Biomedical subjects

J Timmer

Publications and source records attributed to J Timmer.

At least 19 recordsLinked to original sources

PubMed2006

Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways.

Complex cellular networks regulate regeneration, detoxification and differentiation of hepatocytes. By combining experimental data with mathematical modelling, systems biology holds great promises to elucidate the key regulatory mechanisms involved and predict targets for efficient intervention. For the generation of high-quality quantitative data suitable for mathematical modelling a standardised in vitro system is essential. Therefore the authors developed standard operating procedures for the preparation and cultivation of primary mouse hepatocytes. To reliably monitor the dynamic induction of signalling pathways, the authors established starvation conditions and evaluated the extent of starvation-associated stress by quantifying several metabolic functions of cultured primary hepatocytes, namely activities of glutathione-S-transferase, glutamine synthetase, CYP3A as well as secretion of lactate and urea into the culture medium. Establishment of constant metabolic activities after an initial decrease compared with freshly isolated hepatocytes showed that the cultured hepatocytes achieve a new equilibrium state that was not affected by our starving conditions. To verify the highly reproducible dynamic activation of signalling pathways in the in vitro system, the authors examined the JAK-STAT, SMAD, PI3 kinase, MAP kinase, NF-kappaB and Wnt/beta-catenin signalling pathways. For the induction of gp130, JAK1 and STAT3 phosphorylation IL6 was used, whereas TGFbeta was applied to activate the phosphorylation of SMAD1, SMAD2 and SMAD3. Both Akt/PKB and ERK1/2 phosphorylation were stimulated by the addition of hepatocyte growth factor. The time-dependent induction of a pool of signalling competent beta-catenin was monitored in response to the inhibition of GSK3beta. To analyse whether phosphorylation is actually leading to transcriptional responses, luciferase reporter gene constructs driven by multiple copies of TGFbeta-responsive motives were applied, demonstrating a dose-dependent increase in luciferase activity. Moreover, the induction of apoptosis by the TNF-like cytokine Fas ligand was studied in the in vitro system. Thus, the mouse hepatocyte in vitro system provides an important basis for the generation of high-quality quantitative data under standardised cell culture conditions that is essential to elucidate critical hepatocellular functions by the systems biology approach.

Animals↗

PubMed2006

Parameter estimation in stochastic biochemical reactions.

Gene regulatory, signal transduction and metabolic networks are major areas of interest in the newly emerging field of systems biology. In living cells, stochastic dynamics play an important role; however, the kinetic parameters of biochemical reactions necessary for modelling these processes are often not accessible directly through experiments. The problem of estimating stochastic reaction constants from molecule count data measured, with error, at discrete time points is considered. For modelling the system, a hidden Markov process is used, where the hidden states are the true molecule counts, and the transitions between those states correspond to reaction events following collisions of molecules. Two different algorithms are proposed for estimating the unknown model parameters. The first is an approximate maximum likelihood method that gives good estimates of the reaction parameters in systems with few possible reactions in each sampling interval. The second algorithm, treating the data as exact measurements, approximates the number of reactions in each sampling interval by solving a simple linear equation. Maximising the likelihood based on these approximations can provide good results, even in complex reaction systems.

Algorithms↗

PubMed2005

Mixing properties of the Rössler system and consequences for coherence and synchronization analysis.

Cross-spectral and synchronization analysis of two independent, identical chaotic Rössler systems suggest a coupling although there is no interaction. This spuriously detected interaction can either be explained by the absence of mixing or by finite size effects. To decide which alternative holds the phase dynamics is studied by a model of the fluctuations derived from the system's equations. The basic assumption of the model is a diffusive character for the system which corresponds to mixing. Comparison of theoretical properties of the model with empirical properties of the Rössler system suggests that the system is mixing but the rate of mixing appears to be rather low.

Journal Article↗

PubMed2005

Dynamic cerebral autoregulation in acute ischemic stroke assessed from spontaneous blood pressure fluctuations.

BACKGROUND AND PURPOSE: This study investigates dynamic cerebral autoregulation assessed from spontaneous blood pressure (ABP) and cerebral blood flow velocity (CBFV) fluctuations and its time course in acute ischemic stroke. METHODS: Forty patients admitted with acute ischemic stroke in the territory of the middle cerebral artery (MCA) were enrolled. Admission National Institutes of Health Stroke score was 6+/-4. Study 1 was performed within 22 (+/-11) hours and study 2 was performed within 134 (+/-25) hours of ictus. The final analysis comprised 33 and 29 patients for study 1 and study 2, respectively. Twenty-five age- and sex-matched controls were studied. ABP (Finapres method) and CBFV in both MCAs (transcranial Doppler) were recorded over 10 minutes. Correlations between diastolic and mean ABP and CBFV fluctuations were averaged, yielding the correlation coefficient indices (Dx, Mx). Transfer function analysis was applied to obtain phase shift and gain between ABP and CBFV oscillations. RESULTS: No disturbance of autoregulation was indicated by all parameters at study 1. Separate analyses for clinical severity, stroke side, and size did not reveal significant differences for the various autoregulatory indices at study 1 and 2. At study 2, MCA flow velocity was significantly increased on both sides, the autoregulation index Mx was slightly but significantly (P<0.05) worse on both sides in comparison to study 1, and phase showed a trend toward poorer values on affected sides. No significant differences to controls occurred. Clinical outcome in patients completing both studies was good in all but one patient. CONCLUSIONS: Dynamic cerebral autoregulation assessed from spontaneous blood pressure fluctuations does not seem to be relevantly disturbed in early minor MCA stroke. At the subacute stage, slight autoregulatory disturbance may be present.

Adolescent↗

PubMed2005

On studentising and blocklength selection for the bootstrap on time series.

For independent data, non-parametric bootstrap is realised by resampling the data with replacement. This approach fails for dependent data such as time series. If the data generating process is at least stationary and mixing, the blockwise bootstrap by drawing subsamples or blocks of the data saves the concept. For the blockwise bootstrap a blocklength has to be selected. We propose a method for selecting the optimal blocklength. To improve the finite size properties of the blockwise bootstrap, studentised statistics is considered. If the statistic can be represented as a smooth function model this studentisation can be approximated efficiently. The studentised blockwise bootstrap method is applied for testing hypotheses on medical time series.

Algorithms↗

PubMed2005

Quantitative data generation for systems biology: the impact of randomisation, calibrators and normalisers.

Systems biology is an approach to the analysis and prediction of the dynamic behaviour of biological networks through mathematical modelling based on experimental data. The current lack of reliable quantitative data, especially in the field of signal transduction, means that new methodologies in data acquisition and processing are needed. Here, we present methods to advance the established techniques of immunoprecipitation and immunoblotting to more accurate and quantitative procedures. We propose randomisation of sample loading to disrupt lane correlations and the use of normalisers and calibrators for data correction. To predict the impact of each method on improving the data quality we used simulations. These studies showed that randomisation reduces the standard deviation of a smoothed signal by 55% +/- 10%, independently from most experimental settings. Normalisation with appropriate endogenous or external proteins further reduces the deviation from the true values. As the improvement strongly depends on the quality of the normaliser measurement, a criteria-based normalisation procedure was developed. Our approach was experimentally verified by application of the proposed methods to time course data obtained by the immunoblotting technique. This analysis showed that the procedure is robust and can significantly improve the quality of experimental data.

Algorithms↗

PubMed2004

Variations in substitution rate in human and mouse genomes.

We present a method to quantify spatial fluctuations of the substitution rate on different length scales throughout genomes of eukaryotes. The fluctuations on large length scales are found to be predominantly a consequence of a coarse-graining effect of fluctuations on shorter length scales. This is verified for both the mouse and the human genome. We also found that the relative standard deviation of fluctuations in substitution rate is about a factor three smaller in mouse than in human. The method allows furthermore to determine time-resolved substitution rate maps of the genomes, where the corresponding autocorrelation functions quantify the velocity of spatial chromosomal reorganization.

Animals↗

PubMed2004

Phase synchronization from noisy univariate signals.

We present methods for detecting phase synchronization of two unidirectionally coupled, self-sustained noisy oscillators from a signal of the driven oscillator alone. One method detects soft phase locking; another hard phase locking. Both are applied to the problem of detecting phase synchronization in von Kármán vortex flow meters.

Journal Article↗

PubMed2004

Effect of carotid endarterectomy or stenting on impairment of dynamic cerebral autoregulation.

BACKGROUND AND PURPOSE: Analysis of dynamic cerebral autoregulation (DCA) from spontaneous blood pressure fluctuations might contribute to prognosis of severe internal carotid artery stenosis, but its response to carotid recanalization has not been investigated so far. This study investigates the effect of carotid endarterectomy or stenting on various DCA parameters. METHODS: In 58 patients with severe unilateral stenosis undergoing carotid endarterectomy (n=41) or stenting (n=17), cerebral blood flow velocity (CBFV, transcranial Doppler) and arterial blood pressure (ABP, Finapres method) were recorded over 10 minutes before and on average 3 days after carotid recanalization. Nineteen patients were additionally examined after 7 months. Correlations between diastolic and mean ABP and CBFV fluctuations were averaged to form the correlation coefficient indices (diastolic [Dx] and mean values [Mx]). Transfer function parameters (low-frequency phase and high-frequency gain between ABP and CBFV oscillations) were calculated over the same 10 minutes. CO2 reactivity was assessed via inhalation of 7% CO2. RESULTS: Before recanalization, all DCA parameters were clearly impaired ipsilaterally compared with contralateral sides. Phase, Dx, and Mx indicated early normalization of DCA after both endarterectomy and stenting. By multiple regression, the degree of DCA improvement was highly significantly related to the extent of impairment before recanalization. No significant change in DCA was found at follow-up. Ipsilateral gain and CO2 reactivity increased significantly less after endarterectomy than after stenting (P<0.05). CONCLUSIONS: Dynamic cerebral dysautoregulation in patients with severe carotid obstruction is readily and completely remedied by carotid recanalization.

Blood Flow Velocity↗

PubMed2004

Data-driven optimal filtering for phase and frequency of noisy oscillations: Application to vortex flow metering.

A method for measuring the phase of oscillations from noisy time series is proposed. To obtain the phase, the signal is filtered in such a way that the filter output has minimal relative variation in the amplitude over all filters with complex-valued impulse response. The argument of the filter output yields the phase. Implementation of the algorithm and interpretation of the result are discussed. We argue that the phase obtained by the proposed method has a low susceptibility to measurement noise and a low rate of artificial phase slips. The method is applied for the detection and classification of mode locking in vortex flow meters. A measure for the strength of mode locking is proposed.

Journal Article↗

PubMed2004

Tremor analysis in two normal cohorts.

OBJECTIVE: Quantitative tremor analyses using almost identical methods were compared between two independent large normal cohorts, to separate robust measures that may readily be used diagnostically from more critical ones needing lab-specific normalization. METHODS: Hand accelerometry and surface EMG from forearm flexors and extensors were recorded with (500 and 1000 g) and without weight loading under postural conditions in 117 and 67 normal volunteers in two different specialty centers for movement disorders in Germany. RESULTS: Tremor amplitude (total power) and frequency fell within a similar range but differed significantly. A significant reduction of tremor frequency under 1000 g weight load (>1 Hz), and a lack of rhythmic EMG activity at the tremor frequency in around 85-90% of the recordings were robust findings in both centers. CONCLUSIONS: The differences in frequency and total power indicate that these measures critically depend on the details of the recording conditions being slightly different between the two centers. Thus each lab needs to establish its own normative data. We estimate that at least 25 normal subjects have to be recorded to obtain normal values. The reduction of tremor frequency under load and lacking tremor-related EMG activity were well reproducible allowing a differentiation of physiological from low amplitude pathological tremor. SIGNIFICANCE: This study provides a framework for more standardized tremor analyses in clinical neurophysiology.

Adult↗

PubMed2004

Aperiodic flow-induced oscillations of collapsible tubes: a critical reappraisal.

The evidence for the aperiodic self-excited oscillations of flow-conveying collapsible tubes being mathematically chaotic is re-examined. Many cases which powerfully suggest nonlinear deterministic behaviour have not been recorded over time-spans which allow their exhaustive examination. The present investigation centred on a previously recorded robust and generic oscillation, but more recent and more discerning tests were applied. Despite hints that a low embedding dimension might suffice, the data appeared on most indices high-dimensional. A U-shaped return map was found and modelled using both radial basis functions and polynomials, but lack of detailed structure in the map prevented effective parameter estimation. On the basis of power-law rather than exponential divergence of nearby trajectories, and of inability to discriminate against behaviour which would also be manifested by a surrogate consisting of a noise-perturbed nonlinear periodic oscillator, it is concluded that the data do not support the idea that the aperiodicity in the particular oscillation examined is caused by deterministic chaos. There was evidence that the distributed nature of the physical system might underlie aspects of the high dimensionality. We advocate equally searching testing of any future candidate chaotic oscillations in the investigation of collapsed-tube flows.

Biomedical Engineering↗

PubMed2003

Bilateral severe carotid artery stenosis or occlusion - cerebral autoregulation dynamics and collateral flow patterns.

BACKGROUND: Bilateral severe obstruction of the internal carotid artery is a hemodynamically critical state. We aimed to (1) analyze dynamic cerebral autoregulation (DCA) in affected patients, and (2) to correlate DCA data with different collateral flow patterns. METHODS: DCA was assessed noninvasively by transfer function analysis (phase shift) of respiratory-induced oscillations at 0.1 Hz of arterial blood pressure (Finapres method) and cerebral blood flow velocity (transcranial Doppler) in 30 patients with severe bilateral carotid stenosis (> or =75%) or occlusion. CO(2)-reactivity was measured via inhalation of 7% CO(2). 30 patients with unilateral stenosis were recruited as controls. RESULTS: Patients with bilateral 75-89% stenosis had a virtually preserved phase shift. A pronounced reduction was found in bilateral critical stenosis or obstruction (90-100%). Patients with ipsilateral 90-100% and contralateral 75-89% stenosis had a significantly less severe reduction of phase shift on the ipsilateral side. CO(2)-reactivity showed a less marked reduction in patients with bilateral critical stenosis or occlusion. Phase shift was best if "Willisian" collaterals were present. Significantly reduced values were found if only secondary collaterals (ophthalmic artery, leptomeningeal flow) were detected. Poorest values occurred with recruitment of functionally stenosed "Willisian" collaterals. CO(2)-reactivity showed poor values with sole recruitment of secondary collaterals, whereas functionally stenosed primary collaterals did not show values as poor as for phase shift. Clinically symptomatic patients had significantly lower phase shift and CO(2)-reactivity values. CONCLUSIONS: DCA is severely impaired in bilateral critical carotid stenosis or occlusion. Sole recruitment of secondary collaterals and signs of a functional stenosis in primary ("Willisian") collaterals reflect insufficient collateral supply with a poor hemodynamic status. CO(2)-reactivity assessing the vasodilatory reserve and DCA represent different information for characterizing cerebral hemodynamic impairment. Determining transfer function phase might be a physiologically well supported approach for analysis of cerebral hemodynamic compromise.

Aged↗

PubMed2003

How well can epileptic seizures be predicted? An evaluation of a nonlinear method.

The unpredictability of the occurrence of epileptic seizures contributes to the burden of the disease to a major degree. Thus, various methods have been proposed to predict the onset of seizures based on EEG recordings. A nonlinear feature motivated by the correlation dimension is a seemingly promising approach. In a previous study this method was reported to identify 'preictal dimension drops' up to 19 min before seizure onset, exceeding the variability of interictal data sets of 30-50 min duration. Here we have investigated the sensitivity and specificity of this method based on invasive long-term recordings from 21 patients with medically intractable partial epilepsies, who underwent invasive pre-surgical monitoring. The evaluation of interictal 24-h recordings comprising the sleep-wake cycle showed that only one out of 88 seizures was preceded by a significant preictal dimension drop. In a second analysis, the relation between dimension drops within time windows of up to 50 min before seizure onset and interictal periods was investigated. For false-prediction rates below 0.1/h, the sensitivity ranged from 8.3 to 38.3% depending on the prediction window length. Overall, the mean length and amplitude of dimension drops showed no significant differences between interictal and preictal data sets.

Adolescent↗

PubMed2003

Cerebral autoregulation in carotid artery occlusive disease assessed from spontaneous blood pressure fluctuations by the correlation coefficient index.

BACKGROUND AND PURPOSE: Estimation of dynamic cerebral autoregulation from spontaneous fluctuations of arterial blood pressure (ABP) and cerebral blood flow velocity (CBFV) is an attractive monitoring option for cerebral hemodynamic impairment. We evaluated the correlation coefficient index method in patients with severe obstructive carotid disease and compared it with transfer function analysis (frequency domain approach to cerebral autoregulation) and CO2 vasomotor reactivity. METHODS: In 139 patients with severe unilateral carotid stenosis (>or=70%) or occlusion, CBFV (transcranial Doppler) and ABP (Finapres method) were recorded over 10 minutes. Correlations between systolic pressure, diastolic pressure, and mean ABP and CBFV oscillations over 1-minute epochs were averaged over 10 minutes to form the correlation coefficient indexes (Sx, Dx, Mx, respectively). Transfer function parameters (phase shift and gain between ABP and CBFV oscillations) were determined from the entire 10-minute period. CO2 reactivity was assessed by inhalation of 7% CO2. RESULTS: The correlation indexes Dx and Mx were significantly higher ipsilateral to stenosis and increased with degree of stenosis, indicating increasing dependence of CBFV on ABP and thus impairment of cerebral autoregulation. Dx and Mx correlated moderately but highly significantly with transfer function parameters and CO2 reactivity and showed a good level of agreement in detecting pathological values. Patients with a small variance of the 1-minute source correlations of Dx and Mx showed clearly better correlation values. Transfer function parameters and CO2 reactivity but not Dx and Mx were significantly poorer in patients with symptomatic stenosis or occlusion. CONCLUSIONS: The potential of the correlation coefficient indexes Dx and Mx in detecting hemodynamic impairment in patients with carotid stenosis is comparable to that of transfer function analysis and CO2 reactivity testing. In future, a combination of various hemodynamic tests might help to identify patients at risk for ischemic events.

Aged↗

PubMed2003

Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling.

Considerable progress has been made in identifying the molecular composition of complex signaling networks controlling cell proliferation, differentiation, and survival. However, to discover general building principles and predict the dynamic behavior of signaling networks, it is necessary to develop quantitative models based on experimental observations. Here we report a mathematical model of the core module of the Janus family of kinases (JAK)-signal transducer and activator of transcription (STAT) signaling pathway based on time-resolved measurements of receptor and STAT5 phosphorylation. Applying the fitted model, we can determine the quantitative behavior of STAT5 populations not accessible to experimental measurement. By in silico investigations, we identify the parameters of nuclear shuttling as the most sensitive to perturbations and verify experimentally the model prediction that inhibition of nuclear export results in a reduced transcriptional yield. The model reveals that STAT5 undergoes rapid nucleocytoplasmic cycles, continuously coupling receptor activation and target gene transcription, thereby forming a remote sensor between nucleus and receptor. Thus, dynamic modeling of signaling pathways can promote functional understanding at the systems level.

Animals↗

PubMed2003

Detection of very low-frequency oscillations of cerebral haemodynamics is influenced by data detrending.

Recent studies were investigated that report spontaneous oscillations of cerebral perfusion in the very low-frequency range (0.01-0.04 Hz), emphasising details of spectral estimation. The effects of different spectral estimation procedures were compared, using simulated and clinical data. It was shown that data detrending, as used in many studies, can lead to an artifactual peak in the very low-frequency region of estimated power spectra, indicating that the peak cannot be taken as evidence of physiological oscillations. A quantitative, reliable method is described that can be used to assess very low-frequency oscillations. Using the method, very low-frequency oscillations were found in ten out of 17 healthy adults measured with transcranial Doppler (average frequency, 0.021 +/- 0.007 Hz, mean +/- SD), confirming earlier findings based on visual inspection of data.

Adult↗

PubMed2003

Dynamic cerebral autoregulation and collateral flow patterns in patients with severe carotid stenosis or occlusion.

The quality of collateral blood supply in carotid disease is pivotal for the resulting hemodynamic compromise. However, the interrelation between different patterns of collateral blood flow and actual impairment of cerebral autoregulation (CAR) has not been analyzed so far. Dynamic CAR was assessed noninvasively by the phase shift between respiratory-induced 0.1-Hz oscillations of arterial blood pressure (ABP) and cerebral blood flow velocity (CBFV) in 101 patients with severe unilateral carotid stenosis (> or = 75%) or occlusion. CO(2)-vasomotor reactivity was assessed via inhalation of 7% CO(2). Spontaneously activated collaterals via primary (anterior/posterior communicating artery, type I, n = 65) and secondary (ophthalmic artery / leptomeningeal with or without primary pathways, group II, n = 24) pathways were assessed by transcranial Doppler/duplex sonography. Signs of functional stenosis in the anterior collateral pathways were subsumed under type III (n = 12). Best dynamic CAR (phase shift) on affected sides was observed for type I (n = 65), in which values did not differ significantly from contralateral sides. Reduced phase shift values were present in type II; poorest values were observed for type III. CO(2)-reactivity differed mainly between type I and the other types. A less distinct differentiation of autoregulatory impairment was found when dividing patients into groups of different degrees of stenosis. Symptomatic patients (previous TIA/stroke) were significantly less frequent in the group with type I collateral flow and had significantly lower phase shift and CO(2)-reactivity values. In conclusion, we found that dynamic CAR is substantially impaired if secondary collateral pathways are activated or if functional stenosis in the activated anterior collateral pathway is present. These hemodynamic constellations are also associated with a higher proportion of clinically symptomatic patients. Determination of dynamic CAR by transfer function analysis represents a convenient, sensitive method for detection of cerebral hemodynamic compromise in obstructive carotid disease.

Blood Flow Velocity↗