster than the general plasma flow.Comment: Manuscript accepted by Astronomy & Astrophysic

Interband transitions in InxGa1-xAs/In0.52Al0.48As single quantum wells studied by room-temperature modulation spectroscopy

Room-temperature phototransmittance and electrotransmittance of single quantum wells of InxGa1-xAs with In0.52Al0.48As barriers have been used to study the excitonic interband transitions between the confined conduction- and valence-band states. Peak assignment has been confirmed by photocurrent spectroscopy. The lattice-matched (x=0.53) and strained (x=0.6) structures were considered for two different well widths of 50 and 250 Å. Transition energies and broadening parameters were measured from the spectra of the wide well samples and studied as a function of the principal quantum number. Reasonably good agreement between theory and experiment has been achieved by using published values of the electronic band-structure parameters. An observed monotonic increase of the linewidth with the quantum number has been associated with the presence of well-width fluctuations due to rough interfaces

Immune evasion in cancer: mechanistic basis and therapeutic strategies

Cancer immune evasion is a major stumbling block in designing effective anticancer therapeutic strategies. Although considerable progress has been made in understanding how cancers evade destructive immunity, measures to counteract tumor escape have not kept pace. There are a number of factors that contribute to tumor persistence despite having a normal host immune system. Immune editing is one of the key aspects why tumors evade surveillance causing the tumors to lie dormant in patients for years through “equilibrium” and “senescence” before re- emerging. In addition, tumors exploit several immunological processes such as targeting the regulatory T cell function or their secretions, antigen presentation, modifying the production of immune suppressive mediators, tolerance and immune deviation. Besides these, tumor heterogeneity and metastasis also play a critical role in tumor growth. A number of potential targets like promoting Th1, NK cell, γδ T cell responses, inhibiting Treg functionality, induction of IL-12, use of drugs including phytochemicals have been designed to counter tumor progression with much success. Some natural agents and phytochemicals merit further study. For example, use of certain key polysaccharide components from mushrooms and plants have shown possess therapeutic impact on tumor-imposed genetic instability, anti-growth signaling, replicative immortality, deregulated metabolism etc. In this review, we will discuss the advances made towards understanding the basis of cancer immune evasion and summarize the efficacy of various therapeutic measures and targets that have been developed or are being investigated to enhance tumor rejection

Energy efficiency considerations in integrated IT and optical network resilient infrastructures

The European Integrated Project GEYSERS - Generalised Architecture for Dynamic Infrastructure Services - is concentrating on infrastructures incorporating integrated optical network and IT resources in support of the Future Internet with special emphasis on cloud computing. More specifically GEYSERS proposes the concept of Virtual Infrastructures over one or more interconnected Physical Infrastructures comprising both network and IT resources. Taking into consideration the energy consumption levels associated with the ICT today and the expansion of the Internet in size and complexity, that incurring increased energy consumption of both IT and network resources, energy efficient infrastructure design becomes critical. To address this need, in the framework of GEYSERS, we propose energy efficient design of infrastructures incorporating integrated optical network and IT resources, supporting resilient end-to-end services. Our modeling results quantify significant energy savings of the proposed solution by jointly optimizing the allocation of both network and IT resources

Multi-branch convolutional neural network for identification of small non-coding RNA genomic loci

Genomic regions that encode small RNA genes exhibit characteristic patterns in their sequence, secondary structure, and evolutionary conservation. Convolutional Neural Networks are a family of algorithms that can classify data based on learned patterns. Here we present MuStARD an application of Convolutional Neural Networks that can learn patterns associated with user-defined sets of genomic regions, and scan large genomic areas for novel regions exhibiting similar characteristics. We demonstrate that MuStARD is a generic method that can be trained on different classes of human small RNA genomic loci, without need for domain specific knowledge, due to the automated feature and background selection processes built into the model. We also demonstrate the ability of MuStARD for inter-species identification of functional elements by predicting mouse small RNAs (pre-miRNAs and snoRNAs) using models trained on the human genome. MuStARD can be used to filter small RNA-Seq datasets for identification of novel small RNA loci, intra- and inter- species, as demonstrated in three use cases of human, mouse, and fly pre-miRNA prediction. MuStARD is easy to deploy and extend to a variety of genomic classification questions. Code and trained models are freely available at gitlab.com/RBP_Bioinformatics/mustard.peer-reviewe

DIANA-miRGen v4 : indexing promoters and regulators for more than 1500 microRNAs

Deregulation of microRNA (miRNA) expression plays a critical role in the transition from a physiological to a pathological state. The accurate miRNA promoter identification in multiple cell types is a fundamental endeavor towards understanding and characterizing the underlying mechanisms of both physiological as well as pathological conditions. DIANA-miRGen v4 (www.microrna.gr/mirgenv4) provides cell type specific miRNA transcription start sites (TSSs) for over 1500 miRNAs retrieved from the analysis of >1000 cap analysis of gene expression (CAGE) samples corresponding to 133 tissues, cell lines and primary cells available in FANTOM repository. MiRNA TSS locations were associated with transcription factor binding site (TFBSs) annotation, for >280 TFs, derived from analyzing the majority of ENCODE ChIP-Seq datasets. For the first time, clusters of cell types having common miRNA TSSs are characterized and provided through a user friendly interface with multiple layers of customization. DIANA-miRGen v4 significantly improves our understanding of miRNA biogenesis regulation at the transcriptional level by providing a unique integration of high-quality annotations for hundreds of cell specific miRNA promoters with experimentally derived TFBSs.peer-reviewe