Detection of motor imagery based on short-term entropy of time-frequency representations.

BACKGROUND: Motor imagery is a cognitive process of imagining a performance of a motor task without employing the actual movement of muscles. It is often used in rehabilitation and utilized in assistive technologies to control a brain-computer interface (BCI). This paper provides a comparison of different time-frequency representations (TFR) and their Rényi and Shannon entropies for sensorimotor rhythm (SMR) based motor imagery control signals in electroencephalographic (EEG) data. The motor imagery task was guided by visual guidance, visual and vibrotactile (somatosensory) guidance or visual cue only. RESULTS: When using TFR-based entropy features as an input for classification of different interaction intentions, higher accuracies were achieved (up to 99.87%) in comparison to regular time-series amplitude features (for which accuracy was up to 85.91%), which is an increase when compared to existing methods. In particular, the highest accuracy was achieved for the classification of the motor imagery versus the baseline (rest state) when using Shannon entropy with Reassigned Pseudo Wigner-Ville time-frequency representation. CONCLUSIONS: Our findings suggest that the quantity of useful classifiable motor imagery information (entropy output) changes during the period of motor imagery in comparison to baseline period; as a result, there is an increase in the accuracy and F1 score of classification when using entropy features in comparison to the accuracy and the F1 of classification when using amplitude features, hence, it is manifested as an improvement of the ability to detect motor imagery.

Bidirectional meta-Kronecker factored optimizer and Hausdorff distance loss for few-shot medical image segmentation.

To increase the accuracy of medical image analysis using supervised learning-based AI technology, a large amount of accurately labeled training data is required. However, the supervised learning approach may not be applicable to real-world medical imaging due to the lack of labeled data, the privacy of patients, and the cost of specialized knowledge. To handle these issues, we utilized Kronecker-factored decomposition, which enhances both computational efficiency and stability of the learning process. We combined this approach with a model-agnostic meta-learning framework for the parameter optimization. Based on this method, we present a bidirectional meta-Kronecker factored optimizer (BM-KFO) framework to quickly optimize semantic segmentation tasks using just a few magnetic resonance imaging (MRI) images as input. This model-agnostic approach can be implemented without altering network components and is capable of learning the learning process and meta-initial points while training on previously unseen data. We also incorporated a combination of average Hausdorff distance loss (AHD-loss) and cross-entropy loss into our objective function to specifically target the morphology of organs or lesions in medical images. Through evaluation of the proposed method on the abdominal MRI dataset, we obtained an average performance of 78.07% in setting 1 and 79.85% in setting 2. Our experiments demonstrate that BM-KFO with AHD-loss is suitable for general medical image segmentation applications and achieves superior performance compared to the baseline method in few-shot learning tasks. In order to replicate the proposed method, we have shared our code on GitHub. The corresponding URL can be found: https://github.com/YeongjoonKim/BMKFO.git .

Rational Design of Cascade DNA System for Signal Amplification.

System leakage critically confines the development of cascade DNA systems that need to be implemented in a strict order-by-order manner. In principle, ternary DNA reactants, composed of three single-strand DNA (ssDNA) with a strict equimolar ratio (1:1:1), have been indispensable for successfully cascading upstream entropy-driven DNA circuit (EDC) with downstream circuits, and system leakage will occur with any unbalance of the molar ratio. In this work, we proposed "splitting-reconstruction" and "protection-release" strategies on the potential downstream circuit initiator derived from upstream EDC to guide the construction of EDC-involved cascade systems independent of system leakage derived from unpurified reactants. Both the reconstructed and released downstream circuit initiators were in compliance with the principle of the cascade AND logic gate. Using these two strategies, two cascade systems─EDC2-4WJ-TMSDR and EDC3-HCR─were developed to carry out the designed order, which did not require that the ratio of 1:1:1 be maintained. Furthermore, the inherent property of the upstream EDC could transfer into the downstream circuit, endowing the developed cascade systems with a more powerful signal amplification ability for the sensitive detection of the corresponding initiator strand. These two strategies may provide new insights into the process of constructing EDC-like circuit-involved high-order DNA networks.

Enthalpy and entropy synergistic regulation-based programmable DNA motifs for biosensing and information encryption.

Deoxyribonucleic acid (DNA) provides a collection of intelligent tools for the development of information cryptography and biosensors. However, most conventional DNA regulation strategies rely solely on enthalpy regulation, which suffers from unpredictable stimuli-responsive performance and unsatisfactory accuracy due to relatively large energy fluctuations. Here, we report an enthalpy and entropy synergistic regulation-based pH-responsive A+/C DNA motif for programmable biosensing and information encryption. In the DNA motif, the variation in loop length alters entropic contribution, and the number of A+/C bases regulates enthalpy, which is verified through thermodynamic characterizations and analyses. On the basis of this straightforward strategy, the performances, such as pKa, of the DNA motif can be precisely and predictably tuned. The DNA motifs are finally successfully applied for glucose biosensing and crypto-steganography systems, highlighting their potential in the field of biosensing and information encryption.

A comprehensive mortise and tenon structure selection method based on Pugh's controlled convergence and rough Z-number MABAC method.

Mortise and tenon joints are widely used in the building and furniture industries because of their excellent mechanical and eco-friendly properties. In real-life cases, there are usually many available alternative structures for a joint area, it is a challenge to select a proper structure from massively available alternatives. This paper aims to select a proper multiple attribute decision-making method based on massive alternatives and unreliable, uncertain and subjective information. Pugh's controlled convergence, rough number, Z-number, consistency theory and Shannon entropy are integrated and proposed an improved rough Z-number Multi-Attributive Border Approximation Area Comparison (MABAC) method. Firstly, Pugh's controlled convergence is a selection method, simple and rapid, presented in the first phase to eliminate most of the alternatives. In the second phase, an integrated method is proposed. The consistency theory, distance measurement and the Z-number are initially aggregated to calculate the expert weight. The entropy method is then presented to determine the criteria weight. The alternatives are then ranked and the optimal mortise and tenon joint is selected based on the rough Z-number MABAC method. A real-life case is presented, and the proposed method is implemented in the joint of a bucket cabinet. Finally, the efficiency and effectiveness of the proposed method are proved by the case, sensitivity analysis and related comparisons.

Isothermal Titration Calorimetry for Quantification of Protein-Carbohydrate Interactions.

Isothermal titration calorimetry allows the determination of thermodynamic parameters for the interaction between a protein and mono- or oligosaccharides in solution. For the study of protein-carbohydrate interactions, it is a robust way to determine the stoichiometry and affinity, as well as the enthalpic and entropic contributions to this interaction, without the use of labeled proteins or substrates. Here we describe a standard multiple-injection titration experiment for measuring the binding energetics between a carbohydrate-binding protein and an oligosaccharide.

CoT-UNet++: A medical image segmentation method based on contextual transformer and dense connection.

Accurate depiction of individual teeth from CBCT images is a critical step in the diagnosis of oral diseases, and the traditional methods are very tedious and laborious, so automatic segmentation of individual teeth in CBCT images is important to assist physicians in diagnosis and treatment. TransUNet has achieved success in medical image segmentation tasks, which combines the advantages of Transformer and CNN. However, the skip connection taken by TransUNet leads to unnecessary restrictive fusion and also ignores the rich context between adjacent keys. To solve these problems, this paper proposes a context-transformed TransUNet++ (CoT-UNet++) architecture, which consists of a hybrid encoder, a dense connection, and a decoder. To be specific, a hybrid encoder is first used to obtain the contextual information between adjacent keys by CoTNet and the global context encoded by Transformer. Then the decoder upsamples the encoded features by cascading upsamplers to recover the original resolution. Finally, the multi-scale fusion between the encoded and decoded features at different levels is performed by dense concatenation to obtain more accurate location information. In addition, we employ a weighted loss function consisting of focal, dice, and cross-entropy to reduce the training error and achieve pixel-level optimization. Experimental results demonstrate that the proposed CoT-UNet++ method outperforms the baseline models and can obtain better performance in tooth segmentation.

Computational methods of EEG signals analysis for Alzheimer's disease classification.

Computational analysis of electroencephalographic (EEG) signals have shown promising results in detecting brain disorders, such as Alzheimer's disease (AD). AD is a progressive neurological illness that causes neuron cells degeneration, resulting in cognitive impairment. While there is no cure for AD, early diagnosis is critical to improving the quality of life of affected individuals. Here, we apply six computational time-series analysis methods (wavelet coherence, fractal dimension, quadratic entropy, wavelet energy, quantile graphs and visibility graphs) to EEG records from 160 AD patients and 24 healthy controls. Results from raw and wavelet-filtered (alpha, beta, theta and delta bands) EEG signals show that some of the time-series analysis methods tested here, such as wavelet coherence and quantile graphs, can robustly discriminate between AD patients from elderly healthy subjects. They represent a promising non-invasive and low-cost approach to the AD detection in elderly patients.

Entropic control of the free-energy landscape of an archetypal biomolecular machine.

Biomolecular machines are complex macromolecular assemblies that utilize thermal and chemical energy to perform essential, multistep, cellular processes. Despite possessing different architectures and functions, an essential feature of the mechanisms of action of all such machines is that they require dynamic rearrangements of structural components. Surprisingly, biomolecular machines generally possess only a limited set of such motions, suggesting that these dynamics must be repurposed to drive different mechanistic steps. Although ligands that interact with these machines are known to drive such repurposing, the physical and structural mechanisms through which ligands achieve this remain unknown. Using temperature-dependent, single-molecule measurements analyzed with a time-resolution-enhancing algorithm, here, we dissect the free-energy landscape of an archetypal biomolecular machine, the bacterial ribosome, to reveal how its dynamics are repurposed to drive distinct steps during ribosome-catalyzed protein synthesis. Specifically, we show that the free-energy landscape of the ribosome encompasses a network of allosterically coupled structural elements that coordinates the motions of these elements. Moreover, we reveal that ribosomal ligands which participate in disparate steps of the protein synthesis pathway repurpose this network by differentially modulating the structural flexibility of the ribosomal complex (i.e., the entropic component of the free-energy landscape). We propose that such ligand-dependent entropic control of free-energy landscapes has evolved as a general strategy through which ligands may regulate the functions of all biomolecular machines. Such entropic control is therefore an important driver in the evolution of naturally occurring biomolecular machines and a critical consideration for the design of synthetic molecular machines.

Stress Response Analysis via Dynamic Entropy in EEG: Caregivers in View.

According to the World Health Organization (WHO), stress can be defined as any type of alteration that causes physical, emotional, or psychological tension. A very important concept that is sometimes confused with stress is anxiety. The difference between stress and anxiety is that stress usually has an existing cause. Once that activator has passed, stress typically eases. In this respect, according to the American Psychiatric Association, anxiety is a normal response to stress and can even be advantageous in some circumstances. By contrast, anxiety disorders differ from temporary feelings of anxiousness or nervousness with more intense feelings of fear or anxiety. The Diagnostic and Statistical Manual (DSM-5) explicitly describes anxiety as exorbitant concern and fearful expectations, occurring on most days for at least 6 months, about a series of events. Stress can be measured by some standardized questionnaires; however, these resources are characterized by some major disadvantages, the main one being the time consumed to interpret them; i.e., qualitative information must be transformed to quantitative data. Conversely, a physiological recourse has the advantage that it provides quantitative spatiotemporal information directly from brain areas and it processes data faster than qualitative supplies. A typical option for this is an electroencephalographic record (EEG). We propose, as a novelty, the application of time series (TS) entropies developed by us to inspect collections of EEGs obtained during stress situations. We investigated this database related to 23 persons, with 1920 samples (15 s) captured in 14 channels for 12 stressful events. Our parameters reflected that out of 12 events, event 2 (Family/financial instability/maltreatment) and 10 (Fear of disease and missing an important event) created more tension than the others. In addition, the most active lobes reflected by the EEG channels were frontal and temporal. The former is in charge of performing higher functions, self-control, self monitoring, and the latter is in charge of auditory processing, but also emotional handling. Thus, events E2 and E10 triggering frontal and temporal channels revealed the actual state of participants under stressful situations. The coefficient of variation revealed that E7 (Fear of getting cheated/losing someone) and E11 (Fear of suffering a serious illness) were the events with more changes among participants. In the same sense, AF4, FC5, and F7 (mainly frontal lobe channels) were the most irregular on average for all participants. In summary, by means of dynamic entropy analysis, the goal is to process the EEG dataset in order to elucidate which event and brain regions are key for all participants. The latter will allow us to easily determine which was the most stressful and on which brain zone. This study can be applied to other caregivers datasets. All this is a novelty.

Self-Organization of Enzyme-Catalyzed Reactions Studied by the Maximum Entropy Production Principle.

The self-organization of open reaction systems is closely related to specific mechanisms that allow the export of internally generated entropy from systems to their environment. According to the second law of thermodynamics, systems with effective entropy export to the environment are better internally organized. Therefore, they are in thermodynamic states with low entropy. In this context, we study how self-organization in enzymatic reactions depends on their kinetic reaction mechanisms. Enzymatic reactions in an open system are considered to operate in a non-equilibrium steady state, which is achieved by satisfying the principle of maximum entropy production (MEPP). The latter is a general theoretical framework for our theoretical analysis. Detailed theoretical studies and comparisons of the linear irreversible kinetic schemes of an enzyme reaction in two and three states are performed. In both cases, in the optimal and statistically most probable thermodynamic steady state, a diffusion-limited flux is predicted by MEPP. Several thermodynamic quantities and enzymatic kinetic parameters, such as the entropy production rate, the Shannon information entropy, reaction stability, sensitivity, and specificity constants, are predicted. Our results show that the optimal enzyme performance may strongly depend on the number of reaction steps when linear reaction mechanisms are considered. Simple reaction mechanisms with a smaller number of intermediate reaction steps could be better organized internally and could allow fast and stable catalysis. These could be features of the evolutionary mechanisms of highly specialized enzymes.

Structural Preferences Shape the Entropic Force of Disordered Protein Ensembles.

Intrinsically disordered protein regions (IDRs) make up over 30% of the human proteome and exist in a dynamic conformational ensemble instead of a native, well-folded structure. Tethering IDRs to a surface (for example, the surface of a well-folded region of the same protein) can reduce the number of accessible conformations in these ensembles. This reduces the ensemble's conformational entropy, generating an effective entropic force that pulls away from the point of tethering. Recent experimental work has shown that this entropic force causes measurable, physiologically relevant changes to protein function. But how the magnitude of this force depends on IDR sequence remains unexplored. Here, we use all-atom simulations to analyze how structural preferences in IDR ensembles contribute to the entropic force they exert upon tethering. We show that sequence-encoded structural preferences play an important role in determining the magnitude of this force: compact, spherical ensembles generate an entropic force that can be several times higher than more extended ensembles. We further show that changes in the surrounding solution's chemistry can modulate the IDR entropic force strength. We propose that the entropic force is a sequence-dependent, environmentally tunable property of terminal IDR sequences.

Enhancing Hit Discovery in Virtual Screening through Absolute Protein-Ligand Binding Free-Energy Calculations.

In the hit identification stage of drug discovery, a diverse chemical space needs to be explored to identify initial hits. Contrary to empirical scoring functions, absolute protein-ligand binding free-energy perturbation (ABFEP) provides a theoretically more rigorous and accurate description of protein-ligand binding thermodynamics and could, in principle, greatly improve the hit rates in virtual screening. In this work, we describe an implementation of an accurate and reliable ABFEP method in FEP+. We validated the ABFEP method on eight congeneric compound series binding to eight protein receptors including both neutral and charged ligands. For ligands with net charges, the alchemical ion approach is adopted to avoid artifacts in electrostatic potential energy calculations. The calculated binding free energies correlate with experimental results with a weighted average of R2 = 0.55 for the entire dataset. We also observe an overall root-mean-square error (RMSE) of 1.1 kcal/mol after shifting the zero-point of the simulation data to match the average experimental values. Through ABFEP calculations using apo versus holo protein structures, we demonstrated that the protein conformational and protonation state changes between the apo and holo proteins are the main physical factors contributing to the protein reorganization free energy manifested by the overestimation of raw ABFEP calculated binding free energies using the holo structures of the proteins. Furthermore, we performed ABFEP calculations in three virtual screening applications for hit enrichment. ABFEP greatly improves the hit rates as compared to docking scores or other methods like metadynamics. The good performance of ABFEP in rank ordering compounds demonstrated in this work confirms it as a useful tool to improve the hit rates in virtual screening, thus facilitating hit discovery.

Evaluation of the effect of ultrasonic pretreatment on vacuum far-infrared drying characteristics and quality of Angelica sinensis based on entropy weight-coefficient of variation method.

This study investigated the effects of ultrasonic pretreatment time, ultrasonic power, and ultrasonic frequency on the drying characteristics and physicochemical quality of Angelica sinensis, and the physicochemical quality content was selected as the evaluation index, the entropy weight-coefficient of variation method was used to calculate the coupling weight and comprehensive score, and the weighted Technique for Order Preference by Similarity to Ideal Solution method was used to verify the evaluation model. The results showed that the drying rate of materials after ultrasonic treatment was increased by 22.48% to 93.26%, and the effective moisture diffusivity was in the range between 4.6831 × 10-9 and 7.0722 × 10-9  m2 /s, and the drying activation energy was 31.90 kJ/mol. The energy consumption decreased by 5.75% to 25.88%. Compared with the samples without the ultrasonic pretreatment, the chlorogenic acid, ferulic acid, senkyunolide H, senkyunolide I, 3-butenylphthalide, ligustilide, polysaccharides, total phenolic content, total flavonoid content, and antioxidant capacity of A. sinensis were increased after ultrasonic treatment, and the color, rehydration ratio, shrinkage ratio, and microstructure of dried products were improved significantly (p < 0.05). However, the quality of the dried products decreased after ultrasonic treatment for 40 min with an ultrasonic frequency of 60 kHz, and the internal tissue structure was destroyed. In summary, ultrasonic pretreatment at low frequency and high power can significantly increase the drying rate and improve the physicochemical quality of dried products.

Enhanced Thermal Stability and Reduced Aggregation in an Antibody Fab Fragment at Elevated Concentrations.

The aggregation of protein therapeutics such as antibodies remains a major challenge in the biopharmaceutical industry. The present study aimed to characterize the impact of the protein concentration on the mechanisms and potential pathways for aggregation, using the antibody Fab fragment A33 as the model protein. Aggregation kinetics were determined for 0.05 to 100 mg/mL Fab A33, at 65 °C. A surprising trend was observed whereby increasing the concentration decreased the relative aggregation rate, ln(v) (% day-1), from 8.5 at 0.05 mg/mL to 4.4 at 100 mg/mL. The absolute aggregation rate (mol L-1 h-1) increased with the concentration following a rate order of approximately 1 up to a concentration of 25 mg/mL. Above this concentration, there was a transition to an apparently negative rate order of -1.1 up to 100 mg/mL. Several potential mechanisms were examined as possible explanations. A greater apparent conformational stability at 100 mg/mL was observed from an increase in the thermal transition midpoint (Tm) by 7-9 °C, relative to those at 1-4 mg/mL. The associated change in unfolding entropy (△Svh) also increased by 14-18% at 25-100 mg/mL, relative to those at 1-4 mg/mL, indicating reduced conformational flexibility in the native ensemble. Addition of Tween or the crowding agents Ficoll and dextran, showed that neither surface adsorption, diffusion limitations nor simple volume crowding affected the aggregation rate. Fitting of kinetic data to a wide range of mechanistic models implied a reversible two-state conformational switch mechanism from aggregation-prone monomers (N*) into non-aggregating native forms (N) at higher concentrations. kD measurements from DLS data also suggested a weak self-attraction while remaining colloidally stable, consistent with macromolecular self-crowding within weakly associated reversible oligomers. Such a model is also consistent with compaction of the native ensemble observed through changes in Tm and △Svh.

Complexity analysis from EEG data in congestive heart failure: A study via approximate entropy.

AIM: Congestive heart failure (CHF) is a very complex clinical syndrome that may lead to ischemic cerebral hypoxia condition. The aim of the present study is to analyze the effects of CHF on brain activity through electroencephalographic (EEG) complexity measures, like approximate entropy (ApEn). METHODS: Twenty patients with CHF and 18 healthy elderly people were recruited. ApEn values were evaluated in the total spectrum (0.2-47 Hz) and main EEG frequency bands: delta (2-4 Hz), theta (4-8 Hz), alpha 1 (8-11 Hz), alpha 2 (11-13 Hz), beta 1 (13-20 Hz), beta 2 (20-30 Hz), and gamma (30-45 Hz) to identify differences between CHF group and control. Moreover, a correlation analysis was performed between ApEn parameters and clinical data (i.e., B-type natriuretic peptides (BNP), New York Heart Association (NYHA), and systolic blood pressure (SBP)) within the CHF group. RESULTS: Statistical topographic maps showed statistically significant differences between the two groups in the total spectrum and theta frequency band. Within the CHF group, significant negative correlations were found between total ApEn and BNP in O2 channel and between theta ApEn and NYHA scores in Fp1, Fp2, and Fz channels; instead, a significant positive correlation was found between theta ApEn and SBP in C3 channel and a nearly significant positive correlation was obtained between theta ApEn and SBP in F4 channel. CONCLUSION: EEG abnormalities in CHF are very similar to those observed in cognitive-impaired patients, suggesting analogies between the effects of neurodegeneration and brain chronic hypovolaemia due to heart disorder and underlying high brain sensitivity to CHF.

Entropy, complexity, and maturity in children's neural responses to naturalistic video lessons.

Temporal characteristics of neural signals are often overlooked in traditional fMRI developmental studies but are critical to studying brain functions in ecologically valid settings. In the present study, we explore the temporal properties of children's neural responses during naturalistic mathematics and grammar tasks. To do so, we introduce a novel measure in developmental fMRI: neural entropy, which indicates temporal complexity of BOLD signals. We show that temporal patterns of neural activity have lower complexity and greater variability in children than in adults in the association cortex but not in the sensory-motor cortex. We also show that neural entropy is associated with both child-adult similarity in functional connectivity and neural synchrony, and that neural entropy increases with the size of functionally connected networks in the association cortex. In addition, neural entropy increases with functional maturity (i.e., child-adult neural synchrony) in content-specific regions. These exploratory findings suggest the hypothesis that neural entropy indexes the increasing breadth and diversity of neural processes available to children for analyzing mathematical information over development.

A whole-brain model of the neural entropy increase elicited by psychedelic drugs.

Psychedelic drugs, including lysergic acid diethylamide (LSD) and other agonists of the serotonin 2A receptor (5HT2A-R), induce drastic changes in subjective experience, and provide a unique opportunity to study the neurobiological basis of consciousness. One of the most notable neurophysiological signatures of psychedelics, increased entropy in spontaneous neural activity, is thought to be of relevance to the psychedelic experience, mediating both acute alterations in consciousness and long-term effects. However, no clear mechanistic explanation for this entropy increase has been put forward so far. We sought to do this here by building upon a recent whole-brain model of serotonergic neuromodulation, to study the entropic effects of 5HT2A-R activation. Our results reproduce the overall entropy increase observed in previous experiments in vivo, providing the first model-based explanation for this phenomenon. We also found that entropy changes were not uniform across the brain: entropy increased in all regions, but the larger effect were localised in visuo-occipital regions. Interestingly, at the whole-brain level, this reconfiguration was not well explained by 5HT2A-R density, but related closely to the topological properties of the brain's anatomical connectivity. These results help us understand the mechanisms underlying the psychedelic state and, more generally, the pharmacological modulation of whole-brain activity.

Information flow dynamics between geopolitical risk and major asset returns.

We quantify information flows between geopolitical risk (GPR) and global financial assets such as equity, bonds, and commodities, with a focus on the Russian-Ukrainian conflict. We combine transfer entropy and the I-CEEMDAN framework to measure information flows at multi-term scales. Our empirical results indicate that (i) in the short term, crude oil and Russian equity show opposite responses to GPR; (ii) in the medium and long term, GPR information increases the risk in the financial market; and (iii) the efficiency of the financial asset markets can be confirmed on a long-term scale. These findings have important implications for market participants, such as investors, portfolio managers, and policymakers.

The performance evaluation of management mode of small water resources projects.

Due to a series of societal factors, management of small rural water resources projects in China experience management problems. Based on the management mode of small water resources projects in three representative regions of Guangdong Province, the improved TOPSIS model is applied to evaluate the performance of management mode of small water resources projects through the combination with entropy weight method. Compared with the traditional TOPSIS model concerning the evaluation object of this paper, the evaluation value formulas of optimal and worst solutions of TOPSIS method are improved. The evaluation index system takes into account the coverage, hierarchy and systematization of indicators, and maintains a management mode with high environmental adaptability, so that the continuous operation of management mode can guaranteed. The results show that the management mode of water user association is most suitable for the development of small water resources projects in Guangdong Province.