Association between nocturnal oxygen desaturation and ischaemic stroke outcomes

CLINICAL RATIONALE FOR THE STUDY

This study aimed to assess the association between nocturnal hypoxemia and early acute ischaemic stroke (AIS) outcomes in patients without oxygen supplementation.

MATERIAL AND METHODS

One hundred and six AIS patients consecutively admitted to the stroke unit were included in this study. Baseline demographic and medical data and arterial blood saturation (SpO2) measurements during night-sleep (from 10pm to 6am) were examined for their association with stroke outcomes, including the National Institutes of Health Stroke Scale (NIHSS) score on the 7th day or differences between the NIHSS score on the 1st day and the 7th day after stroke onset. Measurements of SpO2 were made using a pulse oximeter of the Spacelabs Medical Inc. (USA) monitoring system, and the number of apnoea episodes and their duration were recorded by ECG Holter with respiration monitoring (CardioMem®, Getamed, GE).

RESULTS

The study showed that age (Spearman's r = 0.207, p = 0.033) and parameters attributable to anaemia (RBC r = -0.205, p = 0.035, Hb r = -0.225, p = 0.02 and HCT r = -0.196, p = 0.044), atrial fibrillation and ischaemic changes in both brain hemispheres (p = 0.023 and 0.01, respectively) were correlated with the study outcomes. In terms of saturation parameters, we demonstrated that the 'total desaturation burden' (i.e. [100% minus actual measured SpO2%] x apnoea duration) and multiple apnoeas of longer than 20 seconds were correlated with worse functional outcomes. Measures of shorter desaturation episodes (i.e. SpO2 oxygen desaturation index (ODI) at 3% and 4%, and time-weighted desaturations below the determined thresholds (SpO2 from 95% to 85%) demonstrated non-significant associations with the study outcomes.

CONCLUSIONS AND CLINICAL IMPLICATIONS

This study demonstrated that long-lasting desaturation episodes during the night, depicted by the 'total desaturation burden', were correlated with worse functional outcomes in AIS, while measures of shorter desaturation episodes were not correlated. In future clinical trials, indications for oxygen supplementation should include the methodology of personalised medicine and introduce individual approaches based on specially formulated, novel multifactorial algorithms.

Stochastic Gene Expression Revisited

We investigate the model of gene expression in the form of Iterated Function System (IFS), where the probability of choice of any iterated map depends on the state of the phase space. Random jump times of the process mark activation periods of the gene when pre-mRNA molecules are produced before mRNA and protein processing phases occur. The main idea is inspired by the continuous-time piecewise deterministic Markov process describing stochastic gene expression. We show that for our system there exists a unique invariant limit measure. We provide full probabilistic description of the process with a comparison of our results to those obtained for the model with continuous time.

Drainage ditches enhance forest succession in a raised bog but do not affect the spatial pattern of tree encroachment

The study was conducted in the raised bog Kusowo (Baltic region, West Pomerania, Poland). Along a transect line crossing two open mires affected by forest succession we analysed tree age distribution. One of those mires had been drained in the past years and still retained some open ditches, while the other one was located far from the ditches. Every 10 meters along the transect line one tree was drilled at the root collar in order to determine its age. We also conducted phytosociological analyses and short-term water level measurements in the sample plots. We expected faster tree encroachment in the undisturbed part of the open mire. The results showed, that there were no significant differences in water table level and in soil moisture indicator values between the formerly drained and undisturbed open mire. There were also no statistically significant differences in tree encroachment between the disturbed and undisturbed mires. Location and the age distribution of the trees suggest that changes in the tree growth conditions cannot be directly explained by the general decreasing of water level in the bog, although periods following drainage works were associated with more numerous establishment of young trees, in the drained part of the bog as well as in the part not directly affected by drainage ditches.

Application of the Goodwin model to autoregulatory feedback for stochastic gene expression

In this paper we analyse stochastic expression of a single gene with its dynamics given by the classical Goodwin model with mRNA and protein contribution. We compare the effect of the presence of positive and negative feedback on the transcription regulation. In such cases we observe two qualitatively different types of asymptotic behaviour. In the case of a negative feedback loop, under sufficient conditions, one can find a stationary density for mRNA and protein molecules. In the case of a positive feedback loop we observe extinction of both types of molecules with time.

Gutzwiller wave function for finite systems: superconductivity in the Hubbard model

We study the superconducting phase of the Hubbard model using the Gutzwiller variational wave function (GWF) and the recently proposed diagrammatic expansion technique (DE-GWF). The DE-GWF method works on the level of the full GWF and in the thermodynamic limit. Here, we consider a finite-size system to study the accuracy of the results as a function of the system size (which is practically unrestricted). We show that the finite-size scaling used, e.g. in the variational Monte Carlo method can lead to significant, uncontrolled errors. The presented research is the first step towards applying the DE-GWF method in studies of inhomogeneous situations, including systems with impurities, defects, inhomogeneous phases, or disorder.

Seqinspector: position-based navigation through the ChIP-seq data landscape to identify gene expression regulators

Background

The regulation of gene expression in eukaryotic cells is a complex process that involves epigenetic modifications and the interaction of DNA with multiple transcription factors. This process can be studied with unprecedented sensitivity using a combination of chromatin immunoprecipitation and next-generation DNA sequencing (ChIP-seq). Available ChIP-seq data can be further utilized to interpret new gene expression profiling experiments.

Results

Here, we describe seqinspector, a tool that accepts any set of genomic coordinates from ChIP-seq or RNA-seq studies to identify shared transcriptional regulators. The presented web resource includes a large collection of publicly available ChIP-seq and RNA-seq experiments (>1300 tracks) performed on transcription factors, histone modifications, RNA polymerases, enhancers and insulators in humans and mice. Over-representation is calculated based on the coverage computed directly from indexed files storing ChIP-seq data (bigwig). Therefore, seqinspector is not limited to pre-computed sets of gene promoters.

Conclusion

The tool can be used to identify common gene expression regulators for sets of co-expressed transcripts (including miRNAs, lncRNAs or any novel unannotated RNAs) or for sets of ChIP-seq peaks to identify putative protein-protein interactions or transcriptional co-factors. The tool is available at http://seqinspector.cremag.org.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-0938-4) contains supplementary material, which is available to authorized users.

On a stochastic gene expression with pre-mRNA, mRNA and protein contribution

In this paper we develop a model of stochastic gene expression, which is an extension of the model investigated in the paper [T. Lipniacki, P. Paszek, A. Marciniak-Czochra, A.R. Brasier, M. Kimmel, Transcriptional stochasticity in gene expression, J. Theor. Biol. 238 (2006) 348-367]. In our model, stochastic effects still originate from random fluctuations in gene activity status, but we precede mRNA production by the formation of pre-mRNA, which enriches classical transcription phase. We obtain a stochastically regulated system of ordinary differential equations (ODEs) describing evolution of pre-mRNA, mRNA and protein levels. We perform mathematical analysis of a long-time behavior of this stochastic process, identified as a piece-wise deterministic Markov process (PDMP). We check exact results using numerical simulations for the distributions of all three types of particles. Moreover, we investigate the deterministic (adiabatic) limit state of the process, when depending on parameters it can exhibit two specific types of behavior: bistability and the existence of the limit cycle. The latter one is not present when only two kinds of gene expression products are considered.