1. Binary coding of resonance graphs of catacondensed polyhexesAleksander Vesel, 2023, original scientific article Abstract: A catacondensed polyhex H is a connected subgraph of a hexagonal system such that any edge of H lies in a hexagon of H, any triple of hexagons of H has an empty intersection and the inner dual of H is a cactus graph. A perfect matching M of a catacondensed polyhex H is relevant if every cycle of the inner dual of H admitsa vertex that corresponds to the hexagon which contributes three edges in M. The vertex set of the graph R˜(H) consists of all relevant perfect matchings of H, two perfect matchings being adjacent whenever their symmetric difference forms the edge set of a hexagon of H. A labeling that assigns in linear time a binary string to every relevant perfect matching of a catacondensed polyhex is presented. The introduced labeling defines an isometric embedding of R˜(H)
into a hypercube. Keywords: graphs, graph theory, resonance graphs Published in DKUM: 07.06.2024; Views: 99; Downloads: 6 Full text (518,69 KB) This document has many files! More... |
2. Insights into the stabilization of interferon alpha by two surfactants revealed by STD-NMR spectroscopyHristo Svilenov, Katharina T. Kopp, Alexander P. Golovanov, Gerhard Winter, Matja Zalar, 2023, other scientific articles Keywords: drug-excipient interactions, protein aggregation, protein formulations, proteins, surfactants, Nuclear Magnetic Resonance, NMR, spectroscopy Published in DKUM: 12.04.2024; Views: 197; Downloads: 17 Full text (1,53 MB) This document has many files! More... |
3. Autolysis affects the iron cargo of ferritins in neurons and glial cells at different rates in the human brainSowmya 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, original scientific article Abstract: 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. Keywords: ferritin, human brain, energy-filtered transmission electron microscopy, quantitative magnetic resonance imaging, autolysis Published in DKUM: 20.03.2024; Views: 228; Downloads: 21 Full text (2,73 MB) This document has many files! More... |
4. Outerplane bipartite graphs with isomorphic resonance graphsSimon Brezovnik, Zhongyuan Che, Niko Tratnik, Petra Žigert Pleteršek, 2024, original scientific article Abstract: We present novel results related to isomorphic resonance graphs of 2-connected outerplane bipartite graphs. As the main result, we provide a structure characterization for 2-connected outerplane bipartite graphs with isomorphic resonance graphs. Three additional characterizations are expressed in terms of resonance digraphs, via local structures of inner duals, as well as using distributive lattices on the set of order ideals of posets defined on inner faces of 2-connected outerplane bipartite graphs. Keywords: distributive lattice, inner dual, isomorphic resonance graphs, order ideal, 2-connected outerplane bipartite graph Published in DKUM: 29.02.2024; Views: 290; Downloads: 9 Link to full text |
5. Measurement of two-particle correlations of hadrons in ▫$e^+ e^-$▫ collisions at BelleY.-C. Chen, Marko Bračko, Samo Korpar, Peter Križan, Tomaž Podobnik, Marko Starič, Luka Šantelj, 2022, original scientific article Abstract: The measurement of two-particle angular correlation functions in high-multiplicity e+e− collisions at √s=10.52 GeV is reported. In this study, the 89.5 fb−1 of hadronic e+e− annihilation data collected by the Belle detector at KEKB are used. Two-particle angular correlation functions are measured in the full relative azimuthal angle (Δϕ) and three units of pseudorapidity (Δη), defined by either the electron beam axis or the event-shape thrust axis, and are studied as a function of charged-particle multiplicity. The measurement in the thrust axis analysis, with mostly outgoing quark pairs determining the reference axis, is sensitive to the region of additional soft gluon emissions. No significant anisotropic collective behavior is observed with either coordinate analyses. Near-side jet correlations appear to be absent in the thrust axis analysis. The measurements are compared to predictions from various event generators and are expected to provide new constraints to the phenomenological models in the low-energy regime. Keywords: Particle & resonance production, Quark & gluon jets, Quark-gluon plasma Published in DKUM: 24.08.2023; Views: 396; Downloads: 9 Full text (634,71 KB) This document has many files! More... |
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7. A microtremor HVSR study of the seismic site effects in the area of the town of Brežice (SE Slovenia)Andrej Gosar, 2009, original scientific article Abstract: The wider region of Brežice is one of the most seismically active areas of Slovenia. The most damaging earthquake occurred in 1917, when Brežice was hit by an ML=5.7 earthquake that had an VIII MSK maximum intensity. Seismic site effects due to Quaternary sediments can be expected in the whole area of the town. Since there is a lack of boreholes and geophysical data to assess the site effects, the microtremor (ambient vibrations) horizontal-to-vertical spectral ratio (HVSR) method was applied at 113 free-field measuring points. In general, clear spectral peaks were obtained, but there were also examples of flat spectral ratios indicating a low impedance contrast between the sediments and the bedrock. A map of the sediment resonance frequency was drawn, which shows a frequency range of 1–15 Hz. In the southern part of the town higher frequencies correspond to the thin sediments (the Brežice terrace and the middle Sava terrace) and the high HVSR peak amplitudes indicate a great impedance contrast with the Sarmatian and Badenian bedrock. The northern part is characterized by very low frequencies, indicating thick sediments (Plio-Quaternary gravel) and a small impedance contrast with Pontian marl. The transition between the high and low frequencies is relatively steep. In addition, measurements were performed in 12 characteristic houses to assess the longitudinal and transverse building frequencies. The established building frequency range of 5–10 Hz indicates some areas in the southern part of the town where there is a potential danger of soil-structure resonance. Two buildings show direct evidence of a potential soil-structure resonance. According to this study, more pronounced seismic site effects are expected in the southern part of Brežice. Keywords: ambient vibrations, microtremors, horizontal-to-vertical spectral ratio (HVSR), seismic site effects, soil-structure resonance Published in DKUM: 06.06.2018; Views: 1396; Downloads: 244 Full text (403,95 KB) This document has many files! More... |
8. The LexA regulated genes of the Clostridium difficileBeata Maria Walter, Maja Rupnik, Vesna Hodnik, Gregor Anderluh, Bruno Dupuy, Nejc Paulič, Darja Žgur-Bertok, Matej Butala, 2014, original scientific article Abstract: Background: The SOS response including two main proteins LexA and RecA, maintains the integrity of bacterial genomes after DNA damage due to metabolic or environmental assaults. Additionally, derepression of LexA-regulated genes can result in mutations, genetic exchange and expression of virulence factors. Here we describe the first comprehensive description of the in silico LexA regulon in Clostridium difficile, an important human pathogen.
Results: We grouped thirty C. difficile strains from different ribotypes and toxinotypes into three clusters according to lexA gene/protein variability. We applied in silico analysis coupled to surface plasmon resonance spectroscopy (SPR) and determined 16 LexA binding sites in C. difficile. Our data indicate that strains within the cluster, as defined by LexA variability, harbour several specific LexA regulon genes. In addition to core SOS genes: lexA, recA, ruvCA and uvrBA, we identified a LexA binding site on the pathogenicity locus (PaLoc) and in the putative promoter region of several genes involved in housekeeping, sporulation and antibiotic resistance.
Conclusions: Results presented here suggest that in C. difficile LexA is not merely a regulator of the DNA damage response genes but also controls the expression of dozen genes involved in various other biological functions. Our in vitro results indicate that in C. difficile inactivation of LexA repressor depends on repressor`s dissociation from the operators. We report that the repressor`s dissociation rates from operators differentiate, thus the determined LexA-DNA dissociation constants imply on the timing of SOS gene expression in C. difficile. Keywords: Clostridium difficile, antibiotic resistance, toxin regulation, SOS system, surface plasmon resonance, SPR, LexA repressor Published in DKUM: 29.06.2017; Views: 1403; Downloads: 375 Full text (1,16 MB) This document has many files! More... |
9. Search for B decays to final states with the η c mesonA. Vinokurova, Marko Bračko, Boštjan Golob, Samo Korpar, Peter Križan, Rok Pestotnik, Marko Petrič, Eva Ribežl, Samo Stanič, Marko Starič, Luka Šantelj, Anže Zupanc, 2015, original scientific article Abstract: We report a search for B decays to selected final states with the ηc meson: B± → K±ηcπ+π−, B± → K±ηcω, B± → K±ηcη and B± → K±ηcπ0. The analysis is based on 772 × 10^6 B¯B pairs collected at the Υ(4S) resonance with the Belle detector at the KEKB asymmetric-energy e+e− collider. We set 90% confidence level upper limits on the branching fractions of the studied B decay modes, independent of intermediate resonances, in the range (0.6–5.3)×10^−4. We also search for molecular-state candidates in the D^0 ¯D^∗0 − ¯D^0D^∗0, D^0 ¯D^0 + ¯D^0D^0 and D^∗0¯D^∗0 + ¯D^∗0D^∗0 combinations, neutral partners of the Z(3900)± and Z(4020)±, and a poorly understood state X(3915) as possible intermediate states in the decay chain, and set 90% confidence level upper limits on the product of branching fractions to the mentioned intermediate states and decay branching fractions of these states in the range (0.6–6.9)×10^−5. Keywords: exotics, quarkonium, e+-e- experiments, B physics, particle and resonance production Published in DKUM: 27.06.2017; Views: 1376; Downloads: 524 Full text (129,32 KB) This document has many files! More... |
10. Autapse-induced multiple coherence resonance in single neurons and neuronal networksErgin Yilmaz, Mahmut Özer, Veli Baysal, Matjaž Perc, 2016, original scientific article Abstract: We study the effects of electrical and chemical autapse on the temporal coherence or firing regularity of single stochastic Hodgkin-Huxley neurons and scale-free neuronal networks. Also, we study the effects of chemical autapse on the occurrence of spatial synchronization in scale-free neuronal networks. Irrespective of the type of autapse, we observe autaptic time delay induced multiple coherence resonance for appropriately tuned autaptic conductance levels in single neurons. More precisely, we show that in the presence of an electrical autapse, there is an optimal intensity of channel noise inducing the multiple coherence resonance, whereas in the presence of chemical autapse the occurrence of multiple coherence resonance is less sensitive to the channel noise intensity. At the network level, we find autaptic time delay induced multiple coherence resonance and synchronization transitions, occurring at approximately the same delay lengths. We show that these two phenomena can arise only at a specific range of the coupling strength, and that they can be observed independently of the average degree of the network. Keywords: neuronal dynamics, autapse, coherence resonance, scale-free network Published in DKUM: 23.06.2017; Views: 1163; Downloads: 438 Full text (1,63 MB) This document has many files! More... |