Altered microRNA and target gene expression related to Tetralogy of Fallot

MicroRNAs (miRNAs) play an important role in guiding development and maintaining function of the human heart. Dysregulation of miRNAs has been linked to various congenital heart diseases including Tetralogy of Fallot (TOF), which represents the most common cyanotic heart malformation in humans. Several studies have identified dysregulated miRNAs in right ventricular (RV) tissues of TOF patients. In this study, we profiled genome-wide the whole transcriptome and analyzed the relationship of miRNAs and mRNAs of RV tissues of a homogeneous group of 22 non-syndromic TOF patients. Observed profiles were compared to profiles obtained from right and left ventricular tissue of normal hearts. To reduce the commonly observed large list of predicted target genes of dysregulated miRNAs, we applied a stringent target prediction pipeline integrating probabilities for miRNA-mRNA interaction. The final list of disease-related miRNA-mRNA pairs comprises novel as well as known miRNAs including miR-1 and miR-133, which are essential to cardiac development and function by regulating KCNJ2, FBN2, SLC38A3 and TNNI1. Overall, our study provides additional insights into post-transcriptional gene regulation of malformed hearts of TOF patients

Quantum critical dynamics of the two-dimensional Bose gas

The dilute, two-dimensional Bose gas exhibits a novel regime of relaxational dynamics in the regime k_B T > |\mu| where T is the absolute temperature and \mu is the chemical potential. This may also be interpreted as the quantum criticality of the zero density quantum critical point at \mu=0. We present a theory for this dynamics, to leading order in 1/\ln (\Lambda/ (k_B T)), where \Lambda is a high energy cutoff. Although pairwise interactions between the bosons are weak at low energy scales, the collective dynamics are strongly coupled even when \ln (\Lambda/T) is large. We argue that the strong-coupling effects can be isolated in an effective classical model, which is then solved numerically. Applications to experiments on the gap-closing transition of spin gap antiferromagnets in an applied field are presented.Comment: 9 pages, 10 figure

Relativistic Equilibrium Distribution by Relative Entropy Maximization

The equilibrium state of a relativistic gas has been calculated based on the maximum entropy principle. Though the relativistic equilibrium state was long believed to be the Juttner distribution, a number of papers have been published in recent years proposing alternative equilibrium states. However, some of these papers do not pay enough attention to the covariance of distribution functions, resulting confusion in equilibrium states. Starting from a fully covariant expression to avoid this confusion, it has been shown in the present paper that the Juttner distribution is the maximum entropy state if we assume the Lorentz symmetry.Comment: Six pages, no figure

SuperCYPsPred - a web server for the prediction of cytochrome activity

Cytochrome P450 enzymes (CYPs)-mediated drug metabolism influences drug pharmacokinetics and results in adverse outcomes in patients through drug-drug interactions (DDIs). Absorption, distribution, metabolism, excretion and toxicity (ADMET) issues are the leading causes for the failure of a drug in the clinical trials. As details on their metabolism are known for just half of the approved drugs, a tool for reliable prediction of CYPs specificity is needed. The SuperCYPsPred web server is currently focused on five major CYPs isoenzymes, which includes CYP1A2, CYP2C19, CYP2D6, CYP2C9 and CYP3A4 that are responsible for more than 80% of the metabolism of clinical drugs. The prediction models for classification of the CYPs inhibition are based on well-established machine learning methods. The models were validated both on cross-validation and external validation sets and achieved good performance. The web server takes a 2D chemical structure as input and reports the CYP inhibition profile of the chemical for 10 models using different molecular fingerprints, along with confidence scores, similar compounds, known CYPs information of drugs-published in literature, detailed interaction profile of individual cytochromes including a DDIs table and an overall CYPs prediction radar chart (http://insilico-cyp.charite.de/SuperCYPsPred/).The web server does not require log in or registration and is free to use

Derivatives of spin dynamics simulations

We report analytical equations for the derivatives of spin dynamics simulations with respect to pulse sequence and spin system parameters. The methods described are significantly faster, more accurate and more reliable than the finite difference approximations typically employed. The resulting derivatives may be used in fitting, optimization, performance evaluation and stability analysis of spin dynamics simulations and experiments. Keywords: NMR, EPR, simulation, analytical derivatives, optimal control, spin chemistry, radical pair.Comment: Accepted by The Journal of Chemical Physic

Stationarity, soft ergodicity, and entropy in relativistic systems

Recent molecular dynamics simulations show that a dilute relativistic gas equilibrates to a Juettner velocity distribution if ensemble velocities are measured simultaneously in the observer frame. The analysis of relativistic Brownian motion processes, on the other hand, implies that stationary one-particle distributions can differ depending on the underlying time-parameterizations. Using molecular dynamics simulations, we demonstrate how this relativistic phenomenon can be understood within a deterministic model system. We show that, depending on the time-parameterization, one can distinguish different types of soft ergodicity on the level of the one-particle distributions. Our analysis further reveals a close connection between time parameters and entropy in special relativity. A combination of different time-parameterizations can potentially be useful in simulations that combine molecular dynamics algorithms with randomized particle creation, annihilation, or decay processes.Comment: 4 page

The Simple Non-degenerate Relativistic Gas: Statistical Properties and Brownian Motion

This paper shows a novel calculation of the mean square displacement of a classical Brownian particle in a relativistic thermal bath. The result is compared with the expressions obtained by other authors. Also, the thermodynamic properties of a non-degenerate simple relativistic gas are reviewed in terms of a treatment performed in velocity space.Comment: 6 pages, 2 figure

Thermal equilibrium and statistical thermometers in special relativity

There is an intense debate in the recent literature about the correct generalization of Maxwell's velocity distribution in special relativity. The most frequently discussed candidate distributions include the Juettner function as well as modifications thereof. Here, we report results from fully relativistic one-dimensional (1D) molecular dynamics (MD) simulations that resolve the ambiguity. The numerical evidence unequivocally favors the Juettner distribution. Moreover, our simulations illustrate that the concept of 'thermal equilibrium' extends naturally to special relativity only if a many-particle system is spatially confined. They make evident that 'temperature' can be statistically defined and measured in an observer frame independent way.Comment: version accepted for publication (5 pages), part of the introduction modified, new figures, additional reference

mVOC: a database of microbial volatiles

Scents are well known to be emitted from flowers and animals. In nature, these volatiles are responsible for inter- and intra-organismic communication, e.g. attraction and defence. Consequently, they influence and improve the establishment of organisms and populations in ecological niches by acting as single compounds or in mixtures. Despite the known wealth of volatile organic compounds (VOCs) from species of the plant and animal kingdom, in the past, less attention has been focused on volatiles of microorganisms. Although fast and affordable sequencing methods facilitate the detection of microbial diseases, however, the analysis of signature or fingerprint volatiles will be faster and easier. Microbial VOCs (mVOCs) are presently used as marker to detect human diseases, food spoilage or moulds in houses. Furthermore, mVOCs exhibited antagonistic potential against pathogens in vitro, but their biological roles in the ecosystems remain to be investigated. Information on volatile emission from bacteria and fungi is presently scattered in the literature, and no public and up-to-date collection on mVOCs is available. To address this need, we have developed mVOC, a database available online at http://bioinformatics.charite.de/mvoc

Estimation of Mechanical Vibrations of the LHC Fast Magnetic Measurement System

Current installation of the Large Hadron Collider (LHC) particle accelerator at CERN has required the use of a harmonic coil magnetic measurement system to quantify the magnetic field harmonic quality of the superconducting, twin aperture LHC dipoles. Current and future needs for measuring fast changing magnetic fields necessitates the use of a rotating unit (RU) and associated electronics to drive this long shaft with increased speed and measurement bandwidth. Therefore, the Fast Magnetic Measurement Equipment (FAME) project has been launched to deliver such a system. A primary obstacle to achieving the goals of the FAME project is the possibility of amplifying mechanical vibrations due to increased speeds. This paper presents the methodology and results of an experimental investigation conducted to estimate mechanical vibrations of the long shaft within a cold-bore mounted anti-cryostat at various rotational speeds using magnetic measurements