@article{PuchkovMuellerLehmannetal.2023, author = {Puchkov, Dmytro and M{\"u}ller, Paul Markus and Lehmann, Martin and Matth{\"a}us, Claudia}, title = {Analyzing the cellular plasma membrane by fast and efficient correlative STED and platinum replica EM}, series = {Frontiers in cell and developmental biology}, volume = {11}, journal = {Frontiers in cell and developmental biology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-634X}, doi = {10.3389/fcell.2023.1305680}, pages = {15}, year = {2023}, abstract = {The plasma membrane of mammalian cells links transmembrane receptors, various structural components, and membrane-binding proteins to subcellular processes, allowing inter- and intracellular communication. Therefore, membrane-binding proteins, together with structural components such as actin filaments, modulate the cell membrane in their flexibility, stiffness, and curvature. Investigating membrane components and curvature in cells remains challenging due to the diffraction limit in light microscopy. Preparation of 5-15-nm-thin plasma membrane sheets and subsequent inspection by metal replica transmission electron microscopy (TEM) reveal detailed information about the cellular membrane topology, including the structure and curvature. However, electron microscopy cannot identify proteins associated with specific plasma membrane domains. Here, we describe a novel adaptation of correlative super-resolution light microscopy and platinum replica TEM (CLEM-PREM), allowing the analysis of plasma membrane sheets with respect to their structural details, curvature, and associated protein composition. We suggest a number of shortcuts and troubleshooting solutions to contemporary PREM protocols. Thus, implementation of super-resolution stimulated emission depletion (STED) microscopy offers significant reduction in sample preparation time and reduced technical challenges for imaging and analysis. Additionally, highly technical challenges associated with replica preparation and transfer on a TEM grid can be overcome by scanning electron microscopy (SEM) imaging. The combination of STED microscopy and platinum replica SEM or TEM provides the highest spatial resolution of plasma membrane proteins and their underlying membrane and is, therefore, a suitable method to study cellular events like endocytosis, membrane trafficking, or membrane tension adaptations.}, language = {en} } @article{QuarmbyZhangGeisleretal.2023, author = {Quarmby, Andrew and Zhang, Martin and Geisler, Moritz and Javorsky, Tomas and Mugele, Hendrik and Cassel, Michael and Lawley, Justin}, title = {Risk factors and injury prevention strategies for overuse injuries in adult climbers}, series = {Frontiers in sports and active living}, volume = {5}, journal = {Frontiers in sports and active living}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2624-9367}, doi = {10.3389/fspor.2023.1269870}, pages = {13}, year = {2023}, abstract = {Introduction Climbing is an increasingly popular activity and imposes specific physiological demands on the human body, which results in unique injury presentations. Of particular concern are overuse injuries (non-traumatic injuries). These injuries tend to present in the upper body and might be preventable with adequate knowledge of risk factors which could inform about injury prevention strategies. Research in this area has recently emerged but has yet to be synthesized comprehensively. Therefore, the aim of this study was to conduct a systematic review of the potential risk factors and injury prevention strategies for overuse injuries in adult climbers. Methods This systematic review was conducted in accordance with the PRISMA guidelines. Databases were searched systematically, and articles were deemed eligible based upon specific criteria. Research included was original and peer-reviewed, involving climbers, and published in English, German or Czech. Outcomes included overuse injury, and at least one or more variable indicating potential risk factors or injury prevention strategies. The methodological quality of the included studies was assessed with the Downs and Black Quality Index. Data were extracted from included studies and reported descriptively for population, climbing sport type, study design, injury definition and incidence/prevalence, risk factors, and injury prevention strategies. Results Out of 1,183 records, a total of 34 studies were included in the final analysis. Higher climbing intensity, bouldering, reduced grip/finger strength, use of a "crimp" grip, and previous injury were associated with an increased risk of overuse injury. Additionally, a strength training intervention prevented shoulder and elbow injuries. BMI/body weight, warm up/cool downs, stretching, taping and hydration were not associated with risk of overuse injury. The evidence for the risk factors of training volume, age/years of climbing experience, and sex was conflicting. Discussion This review presents several risk factors which appear to increase the risk of overuse injury in climbers. Strength and conditioning, load management, and climbing technique could be targeted in injury prevention programs, to enhance the health and wellbeing of climbing athletes. Further research is required to investigate the conflicting findings reported across included studies, and to investigate the effectiveness of injury prevention programs. Systematic Review Registrationhttps://www.crd.york.ac.uk/, PROSPERO (CRD42023404031).}, language = {en} } @article{LangaryKuekenNikoloski2023, author = {Langary, Damoun and K{\"u}ken, Anika and Nikoloski, Zoran}, title = {The effective deficiency of biochemical networks}, series = {Scientific reports}, volume = {13}, journal = {Scientific reports}, publisher = {Springer Nature}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-023-41767-1}, pages = {12}, year = {2023}, abstract = {The deficiency of a (bio)chemical reaction network can be conceptually interpreted as a measure of its ability to support exotic dynamical behavior and/or multistationarity. The classical definition of deficiency relates to the capacity of a network to permit variations of the complex formation rate vector at steady state, irrespective of the network kinetics. However, the deficiency is by definition completely insensitive to the fine details of the directionality of reactions as well as bounds on reaction fluxes. While the classical definition of deficiency can be readily applied in the analysis of unconstrained, weakly reversible networks, it only provides an upper bound in the cases where relevant constraints on reaction fluxes are imposed. Here we propose the concept of effective deficiency, which provides a more accurate assessment of the network's capacity to permit steady state variations at the complex level for constrained networks of any reversibility patterns. The effective deficiency relies on the concept of nonstoichiometric balanced complexes, which we have already shown to be present in real-world biochemical networks operating under flux constraints. Our results demonstrate that the effective deficiency of real-world biochemical networks is smaller than the classical deficiency, indicating the effects of reaction directionality and flux bounds on the variation of the complex formation rate vector at steady state.}, language = {en} } @article{KuekenTrevesNikoloski2023, author = {K{\"u}ken, Anika and Treves, Haim and Nikoloski, Zoran}, title = {A simulation-free constrained regression approach for flux estimation in isotopically nonstationary metabolic flux analysis with applications in microalgae}, series = {Frontiers in plant science : FPLS}, volume = {14}, journal = {Frontiers in plant science : FPLS}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2023.1140829}, pages = {12}, year = {2023}, abstract = {Introduction Flux phenotypes from different organisms and growth conditions allow better understanding of differential metabolic networks functions. Fluxes of metabolic reactions represent the integrated outcome of transcription, translation, and post-translational modifications, and directly affect growth and fitness. However, fluxes of intracellular metabolic reactions cannot be directly measured, but are estimated via metabolic flux analysis (MFA) that integrates data on isotope labeling patterns of metabolites with metabolic models. While the application of metabolomics technologies in photosynthetic organisms have resulted in unprecedented data from 13CO2-labeling experiments, the bottleneck in flux estimation remains the application of isotopically nonstationary MFA (INST-MFA). INST-MFA entails fitting a (large) system of coupled ordinary differential equations, with metabolite pools and reaction fluxes as parameters. Here, we focus on the Calvin-Benson cycle (CBC) as a key pathway for carbon fixation in photosynthesizing organisms and ask if approaches other than classical INST-MFA can provide reliable estimation of fluxes for reactions comprising this pathway. Methods First, we show that flux estimation with the labeling patterns of all CBC intermediates can be formulated as a single constrained regression problem, avoiding the need for repeated simulation of time-resolved labeling patterns. Results We then compare the flux estimates of the simulation-free constrained regression approach with those obtained from the classical INST-MFA based on labeling patterns of metabolites from the microalgae Chlamydomonas reinhardtii, Chlorella sorokiniana and Chlorella ohadii under different growth conditions. Discussion Our findings indicate that, in data-rich scenarios, simulation-free regression-based approaches provide a suitable alternative for flux estimation from classical INST-MFA since we observe a high qualitative agreement (rs=0.89) to predictions obtained from INCA, a state-of-the-art tool for INST-MFA.}, language = {en} } @article{RuszkiewiczEndigGueveretal.2023, author = {Ruszkiewicz, Joanna and Endig, Lisa and G{\"u}ver, Ebru and B{\"u}rkle, Alexander and Mangerich, Aswin}, title = {Life-cycle-dependent toxicities of mono- and bifunctional alkylating agents in the 3R-compliant model organism C. elegans}, series = {Cells : open access journal}, volume = {12}, journal = {Cells : open access journal}, number = {23}, publisher = {MDPI}, address = {Basel}, issn = {2073-4409}, doi = {10.3390/cells12232728}, pages = {16}, year = {2023}, abstract = {Caenorhabditis elegans (C. elegans) is gaining recognition and importance as an organismic model for toxicity testing in line with the 3Rs principle (replace, reduce, refine). In this study, we explored the use of C. elegans to examine the toxicities of alkylating sulphur mustard analogues, specifically the monofunctional agent 2-chloroethyl-ethyl sulphide (CEES) and the bifunctional, crosslinking agent mechlorethamine (HN2). We exposed wild-type worms at different life cycle stages (from larvae L1 to adulthood day 10) to CEES or HN2 and scored their viability 24 h later. The susceptibility of C. elegans to CEES and HN2 paralleled that of human cells, with HN2 exhibiting higher toxicity than CEES, reflected in LC50 values in the high µM to low mM range. Importantly, the effects were dependent on the worms' developmental stage as well as organismic age: the highest susceptibility was observed in L1, whereas the lowest was observed in L4 worms. In adult worms, susceptibility to alkylating agents increased with advanced age, especially to HN2. To examine reproductive effects, L4 worms were exposed to CEES and HN2, and both the offspring and the percentage of unhatched eggs were assessed. Moreover, germline apoptosis was assessed by using ced-1p::GFP (MD701) worms. In contrast to concentrations that elicited low toxicities to L4 worms, CEES and HN2 were highly toxic to germline cells, manifesting as increased germline apoptosis as well as reduced offspring number and percentage of eggs hatched. Again, HN2 exhibited stronger effects than CEES. Compound specificity was also evident in toxicities to dopaminergic neurons-HN2 exposure affected expression of dopamine transporter DAT-1 (strain BY200) at lower concentrations than CEES, suggesting a higher neurotoxic effect. Mechanistically, nicotinamide adenine dinucleotide (NAD+) has been linked to mustard agent toxicities. Therefore, the NAD+-dependent system was investigated in the response to CEES and HN2 treatment. Overall NAD+ levels in worm extracts were revealed to be largely resistant to mustard exposure except for high concentrations, which lowered the NAD+ levels in L4 worms 24 h post-treatment. Interestingly, however, mutant worms lacking components of NAD+-dependent pathways involved in genome maintenance, namely pme-2, parg-2, and sirt-2.1 showed a higher and compound-specific susceptibility, indicating an active role of NAD+ in genotoxic stress response. In conclusion, the present results demonstrate that C. elegans represents an attractive model to study the toxicology of alkylating agents, which supports its use in mechanistic as well as intervention studies with major strength in the possibility to analyze toxicities at different life cycle stages.}, language = {en} } @article{BuergerHeistermann2023, author = {B{\"u}rger, Gerd and Heistermann, Maik}, title = {Shallow and deep learning of extreme rainfall events from convective atmospheres}, series = {Natural hazards and earth system sciences : NHESS}, volume = {23}, journal = {Natural hazards and earth system sciences : NHESS}, number = {9}, publisher = {European Geophysical Society}, address = {Katlenburg-Lindau}, issn = {1684-9981}, doi = {10.5194/nhess-23-3065-2023}, pages = {3065 -- 3077}, year = {2023}, abstract = {Our subject is a new catalogue of radar-based heavy rainfall events (CatRaRE) over Germany and how it relates to the concurrent atmospheric circulation. We classify daily ERA5 fields of convective indices according to CatRaRE, using an array of 13 statistical methods, consisting of 4 conventional ("shallow") and 9 more recent deep machine learning (DL) algorithms; the classifiers are then applied to corresponding fields of simulated present and future atmospheres from the Coordinated Regional Climate Downscaling Experiment (CORDEX) project. The inherent uncertainty of the DL results from the stochastic nature of their optimization is addressed by employing an ensemble approach using 20 runs for each network. The shallow random forest method performs best with an equitable threat score (ETS) around 0.52, followed by the DL networks ALL-CNN and ResNet with an ETS near 0.48. Their success can be understood as a result of conceptual simplicity and parametric parsimony, which obviously best fits the relatively simple classification task. It is found that, on summer days, CatRaRE convective atmospheres over Germany occur with a probability of about 0.5. This probability is projected to increase, regardless of method, both in ERA5-reanalyzed and CORDEX-simulated atmospheres: for the historical period we find a centennial increase of about 0.2 and for the future period one of slightly below 0.1.}, language = {en} } @article{SammoudBouguezziUthoffetal.2023, author = {Sammoud, Senda and Bouguezzi, Raja and Uthoff, Aaron and Ramirez-Campillo, Rodrigo and Moran, Jason and Negra, Yassine and Hachana, Younes and Chaabene, Helmi}, title = {The effects of backward vs. forward running training on measures of physical fitness in young female handball players}, series = {Frontiers in sports and active living}, volume = {5}, journal = {Frontiers in sports and active living}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2624-9367}, doi = {10.3389/fspor.2023.1244369}, pages = {10}, year = {2023}, abstract = {Introduction This study examined the effects of an 8-week backward running (BR) vs. forward running (FR) training programmes on measures of physical fitness in young female handball players. Methods Twenty-nine players participated in this study. Participants were randomly assigned to a FR training group, BR training group, and a control group. Results and discussion Within-group analysis indicated significant, small-to-large improvements in all performance tests (effect size [g] = 0.36 to 1.80), except 5-m forward sprint-time in the BR group and 5- and 10-m forward sprint-time in the FR group. However, the CG significantly decreased forward sprint performance over 10-m and 20-m (g = 0.28 to 0.50) with no changes in the other fitness parameters. No significant differences in the amount of change scores between the BR and FR groups were noted. Both training interventions have led to similar improvements in measures of muscle power, change of direction (CoD) speed, sprint speed either forward or backward, and repeated sprint ability (RSA) in young female handball players, though BR training may have a small advantage over FR training for 10-m forward sprint time and CoD speed, while FR training may provide small improvements over BR training for RSAbest. Practitioners are advised to consider either FR or BR training to improve various measures of physical fitness in young female handball players.}, language = {en} } @article{ZiubanovaLaurinavichyuteParshina2023, author = {Ziubanova, Anastasia A. and Laurinavichyute, Anna and Parshina, Olga}, title = {Does early exposure to spoken and sign language affect reading fluency in deaf and hard-of-hearing adult signers?}, series = {Frontiers in psychology}, volume = {14}, journal = {Frontiers in psychology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-1078}, doi = {10.3389/fpsyg.2023.1145638}, pages = {9}, year = {2023}, abstract = {Introduction Early linguistic background, and in particular, access to language, lays the foundation of future reading skills in deaf and hard-of-hearing signers. The current study aims to estimate the impact of two factors - early access to sign and/or spoken language - on reading fluency in deaf and hard-of-hearing adult Russian Sign Language speakers. Methods In the eye-tracking experiment, 26 deaf and 14 hard-of-hearing native Russian Sign Language speakers read 144 sentences from the Russian Sentence Corpus. Analysis of global eye-movement trajectories (scanpaths) was used to identify clusters of typical reading trajectories. The role of early access to sign and spoken language as well as vocabulary size as predictors of the more fluent reading pattern was tested. Results Hard-of-hearing signers with early access to sign language read more fluently than those who were exposed to sign language later in life or deaf signers without access to speech sounds. No association between early access to spoken language and reading fluency was found. Discussion Our results suggest a unique advantage for the hard-of-hearing individuals from having early access to both sign and spoken language and support the existing claims that early exposure to sign language is beneficial not only for deaf but also for hard-of-hearing children.}, language = {en} } @article{RosenblumPikovsky2023, author = {Rosenblum, Michael and Pikovsky, Arkady}, title = {Inferring connectivity of an oscillatory network via the phase dynamics reconstruction}, series = {Frontiers in network physiology}, volume = {3}, journal = {Frontiers in network physiology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2674-0109}, doi = {10.3389/fnetp.2023.1298228}, pages = {10}, year = {2023}, abstract = {We review an approach for reconstructing oscillatory networks' undirected and directed connectivity from data. The technique relies on inferring the phase dynamics model. The central assumption is that we observe the outputs of all network nodes. We distinguish between two cases. In the first one, the observed signals represent smooth oscillations, while in the second one, the data are pulse-like and can be viewed as point processes. For the first case, we discuss estimating the true phase from a scalar signal, exploiting the protophase-to-phase transformation. With the phases at hand, pairwise and triplet synchronization indices can characterize the undirected connectivity. Next, we demonstrate how to infer the general form of the coupling functions for two or three oscillators and how to use these functions to quantify the directional links. We proceed with a different treatment of networks with more than three nodes. We discuss the difference between the structural and effective phase connectivity that emerges due to high-order terms in the coupling functions. For the second case of point-process data, we use the instants of spikes to infer the phase dynamics model in the Winfree form directly. This way, we obtain the network's coupling matrix in the first approximation in the coupling strength.}, language = {en} } @article{BlaserWeymarWendt2023, author = {Blaser, Berenike Lisa and Weymar, Mathias and Wendt, Julia}, title = {The effect of a single-session heart rate variability biofeedback on attentional control}, series = {Frontiers in psychology}, volume = {14}, journal = {Frontiers in psychology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-1078}, doi = {10.3389/fpsyg.2023.1292983}, pages = {13}, year = {2023}, abstract = {Introduction Vagally mediated heart rate variability is an index of autonomic nervous system activity that is associated with a large variety of outcome variables including psychopathology and self-regulation. While practicing heart rate variability biofeedback over several weeks has been reliably associated with a number of positive outcomes, its acute effects are not well known. As the strongest association with vagally mediated heart rate variability has been found particularly within the attention-related subdomain of self-regulation, we investigated the acute effect of heart rate variability biofeedback on attentional control using the revised Attention Network Test. Methods Fifty-six participants were tested in two sessions. In one session each participant received a heart rate variability biofeedback intervention, and in the other session a control intervention of paced breathing at a normal ventilation rate. After the biofeedback or control intervention, participants completed the Attention Network Test using the Orienting Score as a measure of attentional control. Results Mixed models revealed that higher resting baseline vagally mediated heart rate variability was associated with better performance in attentional control, which suggests more efficient direction of attention to target stimuli. There was no significant main effect of the intervention on attentional control. However, an interaction effect indicated better performance in attentional control after biofeedback in individuals who reported higher current stress levels. Discussion The results point to acute beneficial effects of heart rate variability biofeedback on cognitive performance in highly stressed individuals. Although promising, the results need to be replicated in larger or more targeted samples in order to reach stronger conclusions about the effects.}, language = {en} }