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1.
Assessing different temporal scales of calcium dynamics in networks of beta cell populations
Jan Zmazek, Maša Skelin, Rene Markovič, Jurij Dolenšek, Marko Marhl, Andraž Stožer, Marko Gosak, 2021, izvirni znanstveni članek

Opis: Beta cells within the pancreatic islets of Langerhans respond to stimulation with coherent oscillations of membrane potential and intracellular calcium concentration that presumably drive the pulsatile exocytosis of insulin. Their rhythmic activity is multimodal, resulting from networked feedback interactions of various oscillatory subsystems, such as the glycolytic, mitochondrial, and electrical/calcium components.How these oscillatory modules interact and affect the collective cellular activity, which is a prerequisite for proper hormone release, is incompletely understood. In the present work, we combined advanced confocal Ca2+ imaging in fresh mouse pancreas tissue slices with time series analysis and network science approaches to unveil the glucosedependent characteristics of different oscillatory components on both the intra- and inter-cellular level. Our results reveal an interrelationship between the metabolically driven low-frequency component and the electrically driven high-frequency component, with the latter exhibiting the highest bursting rates around the peaks of the slow component and the lowest around the nadirs. Moreover, the activity, as well as the average synchronicity of the fast component, considerably increased with increasing stimulatory glucose concentration, whereas the stimulation level did not affect any of these parameters in the slow component domain. Remarkably, in both dynamical components, the average correlation decreased similarly with intercellular distance, which implies that intercellular communication affects the synchronicity of both types of oscillations. To explore the intra-islet synchronization patterns in more detail, we constructed functional connectivity maps. The subsequent comparison of network characteristics of different oscillatory components showed more locally clustered and segregated networks of fast oscillatory activity, while the slow oscillations were more global, resulting in several long-range connections and a more cohesive structure. Besides the structural differences, we found a relatively weak relationship between the fast and slow network layer, which suggests that different synchronization mechanisms shape the collective cellular activity in islets, a finding which has to be kept in mind in future studies employing different oscillations for constructing networks.
Ključne besede: islets of Langerhans, beta cell network, calcium oscillations, multimodal activity analysis, confocal imaging, functional connectivity, multiplex network
Objavljeno v DKUM: 06.06.2024; Ogledov: 67; Prenosov: 4
.pdf Celotno besedilo (9,40 MB)
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2.
The effect of forskolin and the role of Epac2A during activation, activity, and deactivation of beta cell networks
Maša Skelin, Jurij Dolenšek, Lidija Križančić Bombek, Viljem Pohorec, Marko Gosak, Marjan Rupnik, Andraž Stožer, 2023, izvirni znanstveni članek

Opis: Beta cells couple stimulation by glucose with insulin secretion and impairments in this coupling play a central role in diabetes mellitus. Cyclic adenosine monophosphate (cAMP) amplifies stimulus-secretion coupling via protein kinase A and guanine nucleotide exchange protein 2 (Epac2A). With the present research, we aimed to clarify the influence of cAMP-elevating diterpene forskolin on cytoplasmic calcium dynamics and intercellular network activity, which are two of the crucial elements of normal beta cell stimulus-secretion coupling, and the role of Epac2A under normal and stimulated conditions. To this end, we performed functional multicellular calcium imaging of beta cells in mouse pancreas tissue slices after stimulation with glucose and forskolin in wild-type and Epac2A knock-out mice. Forskolin evoked calcium signals in otherwise substimulatory glucose and beta cells from Epac2A knock-out mice displayed a faster activation. During the plateau phase, beta cells from Epac2A knock-out mice displayed a slightly higher active time in response to glucose compared with wild-type littermates, and stimulation with forskolin increased the active time via an increase in oscillation frequency and a decrease in oscillation duration in both Epac2A knock-out and wild-type mice. Functional network properties during stimulation with glucose did not differ in Epac2A knock-out mice, but the presence of Epac2A was crucial for the protective effect of stimulation with forskolin in preventing a decline in beta cell functional connectivity with time. Finally, stimulation with forskolin prolonged beta cell activity during deactivation, especially in Epac2A knock-out mice.
Ključne besede: pancreas, tissue slices, beta cells, calcium imaging, amplifying pathway, forskolin, Epac2A KO, intercellular network
Objavljeno v DKUM: 27.05.2024; Ogledov: 98; Prenosov: 2
.pdf Celotno besedilo (12,03 MB)
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3.
Review of bioplastics characterisation by terahertz techniques in the view of ensuring a circular economy
Andreja Abina, Tjaša Korošec, Uroš Puc, Aleksander Zidanšek, 2023, pregledni znanstveni članek

Opis: The increasing scarcity of natural resources, worsening global climate change, environmental degradation, and rising demand for food are forcing the biotechnology and plastics industries to seek and apply circular economy models that would lead to a sustainable transition in the production and use of bioplastics. Circular economy models can improve the economic productivity of bio-based plastics and have a positive impact on the environment by reducing conventional plastic waste and the consumption of petrochemical feedstocks for plastic production. In addition, some agricultural wastes that have the potential to be used as bioplastics can be reused. Terahertz (THz) systems are already used in the plastics and rubber industries for non-destructive testing, detection, imaging, and quality control. Several reports have highlighted the potential applications of THz spectroscopy and imaging in polymer analysis and plastics characterisation. This potential is even greater with chemometric methods and artificial intelligence algorithms. In this review, we focus on applications that support the transformation of the biotechnology sector to the circular economy, particularly via the transition from conventional plastics to bioplastics. In this review, we discuss the potential of THz systems for the characterisation and analysis of bioplastics and biopolymers. The results of previous studies on biopolymers in the THz frequency range are summarised. Furthermore, the potential of using artificial intelligence approaches such as machine learning as advanced analytical methods in THz spectroscopy and imaging, in addition to the conventionally used chemometric methods, is discussed. The results of this review highlight that THz technology can contribute to closed technological circles in important areas of biotechnology and the related plastics and rubber industries.
Ključne besede: terahertz spectroscopy, terahertz imaging, circular economy, biopolymer, biotechnology, bioplastics
Objavljeno v DKUM: 16.04.2024; Ogledov: 252; Prenosov: 179
.pdf Celotno besedilo (5,14 MB)
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4.
Autolysis affects the iron cargo of ferritins in neurons and glial cells at different rates in the human brain
Sowmya Sunkara, Snježana Radulović, Saška Lipovšek Delakorda, Christoph Birkl, Stefan Eggenreich, Anna Maria Birkl-Toeglhofer, Maximilian Schinagl, Daniel Funk, Michael Stöger-Pollach, Johannes Haybaeck, Walter Gössler, Stefan Ropele, Gerd Leitinger, 2023, izvirni znanstveni članek

Opis: Iron is known to accumulate in neurological disorders, so a careful balance of the iron concentration is essential for healthy brain functioning. An imbalance in iron homeostasis could arise due to the dysfunction of proteins involved in iron homeostasis. Here, we focus on ferritin—the primary iron storage protein of the brain. In this study, we aimed to improve a method to measure ferritin-bound iron in the human post-mortem brain, and to discern its distribution in particular cell types and brain regions. Though it is known that glial cells and neurons differ in their ferritin concentration, the change in the number and distribution of iron-filled ferritin cores between different cell types during autolysis has not been revealed yet. Here, we show the cellular and region-wide distribution of ferritin in the human brain using state-of-the-art analytical electron microscopy. We validated the concentration of iron-filled ferritin cores to the absolute iron concentration measured by quantitative MRI and inductively coupled plasma mass spectrometry. We show that ferritins lose iron from their cores with the progression of autolysis whereas the overall iron concentrations were unaffected. Although the highest concentration of ferritin was found in glial cells, as the total ferritin concentration increased in a patient, ferritin accumulated more in neurons than in glial cells. Summed up, our findings point out the unique behaviour of neurons in storing iron during autolysis and explain the differences between the absolute iron concentrations and iron-filled ferritin in a cell-type-dependent manner in the human brain.
Ključne besede: ferritin, human brain, energy-filtered transmission electron microscopy, quantitative magnetic resonance imaging, autolysis
Objavljeno v DKUM: 20.03.2024; Ogledov: 165; Prenosov: 16
.pdf Celotno besedilo (2,73 MB)
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5.
UAV Thermal Imaging for Unexploded Ordnance Detection by Using Deep Learning
Milan Bajić, Jr., Božidar Potočnik, 2023, izvirni znanstveni članek

Opis: A few promising solutions for thermal imaging Unexploded Ordnance (UXO) detection were proposed after the start of the military conflict in Ukraine in 2014. At the same time, most of the landmine clearance protocols and practices are based on old, 20th-century technologies. More than 60 countries worldwide are still affected by explosive remnants of war, and new areas are contaminated almost every day. To date, no automated solutions exist for surface UXO detection by using thermal imaging. One of the reasons is also that there are no publicly available data. This research bridges both gaps by introducing an automated UXO detection method, and by publishing thermal imaging data. During a project in Bosnia and Herzegovina in 2019, an organisation, Norwegian People's Aid, collected data about unexploded ordnances and made them available for this research. Thermal images with a size of 720 x 480 pixels were collected by using an Unmanned Aerial Vehicle at a height of 3 m, thus achieving a very small Ground Sampling Distance (GSD). One of the goals of our research was also to verify if the explosive war remnants' detection accuracy could be improved further by using Convolutional Neural Networks (CNN). We have experimented with various existing modern CNN architectures for object identification, whereat the YOLOv5 model was selected as the most promising for retraining. An eleven-class object detection problem was solved primarily in this study. Our data were annotated semi-manually. Five versions of the YOLOv5 model, fine-tuned with a grid-search, were trained end-to-end on randomly selected 640 training and 80 validation images from our dataset. The trained models were verified on the remaining 88 images from our dataset. Objects from each of the eleven classes were identified with more than 90% probability, whereat the Mean Average Precision (mAP) at a 0.5 threshold was 99.5%, and the mAP at thresholds from 0.5 to 0.95 was 87.0% up to 90.5%, depending on the model's complexity. Our results are comparable to the state-of-the-art, whereat these object detection methods have been tested on other similar small datasets with thermal images. Our study is one of the few in the field of Automated UXO detection by using thermal images, and the first that solves the problem of identifying more than one class of objects. On the other hand, publicly available thermal images with a relatively small GSD will enable and stimulate the development of new detection algorithms, where our method and results can serve as a baseline. Only really accurate automatic UXO detection solutions will help to solve one of the least explored worldwide life-threatening problems.
Ključne besede: unmanned aerial vehicle, unexploded ordnance, thermal imaging, UXOTi_NPA dataset, convolutional neural networks, deep learning
Objavljeno v DKUM: 12.02.2024; Ogledov: 260; Prenosov: 17
.pdf Celotno besedilo (16,94 MB)
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6.
Frequency range optimization for continuous wave Terahertz imaging
Blaž Pongrac, Andrej Sarjaš, Dušan Gleich, izvirni znanstveni članek

Opis: S krajšimi valovnimi dolžinami kot mikrovalovi in večjo globino prodora v material kot infrardeča svetloba, valovi v TeraHertz-nem (THz) spektru ponujajo edinstvene možnosti testiranja materialov. THz tehnologija ponuja neinvazivna in nedestruktivna testiranja v obliki spektroskopije in slikanja. Najbolj uporabljeni sistemi za THz slikanje so sistemi spektroskopije v časovni domeni. Vendar sistemi spektroskopije frekvenčne domene ponujajo odlično frekvenčno ločljivost in so primerni za biomedicinske aplikacije. THz-no slikanje na podlagi spektroskopije v frekvenčnem prostoru je časovno kompleksno in ima pomanjkljivosti zaradi napak pri generiranju THz valov. V tem članku je predstavljen nov princip enodimenzionalnega zajemanja s THz valovi. Predlagana optimizacija frekvenčnega območja temelji na konvolucijski nevronski omreži. Predstavljena je frekvenčna optimizacija za določitev optimalnega frekvenčnega območja za zajem podatkov. Optimalno frekvenčno območje ali pasovna širina morata biti dovolj široka za učinkovito zaznavanje faze in morata biti na presečišču več spektralnih odtisov v opazovanem mediju. Presek spektralnih odtisov je ocenjen z uporabo predlaganega algoritma za optimizacijo frekvenčnega območja, ki temelji na konvolucijski nevronski mreži in algoritmu za občutljivost okluzije. Predlagani algoritem izbira samodejno najobčutljivejši frekvenčni pas THz spektra in omogoča zelo hitre zajeme za pregled in klasifikacijo objektov.
Ključne besede: terahertz, spectroscopy, imaging, convolutional neural network, occlusion sensitivity, optimization
Objavljeno v DKUM: 07.12.2023; Ogledov: 344; Prenosov: 17
.pdf Celotno besedilo (8,82 MB)
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Critical and supercritical spatiotemporal calcium dynamics in beta cells
Marko Gosak, Andraž Stožer, Rene Markovič, Jurij Dolenšek, Matjaž Perc, Marjan Rupnik, Marko Marhl, 2017, izvirni znanstveni članek

Opis: A coordinated functioning of beta cells within pancreatic islets is mediated by oscillatory membrane depolarization and subsequent changes in cytoplasmic calcium concentration. While gap junctions allow for intraislet information exchange, beta cells within islets form complex syncytia that are intrinsically nonlinear and highly heterogeneous. To study spatiotemporal calcium dynamics within these syncytia, we make use of computational modeling and confocal high-speed functional multicellular imaging. We show that model predictions are in good agreement with experimental data, especially if a high degree of heterogeneity in the intercellular coupling term is assumed. In particular, during the first few minutes after stimulation, the probability distribution of calcium wave sizes is characterized by a power law, thus indicating critical behavior. After this period, the dynamics changes qualitatively such that the number of global intercellular calcium events increases to the point where the behavior becomes supercritical. To better mimic normal in vivo conditions, we compare the described behavior during supraphysiological non-oscillatory stimulation with the behavior during exposure to a slightly lower and oscillatory glucose challenge. In the case of this protocol, we observe only critical behavior in both experiment and model. Our results indicate that the loss of oscillatory changes, along with the rise in plasma glucose observed in diabetes, could be associated with a switch to supercritical calcium dynamics and loss of beta cell functionality.
Ključne besede: beta cells, islets of Langerhans, self-organized criticality, intercellular dynamics, calcium waves, glucose oscillations, computational model, confocal calcium imaging
Objavljeno v DKUM: 23.01.2018; Ogledov: 1636; Prenosov: 380
.pdf Celotno besedilo (3,43 MB)
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10.
Particle identification performance of the prototype aerogel RICH counter for the Belle II experiment
S. Iwata, Samo Korpar, Peter Križan, Rok Pestotnik, Luka Šantelj, Andrej Seljak, Elvedin Tahirović, 2016, izvirni znanstveni članek

Opis: We have developed a new type of particle identification device, called an aerogel ring imaging Cherenkov (ARICH) counter, for the Belle II experiment. It uses silica aerogel tiles as Cherenkov radiators. For detection of Cherenkov photons, hybrid avalanche photo-detectors (HAPDs) are used. The designed HAPD has a high sensitivity to single photons under a strong magnetic field. We have confirmed that the HAPD provides high efficiency for single-photon detection even after exposure to neutron and $\gamma$-ray radiation that exceeds the levels expected in the 10-year Belle II operation. In order to confirm the basic performance of the ARICH counter system, we carried out a beam test at the using a prototype of the ARICH counter with six HAPD modules. The results are in agreement with our expectations and confirm the suitability of the ARICH counter for the Belle II experiment. Based on the in-beam performance of the device, we expect that the identification efficiency at $3.5\,{\rm GeV}/c$ is 97.4% and 4.9% for pions and kaons, respectively. This paper summarizes the development of the HAPD for the ARICH and the evaluation of the performance of the prototype ARICH counter built with the final design components.
Ključne besede: H14, elementary particle physics, particle detectors, Belle II detector, ring imaging Cherenkov counters, RICH counters
Objavljeno v DKUM: 21.07.2017; Ogledov: 1271; Prenosov: 470
.pdf Celotno besedilo (1,57 MB)
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