Rate coding
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Recent studies on the theoretical performance of latency and rate code in single neurons have revealed that the ultimate accuracy is affected in a nontrivial way by aspects such as the level of spontaneous activity of presynaptic neurons, amount of neuronal noise or the duration of the time window used to determine the firing rate. This study explores how the optimal decoding performance and the corresponding conditions change when the energy expenditure of a neuron in order to spike and maintain the resting membrane potential is accounted for. It is shown that a nonzero amount of spontaneous activity remains essential for both the latency and the rate coding. Moreover, the optimal level of spontaneous activity does not change so much with respect to the intensity of the applied stimulus. Furthermore, the efficiency of the temporal and the rate code converge to an identical finite value if the neuronal activity is observed for an unlimited period of time.
- Klíčová slova
- Fisher information, Metabolic cost, Rate coding, Temporal coding,
- MeSH
- časové faktory MeSH
- energetický metabolismus * MeSH
- lidé MeSH
- membránové potenciály MeSH
- modely neurologické * MeSH
- nervová síť cytologie fyziologie MeSH
- neuronové sítě * MeSH
- neurony fyziologie MeSH
- počítačová simulace MeSH
- výpočetní biologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- MeSH
- dospělí MeSH
- informační teorie * MeSH
- lidé MeSH
- metody MeSH
- reakční čas MeSH
- srdeční frekvence * MeSH
- systémy člověk-stroj MeSH
- zobrazování dat MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
The apparent stochastic nature of neuronal activity significantly affects the reliability of neuronal coding. To quantify the encountered fluctuations, both in neural data and simulations, the notions of variability and randomness of inter-spike intervals have been proposed and studied. In this article we focus on the concept of the instantaneous firing rate, which is also based on the spike timing. We use several classical statistical models of neuronal activity and we study the corresponding probability distributions of the instantaneous firing rate. To characterize the firing rate variability and randomness under different spiking regimes, we use different indices of statistical dispersion. We find that the relationship between the variability of interspike intervals and the instantaneous firing rate is not straightforward in general. Counter-intuitively, an increase in the randomness (based on entropy) of spike times may either decrease or increase the randomness of instantaneous firing rate, in dependence on the neuronal firing model. Finally, we apply our methods to experimental data, establishing that instantaneous rate analysis can indeed provide additional information about the spiking activity.
- Klíčová slova
- entropy, firing rate, instantaneous firing rate, neural coding, randomness, rate coding, temporal coding, variability,
- Publikační typ
- časopisecké články MeSH
We define an optimal signal in parametric neuronal models on the basis of interspike interval data and rate coding schema. Under the classical approach the optimal signal is located where the frequency transfer function is steepest. Its position coincides with the inflection point of this curve. This concept is extended here by using Fisher information which is the inverse asymptotic variance of the best estimator and its dependence on the parameter value indicates accuracy of estimation. We compare the signal producing maximal Fisher information with the inflection point of the sigmoidal frequency transfer function.
It is widely accepted that neuronal firing rates contain a significant amount of information about the stimulus intensity. Nevertheless, theoretical studies on the coding accuracy inferred from the exact spike counting distributions are rare. We present an analysis based on the number of observed spikes assuming the stochastic perfect integrate-and-fire model with a change point, representing the stimulus onset, for which we calculate the corresponding Fisher information to investigate the accuracy of rate coding. We analyze the effect of changing the duration of the time window and the influence of several parameters of the model, in particular the level of the presynaptic spontaneous activity and the level of random fluctuation of the membrane potential, which can be interpreted as noise of the system. The results show that the Fisher information is nonmonotonic with respect to the length of the observation period. This counterintuitive result is caused by the discrete nature of the count of spikes. We observe also that the signal can be enhanced by noise, since the Fisher information is nonmonotonic with respect to the level of spontaneous activity and, in some cases, also with respect to the level of fluctuation of the membrane potential.
- Publikační typ
- časopisecké články MeSH
Early detection of colorectal cancer (CRC) is the key for prevention and the ability to impact long-term survival of CRC patients. Current CRC screening modalities are inadequate for global application because of low sensitivity and specificity in case of conventional stool-based screening tests, and high costs and a low participation compliance in colonoscopy. An accurate stool- or blood-based screening test with use of innovative biomarkers is an appealing alternative as it is non-invasive and poses minimal risk to patients. It is easy to perform, can be repeated at shorter intervals, and therefore would likely lead to a much higher compliance rates. Non-coding RNAs (ncRNAs) have recently gained attention because of their involvement in different biological processes, such as proliferation, differentiation, migration, angiogenesis and apoptosis. An increasing number of studies have demonstrated that mutations or abnormal expression of ncRNAs are closely associated with various cancers, including CRC. The discovery that ncRNAs (mainly microRNAs) are stable in stool and in blood plasma and serum presents the opportunity to develop novel strategies taking advantage of circulating ncRNAs as early diagnostic biomarkers of CRC. This chapter is a comprehensive examination of aberrant ncRNAs expression levels in tumor tissue, stool and blood of CRC patients and a summary of the current findings on ncRNAs, including microRNAs, small nucleolar RNAs, small nuclear RNAs, Piwi-interacting RNAs, circular RNAs and long ncRNAs in regards to their potential usage for screening or early detection of CRC.
- Klíčová slova
- Colorectal cancer, Early diagnosis, Non-coding RNA, Screening, lncRNA, microRNA, piRNAs, snRNAs, snoRNAs,
- MeSH
- adenokarcinom chemie diagnóza genetika MeSH
- adenom chemie diagnóza genetika MeSH
- časná detekce nádoru metody MeSH
- feces chemie MeSH
- kolorektální nádory chemie diagnóza genetika MeSH
- krevní plazma MeSH
- lidé MeSH
- nádorové biomarkery analýza krev MeSH
- nekódující RNA analýza krev MeSH
- pacientův souhlas se zdravotní péčí MeSH
- polypy tlustého střeva chemie diagnóza genetika MeSH
- regulace genové exprese u nádorů MeSH
- senzitivita a specificita MeSH
- sérum MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- nádorové biomarkery MeSH
- nekódující RNA MeSH
Fast information transfer in neuronal systems rests on series of action potentials, the spike trains, conducted along axons. Methods that compare spike trains are crucial for characterizing different neuronal coding schemes. In this paper we review recent results on the notion of spiking randomness, and discuss its properties with respect to the rate and temporal coding schemes. This method is compared with other widely used characteristics of spiking activity, namely the variability of interspike intervals, and it is shown that randomness and variability provide two distinct views. We demonstrate that estimation of spiking randomness from simulated and experimental data is capable of capturing characteristics that would otherwise be difficult to obtain with conventional methods.
Coat protein (CP) coding regions of six Potato mop-top virus (PMTV) isolates from the Czech Republic and Denmark (54-10, 54-11, 54-15, 54-19, Korneta and Pacov) were sequenced. Comparison of the obtained nucleotide sequences as well as alignment of the deduced amino acid sequences were performed. The obtained results showed that the isolates from different parts of Europe seem to have highly conserved coding regions which is unexpected for a viral RNA genome known for its high mutation rate. Thus considerable differences in virulence and significant variation in biological properties of these isolates should not be attributed to CP but to some other part of the genome.
- MeSH
- klonování DNA MeSH
- molekulární sekvence - údaje MeSH
- nemoci rostlin virologie MeSH
- otevřené čtecí rámce genetika MeSH
- polymerázová řetězová reakce s reverzní transkripcí MeSH
- rostlinné viry genetika izolace a purifikace MeSH
- sekvence aminokyselin MeSH
- sekvence nukleotidů MeSH
- sekvenční seřazení MeSH
- Solanum tuberosum virologie MeSH
- virové plášťové proteiny genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- virové plášťové proteiny MeSH
A model for coding of odor intensity in the first two neuronal layers of olfactory systems is proposed. First, the occupation and activation by odorant molecules of receptor proteins of different types borne by the first order neurons are described as birth and death processes. The occupation (birth) rate depends on the concentration of the odorant, whereas the probability of activation of an occupied receptor depends on the type of the odorant. Second, the spike generation mechanism proposed for the first order neuron depends on the level of the generator potential evoked by the activated receptors and on a time-decaying threshold which is reset to infinity after each spike. The various resulting stochastic regimes of firing activity at different concentrations are described. Third, each second order neuron is influenced by excitation coming from numerous first order neurons, lateral inhibition from other second order neurons, and self-inhibition. All these incoming signals are integrated at the second order neuron. The firing activity of the first and second order neurons is modeled by a first passage time scheme. For both types of neuron the shapes of the curves predicted by the model for the mean firing frequency as a function of stimulus concentration are shown to be in accordance with available experimental results.
- MeSH
- čich fyziologie MeSH
- čichové buňky fyziologie MeSH
- elektrofyziologie MeSH
- modely neurologické MeSH
- odoranty * MeSH
- stochastické procesy MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
BACKGROUND: Breast cancer is the most commonly occurring cancer worldwide and is the main cause of death from cancer in women. Novel biomarkers are highly warranted for this disease. OBJECTIVE: Evaluation of novel long non-coding RNAs biomarkers for breast cancer. METHODS: The study comprised the analysis of the expression of 71 candidate lncRNAs via screening, six of which (four underexpressed, two overexpressed) were validated and analyzed by qPCR in tumor tissues associated with NST breast carcinomas, compared with the benign samples and with respect to their clinicopathological characteristics. RESULTS: The results indicated the tumor suppressor roles of PTENP1, GNG12-AS1, MEG3 and MAGI2-AS3. Low levels of both PTENP1 and GNG12-AS1 were associated with worsened progression-free and overall survival rates. The reduced expression of GNG12-AS1 was linked to the advanced stage. A higher grade was associated with the lower expression of PTENP1, GNG12-AS1 and MAGI2-AS3. Reduced levels of both MEG3 and PTENP1 were linked to Ki-67 positivity. The NRSN2-AS1 and UCA1 lncRNAs were overexpressed; higher levels of UCA1 were associated with multifocality. CONCLUSIONS: The results suggest that the investigated lncRNAs may play important roles in breast cancer and comprise a potential factor that should be further evaluated in clinical studies.
- Klíčová slova
- Breast cancer, GNG12-AS1, MAGI2-AS3, MEG3, NRSN2-AS1, PTENP1, UCA1, clinical outcomes, long non-coding RNAs,
- MeSH
- adaptorové proteiny signální transdukční genetika metabolismus MeSH
- dospělí MeSH
- guanylátkinasy genetika metabolismus MeSH
- lidé středního věku MeSH
- lidé MeSH
- nádorové biomarkery * genetika metabolismus MeSH
- nádory prsu * genetika patologie metabolismus mortalita MeSH
- prognóza MeSH
- regulace genové exprese u nádorů MeSH
- RNA dlouhá nekódující * genetika MeSH
- senioři MeSH
- stupeň nádoru MeSH
- tumor supresorové geny MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- MAGI2 protein, human MeSH Prohlížeč
- MEG3 non-coding RNA, human MeSH Prohlížeč
