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1.
ACTLW - an action-based computation tree logic with unless operator
Robert Meolic, Tatjana Kapus, Zmago Brezočnik, 2008, izvirni znanstveni članek

Opis: Model checkers for systems represented by labelled transition systems are not as extensively used as those for systems represented by Kripke structures. This is partially due to the lack of an elegant formal language for property specification which would not be as raw as, for example, HML yet also not as complex as, for example, -calculus. This paper proposes a new action-based propositional branching-time temporal logic ACTLW, which enhances popular computation tree logic (CTL) with the notion of actions in a similar but more comprehensive way than action-based CTL introduced by De Nicola and Vaandrager [R. De Nicola, F.W. Vaandrager, Action versus logics for transition systems, in: Semantics of Systems of Concurrent Processes, Proceedings LITP Spring School on Theoretical Computer Science, LNCS 469, 1990, pp. 407-419]. ACTLW is defined by using temporal operators until and unless only, whereas all other temporal operators are derived from them. Fixed-point characterisation of the operators together with symbolic algorithms for globalmodel checking are shown. Usage of this new logic is illustrated by an example of verification of mutual-exclusion algorithms.
Ključne besede: formal verification, model checking, action-based temporal logic, fixed point, mutual-exclusion algorithm
Objavljeno: 01.06.2012; Ogledov: 1298; Prenosov: 54
URL Povezava na celotno besedilo

2.
Establishing the stochastic nature of intracellular calcium oscillations from experimental data
Matjaž Perc, Anne K. Green, C. Jane Dixon, Marko Marhl, 2008, izvirni znanstveni članek

Opis: Calcium has been established as a key messenger in both intra- and intercellular signaling. Experimentally observed intracellular calcium responses to different agonists show a variety of behaviors from simple spiking to complex oscillatory regimes. Here we study typical experimental traces of calcium oscillations in hepatocytes obtained in response to phenylephrine and ATP. The traces were analyzed with methods of nonlinear time series analysis in order to determine the stochastic/deterministic nature of the intracellular calcium oscillations. Despite the fact that the oscillations appear, visually, to be deterministic yet perturbed by noise, our analyses provide strong evidence that the measured calcium traces in hepatocytes are prevalently of stochastic nature. In particular, bursting calcium oscillations are temporally correlated Gaussian series distorted by a monotonic, instantaneous, time-independent function, whilst the spiking behavior appears to have a dynamical nonlinear component whereby the overall determinism level is still low. The biological importance of this finding is discussed in relation to the mechanisms incorporated in mathematical models as well as the role of stochasticity and determinism at cellular and tissue levels which resemble typical statistical and thermodynamic effects in physics.
Ključne besede: dynamic systems, stochastic processes, cellular signaling, calcium oscillations, time series analyses, noise, temporal correlation
Objavljeno: 07.06.2012; Ogledov: 965; Prenosov: 62
URL Povezava na celotno besedilo

3.
Spatio-temporal modelling explains the effect of reduced plasma membrane Ca[sup]2+[/sup] efflux on intracellular Ca[sup]2+[/sup] oscillations in hepatocytes
Marko Marhl, Marko Gosak, Matjaž Perc, C. Jane Dixon, Anne K. Green, 2008, izvirni znanstveni članek

Opis: In many non-excitable eukaryotic cells, including hepatocytes, ▫$Ca^{2+}$▫ oscillations play a key role in intra- and intercellular signalling, thus regulating many cellular processes from fertilisation to death. Therefore, understanding the mechanisms underlying these oscillations, and consequently understanding how they may be regulated, is of great interest. In this paper, we study the influence of reduced ▫$Ca^{2+}$▫ plasma membrane efflux on ▫$Ca^{2+}$▫ oscillations in hepatocytes. Our previous experiments with carboxyeosin show that a reduced plasma membrane ▫$Ca^{2+}$▫ efflux increases the frequency of ▫$Ca^{2+}$▫ oscillations, but does not affect the duration of individual transients. This phenomenon can be best explained by taking into account not only the temporal,but also the spatial dynamics underlying the generation of ▫$Ca^{2+}$▫ oscillations in the cell. Here we divide the cell into a grid of elements and treat the ▫$Ca^{2+}$▫ dynamics as a spatio-temporal phenomenon. By converting an existing temporal model into a spatio-temporal one, we obtain theoretical predictions that are in much better agreement with the experimental observations.
Ključne besede: cellular signalling, calcium oscillations, intracellular oscilations, spatio-temporal dynamics, hepatocytes, stochastic simulations
Objavljeno: 07.06.2012; Ogledov: 792; Prenosov: 14
URL Povezava na celotno besedilo

4.
IN VIVO TIME ANALYSIS OF THE DYNAMICS OF QUALITY DEVELOPMENT IN RIPENING APPLE FRUIT
Nadja Sadar, 2013, doktorska disertacija

Opis: Colour and taste are important attributes of apple fruit quality that is generated during the fruit-growing period. Despite a plethora of studies dealing with this topic, the detailed information on how quality is generated is, however, still lacking. This is because traditionally, the obtained agro-morphological and biochemical data are analysed with empirical models using mean values of large samples, without taking the effects of biological variation into account, thus completely masking the spatio-temporal physiological mechanisms. To really understand quality, its generation during fruit growth needs to be monitored and modelled. When knowledge exists on the type and kinetics of the processes involved, the variation in properties can be described and taken into account by using so-called fundamental models, built on theoretical considerations. To understand the behaviour and the variation of colour and taste compounds, within or between individual fruits, and to assess their importance throughout the food supply chain, it is therefore important to understand the dynamics of these compounds during growth. The study consisted of (1) a preliminary experiment, aiming to determine the suitability of the semi-destructive biopsy sampling technique for in-vivo monitoring of certain metabolites during apple fruit development on a tree, (2) an experiment on spatial distribution, and (3) an experiment on temporal distribution of metabolites and colour in developing individual apple fruit. The experiment on spatial distribution was conducted to determine the effect of location on the accumulation of the individual quality components within apple fruit, and the parallel temporal experiment was conducted to monitor the dynamics and mechanisms of these components in apple fruit during on the tree development. Diameter and standard maturity indices of fruit flesh firmness, soluble solids content, starch degradation index, titratable acidity, and Streif maturity index were also determined, to obtain relations between individual quality components. Colour descriptors (L*, a* b*), individual sugars (fructose, sucrose, glucose), sorbitol, and individual organic acids (malic, citric, shikimic, fumaric) were monitored from 40 and 54 days before to 16 and 32 days after the optimum maturity for long term storage on individual apples of cv. ‘Gala’ and cv. ‘Pinova’. Data were analysed with classic empirical statistics as well as with non-linear indexed regression, based on process oriented models, which included biological variation between apples of the same batch. Frequently probelation and quantile regression were applied. The results of the preliminary experiment confirmed that the novel biopsy sampling technique is suitable for in-vivo monitoring of the spatio-temporal distribution of colour and individual taste components during on-tree apple fruit development. In the results from the experiment on spatial distribution, a sinusoidal distribution over locations at 70° above the fruit equator was observed for all the monitored quality components. Descriptor a* was highest at the blush, and b* and L* at the shaded side of the fruit. Citric acid preferentially accumulated at the shaded side of the fruit, whereas fructose in cv. ‘Gala’ tended to accumulate at the blush. Other metabolites were more or less equally distributed within fruit. The results of longitudinal monitoring reveal a sigmoidal increase of a*, an exponential increase of diameter and sugars, and an exponential decrease of organic acids over time. In both cultivars, large variations were observed between individual fruit for all the monitored quality components. When analysed with non-linear indexed regression, based on process-oriented models, and after the probelation combined with quantile regression, the explained parts of the majority of the monitored quality components were well above 90 %. The mechanism of colour development was the same for both cultivars. The biological shift factor for all metabolites and colour had roughly the same value within cultiv
Ključne besede: apple fruit, colour, models, organic acids, spatio-temporal monitoring, sugars
Objavljeno: 19.12.2013; Ogledov: 1734; Prenosov: 197
.pdf Celotno besedilo (3,87 MB)

5.
ACQUIRING TEMPORAL KNOWLEDGE FOR MAKING DECISIONS IN MEDICAL PROCESSES
Aida Kamišalić Latifić, 2014, doktorska disertacija

Opis: A medical process is a set of medical actions performed by healthcare professionals while making observations about signs and symptoms, ordering interventions, prescriptions, tests, and any other actions in order to solve a health problem that is affecting a particular patient. The objective is to offer a curative, chronic, palliative and/or symptomatic treatments. The capability of a physician to propose an appropriate treatment depends on his/her knowledge of similar clinical cases and by following advances in the treatment of particular diseases. Time is an important concept of the real world that has to be considered in regard to medical processes. Clinical Practice Guidelines (CPGs) are a narrative set of recommendations for treating patients suffering from a particular disease. By constantly referring to CPGs physicians can stay up to date with the best evidence-based medical care and with the recommendations of experts. The time dimension is, however, often omitted or only partially covered in CPGs. Some CPGs do contain certain recommendations considering time but often there are huge gaps that are supposed to be overcome by physicians’ own knowledge and experience. At the same time, healthcare centres hold healthcare records and information systems that register medical processes and patients data, including information about the times of any encounters, prescriptions, and other medical actions. Therefore healthcare records and information systems data can be a source for detecting temporal medical knowledge and sound evidence regarding healthcare. This thesis is centred on temporal knowledge acquisition and representation for the purposes of decision-making during medical processes. CPGs were analysed to obtain procedural knowledge models and Extended Timed Transition Diagrams defined for representations of the obtained knowledge. The data about the treatments of patients were analysed in order to detect temporal medical knowledge models that represented those medical procedures that were carried out while the data was being generated. These models thus provided an explicit representation of the time dimensions of past medical procedures. They could be used for complementing the knowledge provided by CPGs, for studying adherences to the CPGs and for representing a basic framework for medical procedural decision support systems development.
Ključne besede: knowledge acquisition, knowledge representation, temporal knowledge, decision-making, medical processes, procedural knowledge modelling
Objavljeno: 25.02.2014; Ogledov: 1023; Prenosov: 72
.pdf Celotno besedilo (2,91 MB)

6.
Comparing Shakespeare`s Othello to Three Film Adaptations
Alenka Gomivnik, 2015, diplomsko delo

Opis: William Shakespeare's plays have had countless adaptations on stage and film, because his 16th century plays can still be made modern and interesting nowadays. They can be adapted to the modern world or played out in costumes and settings appropriate for their original contexts. This thesis will explore whether the temporal and cultural context alters the way the play is interpreted over decades. That is why the thesis will deal with three films: The Tragedy of Othello: The Moor of Venice, directed by Orson Welles, made in 1952; Othello, directed by Oliver Parker, made in 1995; and O, directed by Tim Blake Nelson, made in 2001. Each screenwriter and director has their own vision of a story they are trying to tell, whether it be an adaptation, appropriation or an original work. This thesis will explore whether the main theme of Othello remained intact across all three adaptations or whether, despite being changed to some extent, the adaptation can still be recognised as Othello.
Ključne besede: William Shakespeare, Othello, Iago, Desdemona, adaptation, appropriation, film, play, director, Orson Welles, Oliver Parker, Tim Blake Nelson, theme, cultural context, temporal context
Objavljeno: 04.01.2016; Ogledov: 646; Prenosov: 32
.pdf Celotno besedilo (921,60 KB)

7.
Contribution of temporal data to predictive performance in 30-day readmission of morbidly obese patients
Petra Povalej Bržan, Zoran Obradović, Gregor Štiglic, 2017, izvirni znanstveni članek

Opis: Background: Reduction of readmissions after discharge represents an important challenge for many hospitals and has attracted the interest of many researchers in the past few years. Most of the studies in this field focus on building cross-sectional predictive models that aim to predict the occurrence of readmission within 30-days based on information from the current hospitalization. The aim of this study is demonstration of predictive performance gain obtained by inclusion of information from historical hospitalization records among morbidly obese patients. Methods: The California Statewide inpatient database was used to build regularized logistic regression models for prediction of readmission in morbidly obese patients (n = 18,881). Temporal features were extracted from historical patient hospitalization records in a one-year timeframe. Five different datasets of patients were prepared based on the number of available hospitalizations per patient. Sample size of the five datasets ranged from 4,787 patients with more than five hospitalizations to 20,521 patients with at least two hospitalization records in one year. A 10-fold cross validation was repeted 100 times to assess the variability of the results. Additionally, random forest and extreme gradient boosting were used to confirm the results. Results: Area under the ROC curve increased significantly when including information from up to three historical records on all datasets. The inclusion of more than three historical records was not efficient. Similar results can be observed for Brier score and PPV value. The number of selected predictors corresponded to the complexity of the dataset ranging from an average of 29.50 selected features on the smallest dataset to 184.96 on the largest dataset based on 100 repetitions of 10-fold cross-validation. Discussion: The results show positive influence of adding information from historical hospitalization records on predictive performance using all predictive modeling techniques used in this study. We can conclude that it is advantageous to build separate readmission prediction models in subgroups of patients with more hospital admissions by aggregating information from up to three previous hospitalizations.
Ključne besede: readmission prediction, predictive modelling, temporal data
Objavljeno: 02.08.2017; Ogledov: 547; Prenosov: 160
.pdf Celotno besedilo (1,10 MB)
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