1. EEG + High-density surface EMG recordings of right tibialis anterior muscle during isometric ankle dorsiflexion (HybridNeuro project)Blanka Zicher, Ciaran McGeady, Dario Farina, Nina Murks, Matjaž Divjak, 2025, complete scientific database of research data Abstract: This dataset was prepared in the context of the HybridNeuro project (https://www.hybridneuro.feri.um.si/). It contains a collection of simultaneous EMG and EEG recordings from 7 healthy volunteers. The main purpose of data collection was to investigate the role of beta-band oscillations in motor control by examining how cortical beta activity propagates to the motor unit pool and can be measured at the peripheral level using high-density EMG.
Surface EMG was recorded using 64-channel electrode grids arranged in a 13 × 5 configuration with one missing corner electrode and an interelectrode distance of 4 mm (OT Bioelettronica, Torino, Italy). Signals were amplified (150 V/V), sampled at 2048 Hz using a Quattrocento system (OT Bioelettronica, Torino, Italy), and band-pass filtered between 20 and 500 Hz. Different grid placements were employed to maximize the number of motor units decomposed from the EMG signals.
EEG signals were recorded with 31 active gel-based electrodes positioned according to the International 10–20 system, with FCz as the reference electrode (actiCAP, Brain Products GmbH, Gilching, Germany). Signals were amplified and sampled at 1 kHz using a BrainVision actiCHamp Plus system (Brain Products GmbH, Gilching, Germany).
EEG, EMG, and the exerted force signals were temporally synchronized using a common digital trigger sent to both recording systems.
Participants performed 2 repetitions of 4 sets of trapezoidal submaximal isometric contractions using the right tibialis anterior muscle, at 4 different contraction levels. Total task length was 640 s (not including rests). Each task's data is stored in a separate file in Matlab format (.MAT). Total dataset size is 8.5 GB.
Keywords: surface high density electromyogram (HDEMG), electroencephalogram (EEG), dataset, tibialis anterior, isometric ankle dorsiflexion, beta-band oscillations, motor control, HybridNeuro
Published in DKUM: 06.01.2026; Views: 0; Downloads: 5
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2. Primeri uporabe pregleda grafov v globino : na študijskem programu 2. stopnje MatematikaMaša Galun, 2025, master's thesis Abstract: V magistrski nalogi predstavimo različne algoritme, ki temeljijo na pregledu grafov v globino (DFS). Delovanje DFS algoritma prikažemo na problemih iz teorije grafov in teorije iger. Predstavimo osnovne pojme teorije grafov in analiziramo delovanje ter časovno zahtevnost DFS algoritma.Definiramo pojem krepke povezanosti in krepko povezanih komponent. Obravnavamo dva algoritma za iskanje krepko povezanih komponent v usmerjenih grafih (Kosaraju-Sharirjev in Tarjanov algoritem), ki ju implementiramo v programskem jeziku Python. V zadnjem poglavju preučujemo uporabo DFS algoritma v teoriji iger. Predstavimo minimax algoritem, ki se uporablja za določanje optimalne poteze v igrah z dvema igralcema in ga optimiziramo z alfa-beta obrezovanjem. Predstavljeno implementiramo v programskem jeziku Python, kjer analiziramo delovanje algoritmov na primeru igre križci in krožci.
Keywords: DFS, krepka povezanost, Tarjanov algoritem, Kosaraju-Sharirjev algoritem, minimax, alfa-beta obrezovanje, teorija iger, Python.
Published in DKUM: 10.07.2025; Views: 0; Downloads: 63
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3. Efficient β-galactosidase immobilised on glycidyl methacrylate polyHIPEMuzafera Paljevac, Darja Pečar, Peter Krajnc, 2025, original scientific article Abstract: Poly(glycidyl methacrylate-co-ethyleneglycol dimethacrylate) monoliths (PolyGMA) were synthesized by high internal phase emulsion (HIPE) templating and polymerisation. The porous monoliths exhibited a hierarchical porous structure with primary pores (cavities, average diameter 35 µm) interconnected by secondary pores (average diameter 5 µm). FTIR spectroscopy confirmed the chemical composition and identified characteristic functional groups of both GMA and EGDMA. The polyGMA materials were ground and sieved to obtain particles between 710 µm and 1000 µm in diameter, which were subsequently used to immobilize the enzyme β-galactosidase. Immobilization was performed using two methods, namely direct binding via epoxide groups and binding after the activation with glutaraldehyde. The glutaraldehyde method resulted in higher enzyme loading (0.43 mg of enzyme per 100 mg of polyGMA) and significantly improved catalytic activity compared to direct binding. The immobilized β-galactosidase was used for lactose hydrolysis under various conditions using both batch and flow-through reactors. Optimal activity was observed at pH 6.5 and 35°C, with kinetic parameters vmax = 0.64 mmol∙L -1 ∙min-1 and �� = 38.8 mmol∙mol-1 . Reuse tests showed stable performance over five cycles. Comparatively, non-porous polyGMA exhibited negligible enzymatic activity compared to polyHIPE supported enzyme. In addition, lactose hydrolysis was investigated in a flow-through system at different flow rates (0.5–2.5 mL∙min- ¹). The highest conversion (100%) was observed at a flow rate of 0.5 mL∙min-¹, while a higher flow rate of 2.5 mL∙min-¹ resulted in a lower conversion (approx. 35%), both at the lactose concentration of 4 g∙L - ¹.
Keywords: immobilized enzymes, glycidyl methacrylate, polyHIPE, β-galactosidase, beta-galactosidase
Published in DKUM: 21.03.2025; Views: 0; Downloads: 13
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5. Ultrafast multicellular calcium imaging of calcium spikes in mouse beta cells in tissue slicesJurij Dolenšek, Viljem Pohorec, Maša Skelin, Marko Gosak, Andraž Stožer, 2025, original scientific article Abstract: Background: The crucial steps in beta cell stimulus-secretion coupling upon stimulation with glucose are oscillatory changes in metabolism, membrane potential, intracellular calcium concentration, and exocytosis. The changes in membrane potential consist of bursts of spikes, with silent phases between them being dominated by membrane repolarization and absence of spikes. Assessing intra- and intercellular coupling at the multicellular level is possible with ever-increasing detail, but our current ability to simultaneously resolve spikes from many beta cells remains limited to double-impalement electrophysiological recordings. Methods: Since multicellular calcium imaging of spikes would enable a better understanding of coupling between changes in membrane potential and calcium concentration in beta cell collectives, we set out to design an appropriate methodological approach. Results: Combining the acute tissue slice method with ultrafast calcium imaging, we were able to resolve and quantify individual spikes within bursts at a temporal resolution of >150 Hz over prolonged periods, as well as describe their glucose-dependent properties. In addition, by simultaneous patch-clamp recordings we were able to show that calcium spikes closely follow membrane potential changes. Both bursts and spikes coordinate across islets in the form of intercellular waves, with bursts typically displaying global and spikes more local patterns. Conclusions: This method and the associated findings provide additional insight into the complex signaling within beta cell networks. Once extended to tissue from diabetic animals and human donors, this approach could help us better understand the mechanistic basis of diabetes and find new molecular targets.
Keywords: beta cell, calcium imaging, calcium oscillations, calcium spikes, physiology
Published in DKUM: 24.01.2025; Views: 0; Downloads: 10
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6. From isles of Königsberg to islets of Langerhans: examining the function of the endocrine pancreas through network scienceAndraž Stožer, Marko Šterk, Eva Paradiž, Rene Markovič, Maša Skelin, Cara E. Ellis, Lidija Križančić Bombek, Jurij Dolenšek, Patrick E. MacDonald, Marko Gosak, 2022, review article Abstract: Islets of Langerhans are multicellular microorgans located in the pancreas that play a central role in whole-body energy homeostasis. Through secretion of insulin and other hormones they regulate postprandial storage and interprandial usage of energy-rich nutrients. In these clusters of hormone-secreting endocrine cells, intricate cell-cell communication is essential for proper function. Electrical coupling between the insulin-secreting beta cells through gap junctions composed of connexin36 is particularly important, as it provides the required, most important, basis for coordinated responses of the beta cell population. The increasing evidence that gap-junctional communication and its modulation are vital to well-regulated secretion of insulin has stimulated immense interest in how subpopulations of heterogeneous beta cells are functionally arranged throughout the islets and how they mediate intercellular signals. In the last decade, several novel techniques have been proposed to assess cooperation between cells in islets, including the prosperous combination of multicellular imaging and network science. In the present contribution, we review recent advances related to the application of complex network approaches to uncover the functional connectivity patterns among cells within the islets. We first provide an accessible introduction to the basic principles of network theory, enumerating the measures characterizing the intercellular interactions and quantifying the functional integration and segregation of a multicellular system. Then we describe methodological approaches to construct functional beta cell networks, point out possible pitfalls, and specify the functional implications of beta cell network examinations. We continue by highlighting the recent findings obtained through advanced multicellular imaging techniques supported by network-based analyses, giving special emphasis to the current developments in both mouse and human islets, as well as outlining challenges offered by the multilayer network formalism in exploring the collective activity of islet cell populations. Finally, we emphasize that the combination of these imaging techniques and network-based analyses does not only represent an innovative concept that can be used to describe and interpret the physiology of islets, but also provides fertile ground for delineating normal from pathological function and for quantifying the changes in islet communication networks associated with the development of diabetes mellitus.
Keywords: pancreatic islets, beta cells, calcium imaging, intercellular communication, functional networks, multilayer networks
Published in DKUM: 20.12.2024; Views: 0; Downloads: 91
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7. Both electrical and metabolic coupling shape the collective multimodal activity and functional connectivity patterns in beta cell collectives : a computational model perspectiveMarko Šterk, Uroš Barać, Andraž Stožer, Marko Gosak, 2023, original scientific article Abstract: Pancreatic beta cells are coupled excitable oscillators that synchronize their activity via different communication pathways. Their oscillatory activity manifests itself on multiple timescales and consists of bursting electrical activity, subsequent oscillations in the intracellular Ca 2 + , as well as oscillations in metabolism and exocytosis. The coordination of the intricate activity on the multicellular level plays a key role in the regulation of physiological pulsatile insulin secretion and is incompletely understood. In this paper, we investigate theoretically the principles that give rise to the synchronized activity of beta cell populations by building up a phenomenological multicellular model that incorporates the basic features of beta cell dynamics. Specifically, the model is composed of coupled slow and fast oscillatory units that reflect metabolic processes and electrical activity, respectively. Using a realistic description of the intercellular interactions, we study how the combination of electrical and metabolic coupling generates collective rhythmicity and shapes functional beta cell networks. It turns out that while electrical coupling solely can synchronize the responses, the addition of metabolic interactions further enhances coordination, the spatial range of interactions increases the number of connections in the functional beta cell networks, and ensures a better consistency with experimental findings. Moreover, our computational results provide additional insights into the relationship between beta cell heterogeneity, their activity profiles, and functional connectivity, supplementing thereby recent experimental results on endocrine networks.
Keywords: pancreatic, beta cells, oscilators, calcium signaling, cells signaling
Published in DKUM: 10.12.2024; Views: 0; Downloads: 7
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8. Network representation of multicellular activity in pancreatic islets : Technical considerations for functional connectivity analysisMarko Šterk, Yaowen Zhang, Viljem Pohorec, Eva Paradiž, Jurij Dolenšek, Richard K. P. Benninger, Andraž Stožer, Vira Kravets, Marko Gosak, 2024, original scientific article Abstract: Within the islets of Langerhans, beta cells orchestrate synchronized insulin secretion, a pivotal aspect of metabolic homeostasis. Despite the inherent heterogeneity and multimodal activity of individual cells, intercellular coupling acts as a homogenizing force, enabling coordinated responses through the propagation of intercellular waves. Disruptions in this coordination are implicated in irregular insulin secretion, a hallmark of diabetes. Recently, innovative approaches, such as integrating multicellular calcium imaging with network analysis, have emerged for a quantitative assessment of the cellular activity in islets. However, different groups use distinct experimental preparations, microscopic techniques, apply different methods to process the measured signals and use various methods to derive functional connectivity patterns. This makes comparisons between findings and their integration into a bigger picture difficult and has led to disputes in functional connectivity interpretations. To address these issues, we present here a systematic analysis of how different approaches influence the network representation of islet activity. Our findings show that the choice of methods used to construct networks is not crucial, although care is needed when combining data from different islets. Conversely, the conclusions drawn from network analysis can be heavily affected by the pre-processing of the time series, the type of the oscillatory component in the signals, and by the experimental preparation. Our tutorial-like investigation aims to resolve interpretational issues, reconcile conflicting views, advance functional implications, and encourage researchers to adopt connectivity analysis. As we conclude, we outline challenges for future research, emphasizing the broader applicability of our conclusions to other tissues exhibiting complex multicellular dynamics.
Keywords: islets of Langerhans, beta cells, calcium signaling, intercellular communication, functional networks, myosin model
Published in DKUM: 09.12.2024; Views: 0; Downloads: 6
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9. Brain dynamics underlying preserved cycling ability in patients with Parkinson’s disease and freezing of gaitTeja Ličen, Martin Rakuša, Nicolaas I. Bohnen, Paolo Manganotti, Uroš Marušič, 2022, review article Abstract: Parkinson’s disease (PD) is generally associated with abnormally increased beta band oscillations in the cortico-basal ganglia loop during walking. PD patients with freezing of gait (FOG) exhibit a more distinct, prolonged narrow band of beta oscillations that are locked to the initiation of movement at ∼18 Hz. Upon initiation of cycling movements, this oscillation has been reported to be weaker and rather brief in duration. Due to the suppression of the overall beta band power during cycling and its continuous nature of the movement, cycling is considered to be less demanding for cortical networks compared to walking, including reduced need for sensorimotor processing, and thus unimpaired continuous cycling motion. Furthermore, cycling has been considered one of the most efficient non-pharmacological therapies with an influence on the subthalamic nucleus (STN) beta rhythms implicative of the deep brain stimulation effects. In the current review, we provide an overview of the currently available studies and discuss the underlying mechanism of preserved cycling ability in relation to the FOG in PD patients. The mechanisms are presented in detail using a graphical scheme comparing cortical oscillations during walking and cycling in PD.
Keywords: gait, freezing of gait, Parkinson's disease, cycling, cortical oscillations, beta band
Published in DKUM: 04.12.2024; Views: 0; Downloads: 9
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10. NMDA receptor inhibition increases, synchronizes, and stabilizes the collective pancreatic beta cell activity : insights through multilayer network analysisMarko Šterk, Lidija Križančić Bombek, Maša Skelin, Marjan Rupnik, Marko Marhl, Andraž Stožer, Marko Gosak, 2021, original scientific article Abstract: NMDA receptors promote repolarization in pancreatic beta cells and thereby reduce glucose-stimulated insulin secretion. Therefore, NMDA receptors are a potential therapeutic target for diabetes. While the mechanism of NMDA receptor inhibition in beta cells is rather well understood at the molecular level, its possible effects on the collective cellular activity have not been addressed to date, even though proper insulin secretion patterns result from well-synchronized beta cell behavior. The latter is enabled by strong intercellular connectivity, which governs propagating calcium waves across the islets and makes the heterogeneous beta cell population work in synchrony. Since a disrupted collective activity is an important and possibly early contributor to impaired insulin secretion and glucose intolerance, it is of utmost importance to understand possible effects of NMDA receptor inhibition on beta cell functional connectivity. To address this issue, we combined confocal functional
multicellular calcium imaging in mouse tissue slices with network science approaches. Our results revealed that NMDA receptor inhibition increases, synchronizes, and stabilizes beta cell activity without affecting the velocity or size of calcium waves. To explore intercellular interactions more precisely, we made use of the multilayer network formalism by regarding each calcium wave as an individual network layer, with weighted directed connections portraying the intercellular propagation. NMDA receptor inhibition stabilized both the role of wave initiators and the course of waves. The findings obtained with the experimental antagonist of NMDA receptors, MK-801, were additionally validated with dextrorphan, the active metabolite of the approved drug dextromethorphan, as well as with experiments on NMDA receptor KO mice. In sum, our results provide additional and new evidence for a possible
role of NMDA receptor inhibition in treatment of type 2 diabetes and introduce the multilayer network paradigm as a general strategy to examine effects of drugs on connectivity in multicellular systems.
Keywords: pancreas, beta cells, insulin, Islets of Langerhans
Published in DKUM: 29.11.2024; Views: 0; Downloads: 6
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