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Results for “Deterministic Measurement”

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At least 343 records · Page 19Linked to original sources

PubMed2005

GeneMCL in microarray analysis.

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5,730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms.

Algorithms↗

PubMedDate not supplied

Origin of chaos in the circulation: open loop analysis with an artificial heart.

To develop the optimal automatic control algorithm for an in vivo artificial heart system, investigation of the basic characteristics of the cardiovascular system may be important. The clinical significance of chaotic dynamics in the cardiovascular system has attracted attention. The circulation is a so-called complex system with many feedback circuits, making it very difficult to investigate the origin of chaos within the system. In this study, we investigated the origin of chaos by open loop analysis with an artificial heart (which has no fluctuation in pumping rate or contraction power) in chronic animal experiments with healthy adult goats. As a result, in the artificial heart circulatory time series data, low dimensional deterministic chaos was discovered by nonlinear mathematical analysis, suggesting the importance of blood vessels in the chaotic dynamics of the cardiovascular system. To investigate the origin of chaos further, sympathetic activity was directly measured in animals with artificial hearts. Chaotic dynamics was also recognized in sympathetic action potentials, even during artificial heart circulation. Coupling of the nonlinear information between blood vessels and sympathetic activity was suggested by analysis of mutual information. In chaotic dynamics, the central nervous system (CNS) played an important role through sympathetic activity. These findings may be useful for the development of an automatic control algorithm for an artificial heart.

Algorithms↗

PubMed2004

Distinguishability and indistinguishability by local operations and classical communication.

It is well known that orthogonal quantum states can be distinguished perfectly. However, if we assume that these orthogonal quantum states are shared by spatially separated parties, the distinguishability of these shared quantum states may be completely different. We show that a set of linearly independent quantum states [formula: see text] where U(m,n) are generalized Pauli matrices, cannot be discriminated deterministically or probabilistically by local operations and classical communication. On the other hand, any l maximally entangled states from this set are locally distinguishable if l(l-1)< or =2d. The explicit projecting measurements are obtained to locally discriminate these states. As an example, we show that four Werner states are locally indistinguishable.

Journal Article↗

PubMed1997

Non-linear dynamics of alpha and theta rhythm: correlation dimensions and Lyapunov exponents from healthy subject's spontaneous EEG.

The aim of the present paper was to analyze some non-linear dynamic properties of the resting EEG from healthy subjects under eyes closed conditions. For this purpose we digitally filtered the spontaneous EEG in the theta (3-8 Hz) and alpha frequency range (8-13 Hz) and considered these independent rhythms as signals from a deterministic system. Under certain conditions non-linear dynamic systems are able to generate deterministic chaos, which means that similar causes do not produce similar effects. This phenomenon is called sensitive dependence on initial conditions. From different lead positions (F3, F4, Cz, P3, P4, O1 and O2) we calculated the so-called correlation dimension D2, which is assumed to be an estimation of the system's complexity, and the Lyapunov exponent L, which appears to be a measure of the sensitive dependence on initial conditions. Our investigations revealed that the dimensionality of the theta- and alpha-rhythm varies within subjects across the experimental session in wide ranges. The degrees of freedom of the alpha and theta rhythms across the scalp are in the same order, indicating dynamic processes which can not be differentiated by applying the Grassberger-Procaccia algorithm. The Lyapunov-exponents, indicating 'how chaotic a deterministic process is', are in general smaller for the theta than for the alpha activity. Across the scalp there is no evidence for different dynamics of the theta rhythm. The dynamics of the alpha rhythm, on the contrary, appears to be different at various lead positions. It appears justified to state that the dynamics of the frontal alpha activity is functionally different from the alpha activity recorded at other topographic locations.

Algorithms↗

PubMed2004

Robust control of initiation of prokaryotic chromosome replication: essential considerations for a minimal cell.

A genomically and chemically detailed mathematical model of a "minimal cell" would be useful to understand better the "design logic" of cellular regulation. A "minimal cell" will be a prokaryote with the minimum number of genes necessary for growth and replication in an ideal environment (i.e., preformed precursors, constant temperature, etc.). The Cornell single-cell model of Escherichia coli serves as the basic framework upon which a minimal cell model can be constructed. A critical issue for any cell model is to describe a mechanism for control of initiation of chromosome replication. There is strong evidence that the essence of chromosome replication control is highly conserved in eubacteria and even extends to the archae. A generalized mechanism is possible based on binding of the protein DnaA-ATP to the origin of replication (oriC) as a primary control. Other features, such as regulatory inactivation of DnaA (RIDA) by conversion of DnaA-ATP to DnaA-ADP and titration of DnaA by binding to other DnaA boxes on the chromosome, have emerged as critical elements in obtaining a functional system to control initiation of chromosome synthesis. We describe a biologically realistic model of chromosome replication initiation control embedded in a complete whole-cell model that explicitly links the external environment to the mechanism of replication control. The base model is deterministic and then modified to include stochastic variation in the components for replication control. The stochastic model allows evaluation of the model's robustness, employing a low standard deviation of interinitiation time as a measure of robustness. Four factors were examined: DnaA synthesis rate; DnaA-ATP binding sites at oriC; the binding rate of DnaA-ATP to the nonfunctional DnaA boxes; and the effect of changing the number of nonfunctional binding sites. The observed DnaA synthesis rate (2000 molecules/cell) and the number of DnaA binding sites per origin (30) are close to the values predicted by the model to provide good control (low variance of interinitiation time), with a reasonable expenditure of cell resources. At relatively high binding rates for DnaA-ATP to the DnaA boxes (10(16) M(-1) s(-1)), increasing the number of DnaA binding sites to about 300, improved control (but little further improvement was seen by extension to 1000 boxes); however, at a low binding rate (10(10) M(-1) s(-1)), an increase in DnaA boxes had an adverse effect on control. The combination of all four factors is probably necessary to obtain a robust control system. Although this mechanism of replication initiation control is highly conserved, it is not clear if simpler control in a minimal cell might exist based on experimental observations with Mycoplasma. This issue is discussed in this investigation.

Bacterial Proteins↗

PubMed1999

Using Boolean reasoning to anonymize databases.

This paper investigates how Boolean reasoning can be used to make the records in a database anonymous. In a medical setting, this is of particular interest due to privacy issues and to prevent the possible misuse of confidential information. As electronic medical records and medical data repositories get more common and widespread, the issue of making sensitive data anonymous becomes increasingly important. A theoretically well-founded algorithm is proposed that via cell suppression can be used to make a database anonymous before releasing or sharing it to the outside world. The degree of anonymity can be tailored according to the specific needs of the recipient, and according to the amount of trust we place in the recipient. Furthermore, the required measure of anonymity can be specified as far down as to the individual objects in the database. The algorithm can also be used for anonymization relative to a particular piece of information, effectively blocking deterministic inferences about sensitive database fields.

Adult↗

PubMed2002

Evaluation of the peripheral dose to uterus in breast carcinoma radiotherapy.

The absorbed dose outside of the direct fields of radiotherapy treatment (or peripheral dose, PD) is responsible for radiation exposure of the fetus in pregnant women. Because the radiological protection of the unborn child is of particular concern in the early period of the pregnancy, the aim of this study is to estimate the PD in order to assess the absorbed dose in the uterus in a pregnant patient irradiated for breast carcinoma therapy. The treatment was simulated on an Alderson-Rando anthropomorphic phantom, and the radiation dose to the fetus was measured using an ionisation chamber and thermoluminescence dosemeters. Two similar treatments plans with and without wedges were delivered, using a 6 MV photon beam with two isocentric opposite tangential fields with a total dose of 50 Gy, in accordance with common established procedures. Average field parameters for more than 300 patients were studied. Measurements showed the fetal dose to be slightly lower than 50 mGy, a level at which the risk to the fetus is uncertain, although several authors consider this value as the dose threshold for deterministic effects. The planning system (PS) underestimated PD values and no significant influence was found with the use of wedge filters.

Breast Neoplasms↗

PubMed2002

Detecting determinism in short time series, with an application to the analysis of a stationary EEG recording.

We have developed a new method for detecting determinism in a short time series and used this method to examine whether a stationary EEG is deterministic or stochastic. The method is based on the observation that the trajectory of a time series generated from a differentiable dynamical system behaves smoothly in an embedded phase space. The angles between two successive directional vectors in the trajectory reconstructed from a time series at a minimum embedding dimension were calculated as a function of time. We measured the irregularity of the angle variations obtained from the time series using second-order difference plots and central tendency measures, and compared these values with those from surrogate data. The ability of the proposed method to distinguish between chaotic and stochastic dynamics is demonstrated through a number of simulated time series, including data from Lorenz, Rössler, and Van der Pol attractors, high-dimensional equations, and 1/f noise. We then applied this method to the analysis of stationary segments of EEG recordings consisting of 750 data points (6-s segments) from five normal subjects. The stationary EEG segments were not found to exhibit deterministic components. This method can be used to analyze determinism in short time series, such as those from physiological recordings, that can be modeled using differentiable dynamical processes.

Algorithms↗

PubMedDate not supplied

Radiation exposure to patient and staff in hepatic chemoembolization: risk estimation of cancer and deterministic effects.

The purpose of the study was to determine the risks of radiation-induced cancer and deterministic effects for the patient and staff in transarterial chemoembolization (TACE) of hepatocellular carcinoma (HCC). Sixty-five patients with HCC underwent the first cycle of TACE. Thermoluminescence dosemeters and conversion factors were used to measure surface doses and to calculate organ doses and effective dose. For the patient, the risk of fatal cancer and severe genetic defect was in the magnitude of 10(-4) and 10(-5), respectively. Five patients showed surface doses over the first lumbar vertebra exceeding 2000 mSv and 45 patients showed doses over the spine or the liver region above 500 mSv. The risk of fatal cancer and severe genetic defect for the radiologist and assistant was in the magnitude of 10(-7) to 10(-8). They could exceed the threshold for lens opacity in the case of more than 490 and 1613 TACE yearly for a period of many years, respectively. Radiation dose could lead to local transient erythema and/or local depression of hematopoiesis in many patients after TACE. For the radiologist and assistant, risk of fatal cancer and genetic defect and lens opacity might arise when they perform interventions such as TACE intensively.

Adult↗

PubMed1989

A methodological study of a nonlinear stochastic model of an AIDS epidemic with recruitment.

A nonlinear stochastic model of an AIDS epidemic with recruitment of infectives, susceptibles, and AIDS cases into a randomly mixing population of male homosexuals was formulated and studied from a methodological point of view through intensive computer experimentation. Probability generating functions were used to formulate a model for the monthly probability that a susceptible individual becomes infected with HIV, under the assumption that the probability of infection per sexual contact varies as a function of the duration of infection. A method for taking into account the use of condoms to prevent infection with HIV was also introduced. Nonlinear difference equations, resembling deterministic epidemic models, were embedded in the stochastic population process by iterating an initial conditional expectation. Examples of Monte Carlo experiments are presented, illustrating that solutions of these nonlinear difference equations are not always good measures of central tendency for variations in the sample functions of the process. Two important substantive conclusions drawn from the Monte Carlo experiments were that efforts should be made to collect quantitative information on the probability of infection per sexual contact as a function of duration of infection and the frequency of condom use within and among risk categories in a population.

Acquired Immunodeficiency Syndrome↗

PubMed1999

Are societal judgments being incorporated into the uncertainty factors used in toxicological risk assessment?

The aim of this paper is to show that the uncertainty factors used in toxic risk assessment to develop exposure standards do contain societal judgments as well as technical judgments. The process generally used today originated in the 1950s, when a deterministic approach to risk was the norm. Technical judgments are required concerning the nature and the quality of the evidence used in the risk assessment. Judgments taken are essentially cautious. This caution may not matter when measured exposure is significantly below the standard and may be accepted when exposure occurs only following an approval process based on "gate keeping." More sophisticated judgments are required when actual exposure may exceed this type of standard or when risk needs to be compared with benefit. These circumstances can occur with patient exposure to human medicines and with occupational exposure to chemicals. Under these circumstances more explicitly considered societal judgments concerning what constitute "broadly acceptable" and "tolerable" risk criteria, and hence what are appropriate uncertainty factors, are required. The outcomes of those societal judgments are likely to vary according to the circumstances surrounding the exposure and have led to smaller uncertainty factors being considered appropriate for occupational exposure, when compared with widespread public exposure.

Humans↗

PubMed2005

A new model validation tool using kernel regression and density estimation.

In physiological system modelling for control or decision support, model validation is a critical element. A nonparametric approach for assessing the validity of deterministic dynamic models against empirical data is developed, based on kernel regression and kernel density estimation, yielding visual graphical assessment tools as well as numerical metrics of compatibility between the model and the data. Nonparametric regression has been suggested for assessing a parametric statistical model by constructing a confidence band for the proposed model and then checking whether the nonparametric regression curve lies within the band. However, for deterministic models, there is no confidence band that can be constructed. A reversal of roles is therefore suggested--construct a probability band for the nonparametric regression curve and check whether the proposed model lies within the band. This approach extends the utility of nonparametric regression for model assessment to deterministic models. Weighted kernel density estimation is incorporated to derive a density profile for the regression curve, creating a local graphical validation tool. In addition, the density profile is used to define and compute two numerical measures--average normalized density (AND) and relative average normalized density (RAND), representing global statistical validity measures. These tools are demonstrated using a biomedical system model for agitation-sedation and sedation management control.

Humans↗

PubMed1998

Complete calibration of a stereo photogrammetric system through control points of unknown coordinates.

This paper presents a new method for calibrating a video 3D stereo-photogrammetric system. The external parameters and the focal lengths of the cameras are determined from the epipolar constraint and the principal points are computed through the minimisation of a cost function carried out through an evolutionary optimisation. The method has been made more robust with a deterministic annealing procedure of the search region amplitude. Calibration is carried out by moving a rigid bar, carrying two markers on its extremities, inside the working volume. The distance between the two markers is the only measure required. Tests on real data are reported which show that the obtained accuracy is comparable to the one achieved calibrating with control points of known 3D coordinates.

Calibration↗

PubMed2005

High-efficiency deterministic Josephson vortex ratchet.

We investigate experimentally a Josephson vortex ratchet--a fluxon in an asymmetric periodic potential driven by a deterministic force with zero time average. The highly asymmetric periodic potential is created in an underdamped annular long Josephson junction by means of a current injector providing an efficiency of the device up to 91%. We measured the ratchet effect for driving forces with different spectral content. For monochromatic high-frequency drive the rectified voltage becomes quantized. At high driving frequencies we also observe chaos, subharmonic dynamics, and voltage reversal due to the inertial mass of a fluxon.

Journal Article↗

PubMed2006

Quantum feedback control for deterministic entangled photon generation.

We present quantum feedback control for deterministic entanglement generation at the single-photon level. The protocol of controlling both total photon number and phase difference is based on the cascade structure of cavities placed in an optical closed loop, quantum nondemolition measurement with cross-Kerr interactions, and Lyapunov stability for feedback design.

Journal Article↗

PubMed2004

Quantifying variability in neural responses and its application for the validation of model predictions.

A rate code assumes that a neuron's response is completely characterized by its time-varying mean firing rate. This assumption has successfully described neural responses in many systems. The noise in rate coding neurons can be quantified by the coherence function or the correlation coefficient between the neuron's deterministic time-varying mean rate and noise corrupted single spike trains. Because of the finite data size, the mean rate cannot be known exactly and must be approximated. We introduce novel unbiased estimators for the measures of coherence and correlation which are based on the extrapolation of the signal to noise ratio in the neural response to infinite data size. We then describe the application of these estimates to the validation of the class of stimulus-response models that assume that the mean firing rate captures all the information embedded in the neural response. We explain how these quantifiers can be used to separate response prediction errors that are due to inaccurate model assumptions from errors due to noise inherent in neuronal spike trains.

Action Potentials↗

PubMedDate not supplied

Evidence of deterministic chaos in the myoelectric signal.

Our aim was to study whether the myoelectric signals can be better modelled as outputs of a nonlinear dynamic system rather than as random stochastic signals. Both the nonlinear predictability and the dimensionality of the signals were studied using methods of nonlinear dynamics. The signals were measured from the biceps brachii muscle during both fatiguing and non-fatiguing isometric contractions at low load levels. The myoelectric signals were found to be nonlinear and to have a structure statistically distinguishable from random noise. The correlation dimension describing the dimensionality of the myoelectric signal decreased during local muscular fatigue. The results support the use of the theory of nonlinear dynamics for the modelling of the myoelectric signals.

Adult↗

PubMed1996

Quantal transmitter release at somatic motor-nerve terminals: stochastic analysis of the subunit hypothesis.

Here we analyze the problem of determining whether experimentally measured spontaneous miniature end-plate currents (MEPCs) indicate that quanta are composed of subunits. The properties of MEPCs at end plates with or without secondary clefts at the neuromuscular junction are investigated, using both stochastic and deterministic models of the action of a quantum of transmitter. It is shown that as the amount of transmitter in a quantum is increased above about 4000 acetylcholine (ACh) molecules there is a linear increase in the size of the MEPC. It is possible to then use amplitude-frequency histograms of such MEPCs to detect a subunit structure, as there is little potentiation effect above 4000 ACh molecules. Autocorrelation and power spectral analyses of such histograms establish that their subunit structure can be detected if the coefficient of variation of the subunit size is less than about 0.12 or, if electrical noise is added, about 0.1. Positive gradients relate the rise time and half-decay times of MEPCs to their amplitude, even in the absence of potentiating effects; these gradients are shallower at motor nerve terminals that possess secondary clefts. The effect of asynchronous release of subunits is also investigated. The criteria determined by this analysis for identifying a subunit composition in the quantum are applied to an amplitude-frequency histogram of MEPCs recorded from a small group of active zones at a visualized amphibian motor-nerve terminal. This did not provide evidence for a subunit structure.

Acetylcholine↗