Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions

<p>Abstract</p> <p>Background</p> <p>In all eukaryotic species examined, genes that are chromosomal neighbours are more similar in their expression than random gene pairs. Currently, it is still unclear how much of this local co-expression is caused by direct transcriptional interactions, and how much is due to shared chromatin environments.</p> <p>Results</p> <p>We analysed neighbouring genes in <it>Arabidopsis thaliana</it>. At large intergenic distances (>400 bp), divergently and convergently transcribed gene pairs show very similar levels of co-expression, mediated most likely by shared chromatin environments. At gene distances below 400 bp, co-expression is strongly enhanced only for divergently transcribed gene pairs, indicating bi-directional transcription from a single promoter. Conversely, co-expression is suppressed for short convergently or uni-directionally transcribed pairs. This suppression points to transcriptional interference concentrated at the 3' end, e.g., in the context of transcription termination.</p> <p>Conclusions</p> <p>Classifying linked gene pairs by their orientation, we are able to partially tease apart the different levels of regional expression modulation. (i) Regional chromatin characteristics modulate the accessibility for regulation and transcription, regardless of gene orientation; the strength of this chromatin effect can be assessed from divergently or convergently transcribed distant neighbours. (ii) Shared promoter regions up to 400 bp in length enhance the co-expression of close bi-directional neighbours. (iii) Transcriptional interference of close neighbours is concentrated at the 3' ends of genes, and reduces co-expression on average by 40%.</p

Probing gluon helicity distribution and quark transversity through hyperon polarization in singly polarized pp collisions

We study the polarization of hyperon in different processes in singly polarized $pp$ collisions, in particular its relation to the polarized parton distributions. We show that by measuring hyperon polarization in particularly chosen processes, one can extract useful information on these parton distributions. We show in particular that, by measuring the $\Sigma^+$ polarization in high $p_T$ direct photon production process, one can extract information on the gluon helicity distribution; and by measuring the transverse polarization of hyeprons with high $p_T$ in singly polarized reactions, one can obtain useful information on the transversity distribution. We present the numerical results obtained for those hyperon polarizations using different models for parton distribution function and those for the spin transfer in fragmentation processes.Comment: 25 pages, 8 figures, to appear in Phys. Rev.

Integral Field Spectroscopy of the Central Regions of 3C 120: Evidence of a Past Merging Event

IFS combined with HST WFPC imaging were used to characterize the central regions of the Seyfert 1 radio galaxy 3C 120. We carried out the analysis of the data, deriving intensity maps of different emission lines and the continua at different wavelengths from the observed spectra. Applying a 2D modeling to the HST images we decoupled the nucleus and the host galaxy, and analyzed the host morphology. The host is a highly distorted bulge dominated galaxy, rich in substructures. We developed a new technique to model the IFS data extending the 2D modeling. Using this technique we separated the Seyfert nucleus and the host galaxy spectra, and derived a residual data cube with spectral and spatial information of the different structures in 3C 120. Three continuum-dominated structures (named A, B, and C) and other three extended emission line regions (EELRs, named E1, E2 and E3) are found in 3C 120 which does not follow the general behavior of a bulge dominated galaxy. We also found shells in the central kpc that may be remnants of a past merging event in this galaxy. The origin of E1 is most probably due to the interaction of the radio-jet of 3C 120 with the intergalactic medium. Structures A, B, and the shell at the southeast of the nucleus seem to correspond to a larger morphological clumpy structure that may be a tidal tail, consequence of the past merging event. We found a bright EELR (E2) in the innermost part of this tidal tail, nearby the nucleus, which shows a high ionization level. The kinematics of the E2 region and its connection to the tidal tail suggest that the tail has channeled gas from the outer regions to the center.Comment: 55 pages, 18 figures and 5 tables Accepted by AP

Intermediate Tail Dependence: A Review and Some New Results

The concept of intermediate tail dependence is useful if one wants to quantify the degree of positive dependence in the tails when there is no strong evidence of presence of the usual tail dependence. We first review existing studies on intermediate tail dependence, and then we report new results to supplement the review. Intermediate tail dependence for elliptical, extreme value and Archimedean copulas are reviewed and further studied, respectively. For Archimedean copulas, we not only consider the frailty model but also the recently studied scale mixture model; for the latter, conditions leading to upper intermediate tail dependence are presented, and it provides a useful way to simulate copulas with desirable intermediate tail dependence structures.Comment: 25 pages, 1 figur

Integrable theory of quantum transport in chaotic cavities

The problem of quantum transport in chaotic cavities with broken time-reversal symmetry is shown to be completely integrable in the universal limit. This observation is utilised to determine the cumulants and the distribution function of conductance for a cavity with ideal leads supporting an arbitrary number $n$ of propagating modes. Expressed in terms of solutions to the fifth Painlev\'e transcendent and/or the Toda lattice equation, the conductance distribution is further analysed in the large-$n$ limit that reveals long exponential tails in the otherwise Gaussian curve.Comment: 4 pages; final version to appear in Physical Review Letter

Radio Sensing with Large Intelligent Surface for 6G

This paper leverages the potential of Large Intelligent Surface (LIS) for radio sensing in 6G wireless networks. Major research has been undergone about its communication capabilities but it can be exploited as a formidable tool for radio sensing. By taking advantage of arbitrary communication signals occurring in the scenario, we apply direct processing to the output signal from the LIS to obtain a radio map that describes the physical presence of passive devices (scatterers, humans) which act as virtual sources due to the communication signal reflections. We then assess the usage of machine learning (k-means clustering), image processing and computer vision (template matching and component labeling) to extract meaningful information from these radio maps. As an exemplary use case, we evaluate this method for both active and passive user detection in an indoor setting. The results show that the presented method has high application potential as we are able to detect around 98% of humans passively and 100% active users by just using communication signals of commodity devices even in quite unfavorable Signal-to-Noise Ratio (SNR) conditions

What’s so bad about scientism?

In their attempt to defend philosophy from accusations of uselessness made by prominent scientists, such as Stephen Hawking, some philosophers respond with the charge of ‘scientism.’ This charge makes endorsing a scientistic stance, a mistake by definition. For this reason, it begs the question against these critics of philosophy, or anyone who is inclined to endorse a scientistic stance, and turns the scientism debate into a verbal dispute. In this paper, I propose a different definition of scientism, and thus a new way of looking at the scientism debate. Those philosophers who seek to defend philosophy against accusations of uselessness would do philosophy a much better service, I submit, if they were to engage with the definition of scientism put forth in this paper, rather than simply make it analytic that scientism is a mistake

Pharmacological profile of the sodium current in human stem cell-derived cardiomyocytes compares to heterologous Nav1.5+β1 model

The cardiac Nav1.5 mediated sodium current (I-Na) generates the upstroke of the action potential in atrial and ventricular myocytes. Drugs that modulate this current can therefore be antiarrhythmic or proarrhythmic, which requires preclinical evaluation of their potential drug-induced inhibition or modulation of Nav1.5. Since Nav1.5 assembles with, and is modulated by, the auxiliary beta 1-subunit, this subunit can also affect the channel's pharmacological response. To investigate this, the effect of known Nav1.5 inhibitors was compared between COS-7 cells expressing Nav1.5 or Nav1.5+beta 1 using whole-cell voltage clamp experiments. For the open state class Ia blockers ajmaline and quinidine, and class Ic drug flecainide, the affinity did not differ between both models. For class Ib drugs phenytoin and lidocaine, which are inactivated state blockers, the affinity decreased more than a twofold when beta 1 was present. Thus, beta 1 did not influence the affinity for the class Ia and Ic compounds but it did so for the class Ib drugs. Human stem cell-derived cardiomyocytes (hSC-CMs) are a promising translational cell source for in vitro models that express a representative repertoire of channels and auxiliary proteins, including beta 1. Therefore, we subsequently evaluated the same drugs for their response on the I-Na in hSC-CMs. Consequently, it was expected and confirmed that the drug response of I-Na in hSC-CMs compares best to I-Na expressed by Nav1.5+beta 1

Tensor Regression with Applications in Neuroimaging Data Analysis

Classical regression methods treat covariates as a vector and estimate a corresponding vector of regression coefficients. Modern applications in medical imaging generate covariates of more complex form such as multidimensional arrays (tensors). Traditional statistical and computational methods are proving insufficient for analysis of these high-throughput data due to their ultrahigh dimensionality as well as complex structure. In this article, we propose a new family of tensor regression models that efficiently exploit the special structure of tensor covariates. Under this framework, ultrahigh dimensionality is reduced to a manageable level, resulting in efficient estimation and prediction. A fast and highly scalable estimation algorithm is proposed for maximum likelihood estimation and its associated asymptotic properties are studied. Effectiveness of the new methods is demonstrated on both synthetic and real MRI imaging data.Comment: 27 pages, 4 figure