TY - JOUR A1 - Schlappa, Stephanie A1 - Bressel, Lena A1 - Reich, Oliver A1 - Münzberg, Marvin T1 - Advanced particle size analysis in high-solid-content polymer dispersions using photon density wave spectroscopy JF - Polymers N2 - High-solid-content polystyrene and polyvinyl acetate dispersions of polymer particles with a 50 nm to 500 nm mean particle diameter and 12-55% (w/w) solid content have been produced via emulsion polymerization and characterized regarding their optical and physical properties. Both systems have been analyzed with common particle-size-measuring techniques like dynamic light scattering (DLS) and static light scattering (SLS) and compared to inline particle size distribution (PSD) measurements via photon density wave (PDW) spectroscopy in undiluted samples. It is shown that particle size measurements of undiluted polystyrene dispersions are in good agreement between analysis methods. However, for polyvinyl acetate particles, size determination is challenging due to bound water in the produced polymer. For the first time, water-swelling factors were determined via an iterative approach of PDW spectroscopy error (X-2) minimization. It is shown that water-swollen particles can be analyzed in high-solid-content solutions and their physical properties can be assumed to determine the refractive index, density, and volume fraction in dispersion. It was found that assumed water swelling improved the reduced scattering coefficient fit by PDW spectroscopy by up to ten times and particle size determination was refined and enabled. Particle size analysis of the water-swollen particles agreed well with offline-based state-of-the-art techniques. KW - emulsion polymerization KW - multiple light scattering KW - photon density wave KW - spectroscopy KW - particle sizing KW - swelling of polymers Y1 - 2023 U6 - https://doi.org/10.3390/polym15153181 SN - 2073-4360 VL - 15 IS - 15 PB - MDPI CY - Basel ER - TY - JOUR A1 - Hollenstein, Nora A1 - Trondle, Marius A1 - Plomecka, Martyna A1 - Kiegeland, Samuel A1 - Ozyurt, Yilmazcan A1 - Jäger, Lena Ann A1 - Langer, Nicolas T1 - The ZuCo benchmark on cross-subject reading task classification with EEG and eye-tracking data JF - Frontiers in psychology N2 - We present a new machine learning benchmark for reading task classification with the goal of advancing EEG and eye-tracking research at the intersection between computational language processing and cognitive neuroscience. The benchmark task consists of a cross-subject classification to distinguish between two reading paradigms: normal reading and task-specific reading. The data for the benchmark is based on the Zurich Cognitive Language Processing Corpus (ZuCo 2.0), which provides simultaneous eye-tracking and EEG signals from natural reading of English sentences. The training dataset is publicly available, and we present a newly recorded hidden testset. We provide multiple solid baseline methods for this task and discuss future improvements. We release our code and provide an easy-to-use interface to evaluate new approaches with an accompanying public leaderboard: . KW - reading task classification KW - eye-tracking KW - EEG KW - machine learning KW - reading research KW - cross-subject evaluation Y1 - 2023 U6 - https://doi.org/10.3389/fpsyg.2022.1028824 SN - 1664-1078 VL - 13 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Michelet, Robin A1 - Bindellini, Davide A1 - Melin, Johanna A1 - Neumann, Uta A1 - Blankenstein, Oliver A1 - Huisinga, Wilhelm A1 - Johnson, Trevor N. A1 - Whitaker, Martin J. A1 - Ross, Richard A1 - Kloft, Charlotte T1 - Insights in the maturational processes influencing hydrocortisone pharmacokinetics in congenital adrenal hyperplasia patients using a middle-out approach JF - Frontiers in Pharmacology N2 - Introduction: Hydrocortisone is the standard of care in cortisol replacement therapy for congenital adrenal hyperplasia patients. Challenges in mimicking cortisol circadian rhythm and dosing individualization can be overcome by the support of mathematical modelling. Previously, a non-linear mixed-effects (NLME) model was developed based on clinical hydrocortisone pharmacokinetic (PK) pediatric and adult data. Additionally, a physiologically-based pharmacokinetic (PBPK) model was developed for adults and a pediatric model was obtained using maturation functions for relevant processes. In this work, a middle-out approach was applied. The aim was to investigate whether PBPK-derived maturation functions could provide a better description of hydrocortisone PK inter-individual variability when implemented in the NLME framework, with the goal of providing better individual predictions towards precision dosing at the patient level. Methods: Hydrocortisone PK data from 24 adrenal insufficiency pediatric patients and 30 adult healthy volunteers were used for NLME model development, while the PBPK model and maturation functions of clearance and cortisol binding globulin (CBG) were developed based on previous studies published in the literature. Results: Clearance (CL) estimates from both approaches were similar for children older than 1 year (CL/F increasing from around 150 L/h to 500 L/h), while CBG concentrations differed across the whole age range (CBG(NLME) stable around 0.5 mu M vs. steady increase from 0.35 to 0.8 mu M for CBG (PBPK)). PBPK-derived maturation functions were subsequently included in the NLME model. After inclusion of the maturation functions, none, a part of, or all parameters were re-estimated. However, the inclusion of CL and/or CBG maturation functions in the NLME model did not result in improved model performance for the CL maturation function (& UDelta;OFV > -15.36) and the re-estimation of parameters using the CBG maturation function most often led to unstable models or individual CL prediction bias. Discussion: Three explanations for the observed discrepancies could be postulated, i) non-considered maturation of processes such as absorption or first-pass effect, ii) lack of patients between 1 and 12 months, iii) lack of correction of PBPK CL maturation functions derived from urinary concentration ratio data for the renal function relative to adults. These should be investigated in the future to determine how NLME and PBPK methods can work towards deriving insights into pediatric hydrocortisone PK. KW - hydrocortisone KW - congenital adrenal hyperplasia KW - population pharmacokinetics KW - middle-out approach KW - pediatrics KW - physiologically-based pharmacokinetics (PBPK) KW - non-linear mixed effects modelling (NLME); KW - maturation Y1 - 2023 U6 - https://doi.org/10.3389/fphar.2022.1090554 SN - 1663-9812 VL - 13 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Nordmeyer, Sarah A1 - Kraus, Milena A1 - Ziehm, Matthias A1 - Kirchner, Marieluise A1 - Schafstedde, Marie A1 - Kelm, Marcus A1 - Niquet, Sylvia A1 - Stephen, Mariet Mathew A1 - Baczko, Istvan A1 - Knosalla, Christoph A1 - Schapranow, Matthieu-Patrick A1 - Dittmar, Gunnar A1 - Gotthardt, Michael A1 - Falcke, Martin A1 - Regitz-Zagrosek, Vera A1 - Kuehne, Titus A1 - Mertins, Philipp T1 - Disease- and sex-specific differences in patients with heart valve disease BT - a proteome study JF - Life Science Alliance N2 - Pressure overload in patients with aortic valve stenosis and volume overload in mitral valve regurgitation trigger specific forms of cardiac remodeling; however, little is known about similarities and differences in myocardial proteome regulation. We performed proteome profiling of 75 human left ventricular myocardial biopsies (aortic stenosis = 41, mitral regurgitation = 17, and controls = 17) using high-resolution tandem mass spectrometry next to clinical and hemodynamic parameter acquisition. In patients of both disease groups, proteins related to ECM and cytoskeleton were more abundant, whereas those related to energy metabolism and proteostasis were less abundant compared with controls. In addition, disease group-specific and sex-specific differences have been observed. Male patients with aortic stenosis showed more proteins related to fibrosis and less to energy metabolism, whereas female patients showed strong reduction in proteostasis-related proteins. Clinical imaging was in line with proteomic findings, showing elevation of fibrosis in both patient groups and sex differences. Disease-and sex-specific proteomic profiles provide insight into cardiac remodeling in patients with heart valve disease and might help improve the understanding of molecular mechanisms and the development of individualized treatment strategies. Y1 - 2023 U6 - https://doi.org/10.26508/lsa.202201411 SN - 2575-1077 VL - 6 IS - 3 PB - EMBO Press CY - Heidelberg ER - TY - JOUR A1 - Teich, Paula A1 - Fühner, Thea Heidi A1 - Granacher, Urs A1 - Kliegl, Reinhold T1 - Physical fitness of primary school children differs depending on their timing of school enrollment JF - Scientific reports N2 - Previous research has shown that children who were enrolled to school according to the legal key date (i.e., keyage children, between eight and nine years in third grade) exhibited a linear physical fitness development in the ninth year of life. In contrast, children who were enrolled with a delay (i.e., older-than-keyage children [OTK], between nine and ten years in third grade) exhibited a lower physical fitness compared to what would be expected for their age. In these studies, cross-sectional age differences within third grade and timing of school enrollment were confounded. The present study investigated the longitudinal development of keyage and OTK children from third to fifth grade. This design also afforded a comparison of the two groups at the same average chronological age, that is a dissociation of the effects of timing of school enrollment and age. We tested six physical fitness components: cardiorespiratory endurance, coordination, speed, power of lower and upper limbs, and static balance. 1502 children (i.e., 1206 keyage and 296 OTK children) from 35 schools were tested in third, fourth, and fifth grade. Except for cardiorespiratory endurance, both groups developed from third to fourth and from fourth to fifth grade and keyage children outperformed OTK children at the average ages of 9.5 or 10.5 years. For cardiorespiratory endurance, there was no significant gain from fourth to fifth grade and keyage and OTK children did not differ significantly at 10.5 years of age. One reason for a delayed school enrollment could be that a child is (or is perceived as) biologically younger than their chronological age at the school entry examination, implying a negative correlation between chronological and biological age for OTK children. Indeed, a simple reflection of chronological age brought the developmental rate of the chronologically youngest OTK children in line with the developmental rate observed for keyage children, but did not eliminate all differences. The mapping of chronological and biological age of OTK children and other possible reasons for lower physical fitness of OTK children remain a task for future research. KW - Health care KW - Paediatrics KW - Physiology Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-35727-y SN - 2045-2322 VL - 13 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - Petrich, Annett A1 - Aji, Amit Koikkarah A1 - Dunsing, Valentin A1 - Chiantia, Salvatore T1 - Benchmarking of novel green fluorescent proteins for the quantification of protein oligomerization in living cells JF - PLoS one N2 - Protein-protein-interactions play an important role in many cellular functions. Quantitative non-invasive techniques are applied in living cells to evaluate such interactions, thereby providing a broader understanding of complex biological processes. Fluorescence fluctuation spectroscopy describes a group of quantitative microscopy approaches for the characterization of molecular interactions at single cell resolution. Through the obtained molecular brightness, it is possible to determine the oligomeric state of proteins. This is usually achieved by fusing fluorescent proteins (FPs) to the protein of interest. Recently, the number of novel green FPs has increased, with consequent improvements to the quality of fluctuation-based measurements. The photophysical behavior of FPs is influenced by multiple factors (including photobleaching, protonation-induced "blinking" and long-lived dark states). Assessing these factors is critical for selecting the appropriate fluorescent tag for live cell imaging applications. In this work, we focus on novel green FPs that are extensively used in live cell imaging. A systematic performance comparison of several green FPs in living cells under different pH conditions using Number & Brightness (N & B) analysis and scanning fluorescence correlation spectroscopy was performed. Our results show that the new FP Gamillus exhibits higher brightness at the cost of lower photostability and fluorescence probability (pf), especially at lower pH. mGreenLantern, on the other hand, thanks to a very high pf, is best suited for multimerization quantification at neutral pH. At lower pH, mEGFP remains apparently the best choice for multimerization investigation. These guidelines provide the information needed to plan quantitative fluorescence microscopy involving these FPs, both for general imaging or for protein-protein-interactions quantification via fluorescence fluctuation-based methods. Y1 - 2023 U6 - https://doi.org/10.1371/journal.pone.0285486 SN - 1932-6203 VL - 18 IS - 8 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Kappel, Christian A1 - Friedrich, Thomas A1 - Oberkofler, Vicky A1 - Jiang, Li A1 - Crawford, Tim A1 - Lenhard, Michael A1 - Bäurle, Isabel T1 - Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis JF - Genome biology : biology for the post-genomic era N2 - Background Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq. Results HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. Conclusions Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior. KW - Transcriptional memory KW - Priming KW - Heat stress KW - HSFA2 KW - HSFA3 KW - Arabidopsis thaliana KW - Histone H3K4 trimethylation KW - ChIP-seq Y1 - 2023 U6 - https://doi.org/10.1186/s13059-023-02970-5 SN - 1474-760X VL - 24 IS - 1 PB - BioMed Central CY - London ER - TY - JOUR A1 - Ferreira, Clara Mendes A1 - Dammhahn, Melanie A1 - Eccard, Jana T1 - So many choices, so little time BT - food preference and movement vary with the landscape of fear JF - Ecology and evolution N2 - Spatial and temporal variation in perceived predation risk is an important determinant of movement and foraging activity of animals. Foraging in this landscape of fear, individuals need to decide where and when to move, and what resources to choose. Foraging theory predicts the outcome of these decisions based on energetic trade-offs, but complex interactions between perceived predation risk and preferences of foragers for certain functional traits of their resources are rarely considered. Here, we studied the interactive effects of perceived predation risk on food trait preferences and foraging behavior in bank voles (Myodes glareolus) in experimental landscapes. Individuals (n = 19) were subjected for periods of 24 h to two extreme, risk-uniform landscapes (either risky or safe), containing 25 discrete food patches, filled with seeds of four plant species in even amounts. Seeds varied in functional traits: size, nutrients, and shape. We evaluated whether and how risk modifies forager preference for functional traits. We also investigated whether perceived risk and distance from shelter affected giving-up density (GUD), time in patches, and number of patch visits. In safe landscapes, individuals increased time spent in patches, lowered GUD and visited distant patches more often compared to risky landscapes. Individuals preferred bigger seeds independent of risk, but in the safe treatment they preferred fat-rich over carb-rich seeds. Thus, higher densities of resource levels remained in risky landscapes, while in safe landscapes resource density was lower and less diverse due to selective foraging. Our results suggest that the interaction of perceived risk and dietary preference adds an additional layer to the cascading effects of a landscape of fear which affects biodiversity at resource level. KW - foraging behavior KW - functional traits KW - giving-up density KW - myodes glareolus KW - perceived predation risk KW - seed ecology Y1 - 2023 U6 - https://doi.org/10.1002/ece3.10330 SN - 2045-7758 VL - 13 IS - 7 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Stoltnow, Malte A1 - Weis, Philipp A1 - Korges, Maximilian T1 - Hydrological controls on base metal precipitation and zoning at the porphyry-epithermal transition constrained by numerical modeling JF - Scientific reports N2 - Ore precipitation in porphyry copper systems is generally characterized by metal zoning (Cu-Mo to Zn-Pb-Ag), which is suggested to be variably related to solubility decreases during fluid cooling, fluid-rock interactions, partitioning during fluid phase separation and mixing with external fluids. Here, we present new advances of a numerical process model by considering published constraints on the temperature- and salinity-dependent solubility of Cu, Pb and Zn in the ore fluid. We quantitatively investigate the roles of vapor-brine separation, halite saturation, initial metal contents, fluid mixing and remobilization as first-order controls of the physical hydrology on ore formation. The results show that the magmatic vapor and brine phases ascend with different residence times but as miscible fluid mixtures, with salinity increases generating metal-undersaturated bulk fluids. The release rates of magmatic fluids affect the location of the thermohaline fronts, leading to contrasting mechanisms for ore precipitation: higher rates result in halite saturation without significant metal zoning, lower rates produce zoned ore shells due to mixing with meteoric water. Varying metal contents can affect the order of the final metal precipitation sequence. Redissolution of precipitated metals results in zoned ore shell patterns in more peripheral locations and also decouples halite saturation from ore precipitation. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-30572-5 SN - 2045-2322 VL - 13 IS - 1 PB - Springer Nature CY - London ER - TY - JOUR A1 - Apriyanto, Ardha A1 - Compart, Julia A1 - Fettke, Jörg T1 - Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield JF - Frontiers in plant science N2 - The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches. KW - starch KW - oil yield KW - fruit development KW - gene expression KW - RNA-seq KW - and palm KW - oil KW - Elaeis guineensis Jacq Y1 - 2023 U6 - https://doi.org/10.3389/fpls.2023.1220237 SN - 1664-462X VL - 14 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Compart, Julia A1 - Singh, Aakanksha A1 - Fettke, Jörg A1 - Apriyanto, Ardha T1 - Customizing starch properties BT - a review of starch modifications and their applications JF - Polymers N2 - Starch has been a convenient, economically important polymer with substantial applications in the food and processing industry. However, native starches present restricted applications, which hinder their industrial usage. Therefore, modification of starch is carried out to augment the positive characteristics and eliminate the limitations of the native starches. Modifications of starch can result in generating novel polymers with numerous functional and value-added properties that suit the needs of the industry. Here, we summarize the possible starch modifications in planta and outside the plant system (physical, chemical, and enzymatic) and their corresponding applications. In addition, this review will highlight the implications of each starch property adjustment. KW - starch KW - starch modification KW - in planta modification KW - physical modification KW - chemical modification KW - enzymatic modification KW - starch application Y1 - 2023 U6 - https://doi.org/10.3390/polym15163491 SN - 2073-4360 VL - 15 IS - 16 PB - MDPI CY - Basel ER - TY - JOUR A1 - Berry, Paul E. A1 - Dammhahn, Melanie A1 - Blaum, Niels T1 - Keeping cool on hot days BT - activity responses of African antelope to heat extremes JF - Frontiers in ecology and evolution N2 - Long-lived organisms are likely to respond to a rapidly changing climate with behavioral flexibility. Animals inhabiting the arid parts of southern Africa face a particularly rapid rise in temperature which in combination with food and water scarcity places substantial constraints on the ability of animals to tolerate heat. We investigated how three species of African antelope-springbok Antidorcas marsupialis, kudu Tragelaphus strepsiceros and eland T. oryx-differing in body size, habitat preference and movement ecology, change their activity in response to extreme heat in an arid savanna. Serving as a proxy for activity, dynamic body acceleration data recorded every five minutes were analyzed for seven to eight individuals per species for the three hottest months of the year. Activity responses to heat during the hottest time of day (the afternoons) were investigated and diel activity patterns were compared between hot and cool days. Springbok, which prefer open habitat, are highly mobile and the smallest of the species studied, showed the greatest decrease in activity with rising temperature. Furthermore, springbok showed reduced mean activity over the 24 h cycle on hot days compared to cool days. Large-bodied eland seemed less affected by afternoon heat than springbok. While eland also reduced diurnal activity on hot days compared to cool days, they compensated for this by increasing nocturnal activity, possibly because their predation risk is lower. Kudu, which are comparatively sedentary and typically occupy shady habitat, seemed least affected during the hottest time of day and showed no appreciable difference in diel activity patterns between hot and cool days. The interplay between habitat preference, body size, movement patterns, and other factors seems complex and even sub-lethal levels of heat stress have been shown to impact an animal's long-term survival and reproduction. Thus, differing heat tolerances among species could result in a shift in the composition of African herbivore communities as temperatures continue to rise, with significant implications for economically important wildlife-based land use and conservation. KW - springbok KW - kudu KW - eland KW - dynamic body acceleration KW - tri-axial accelerometers KW - behavioral flexibility KW - climate change KW - savanna ecology Y1 - 2023 U6 - https://doi.org/10.3389/fevo.2023.1172303 SN - 2296-701X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Stiegler, Jonas A1 - Pahl, Janice A1 - Guillen, Rafael Arce A1 - Ullmann, Wiebke A1 - Blaum, Niels T1 - The heat is on BT - impacts of rising temperature on the activity of a common European mammal JF - Frontiers in Ecology and Evolution N2 - Climate conditions severely impact the activity and, consequently, the fitness of wildlife species across the globe. Wildlife can respond to new climatic conditions, but the pace of human-induced change limits opportunities for adaptation or migration. Thus, how these changes affect behavior, movement patterns, and activity levels remains unclear. In this study, we investigate how extreme weather conditions affect the activity of European hares (Lepus europaeus) during their peak reproduction period. When hares must additionally invest energy in mating, prevailing against competitors, or lactating, we investigated their sensitivities to rising temperatures, wind speed, and humidity. To quantify their activity, we used the overall dynamic body acceleration (ODBA) calculated from tri-axial acceleration measurements of 33 GPS-collared hares. Our analysis revealed that temperature, humidity, and wind speed are important in explaining changes in activity, with a strong response for high temperatures above 25 & DEG;C and the highest change in activity during temperature extremes of over 35 & DEG;C during their inactive period. Further, we found a non-linear relationship between temperature and activity and an interaction of activity changes between day and night. Activity increased at higher temperatures during the inactive period (day) and decreased during the active period (night). This decrease was strongest during hot tropical nights. At a stage of life when mammals such as hares must substantially invest in reproduction, the sensitivity of females to extreme temperatures was particularly pronounced. Similarly, both sexes increased their activity at high humidity levels during the day and low wind speeds, irrespective of the time of day, while the effect of humidity was stronger for males. Our findings highlight the importance of understanding the complex relationships between extreme weather conditions and mammal behavior, critical for conservation and management. With ongoing climate change, extreme weather events such as heat waves and heavy rainfall are predicted to occur more often and last longer. These events will directly impact the fitness of hares and other wildlife species and hence the population dynamics of already declining populations across Europe. KW - activity KW - ODBA KW - animal tracking KW - European hare KW - extreme weather events KW - climate change Y1 - 2023 U6 - https://doi.org/10.3389/fevo.2023.1193861 SN - 2296-701X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Cohen, Sarel A1 - Hershcovitch, Moshik A1 - Taraz, Martin A1 - Kissig, Otto A1 - Issac, Davis A1 - Wood, Andrew A1 - Waddington, Daniel A1 - Chin, Peter A1 - Friedrich, Tobias T1 - Improved and optimized drug repurposing for the SARS-CoV-2 pandemic JF - PLoS one N2 - The active global SARS-CoV-2 pandemic caused more than 426 million cases and 5.8 million deaths worldwide. The development of completely new drugs for such a novel disease is a challenging, time intensive process. Despite researchers around the world working on this task, no effective treatments have been developed yet. This emphasizes the importance of drug repurposing, where treatments are found among existing drugs that are meant for different diseases. A common approach to this is based on knowledge graphs, that condense relationships between entities like drugs, diseases and genes. Graph neural networks (GNNs) can then be used for the task at hand by predicting links in such knowledge graphs. Expanding on state-of-the-art GNN research, Doshi et al. recently developed the Dr-COVID model. We further extend their work using additional output interpretation strategies. The best aggregation strategy derives a top-100 ranking of 8,070 candidate drugs, 32 of which are currently being tested in COVID-19-related clinical trials. Moreover, we present an alternative application for the model, the generation of additional candidates based on a given pre-selection of drug candidates using collaborative filtering. In addition, we improved the implementation of the Dr-COVID model by significantly shortening the inference and pre-processing time by exploiting data-parallelism. As drug repurposing is a task that requires high computation and memory resources, we further accelerate the post-processing phase using a new emerging hardware-we propose a new approach to leverage the use of high-capacity Non-Volatile Memory for aggregate drug ranking. Y1 - 2023 U6 - https://doi.org/10.1371/journal.pone.0266572 SN - 1932-6203 VL - 18 IS - 3 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Kappattanavar, Arpita Mallikarjuna A1 - Hecker, Pascal A1 - Moontaha, Sidratul A1 - Steckhan, Nico A1 - Arnrich, Bert T1 - Food choices after cognitive load BT - an affective computing approach JF - Sensors N2 - Psychology and nutritional science research has highlighted the impact of negative emotions and cognitive load on calorie consumption behaviour using subjective questionnaires. Isolated studies in other domains objectively assess cognitive load without considering its effects on eating behaviour. This study aims to explore the potential for developing an integrated eating behaviour assistant system that incorporates cognitive load factors. Two experimental sessions were conducted using custom-developed experimentation software to induce different stimuli. During these sessions, we collected 30 h of physiological, food consumption, and affective states questionnaires data to automatically detect cognitive load and analyse its effect on food choice. Utilising grid search optimisation and leave-one-subject-out cross-validation, a support vector machine model achieved a mean classification accuracy of 85.12% for the two cognitive load tasks using eight relevant features. Statistical analysis was performed on calorie consumption and questionnaire data. Furthermore, 75% of the subjects with higher negative affect significantly increased consumption of specific foods after high-cognitive-load tasks. These findings offer insights into the intricate relationship between cognitive load, affective states, and food choice, paving the way for an eating behaviour assistant system to manage food choices during cognitive load. Future research should enhance system capabilities and explore real-world applications. KW - cognitive load KW - eating behaviour KW - machine learning KW - physiological signals KW - photoplethysmography KW - electrodermal activity KW - sensors Y1 - 2023 U6 - https://doi.org/10.3390/s23146597 SN - 1424-8220 VL - 23 IS - 14 PB - MDPI CY - Basel ER - TY - JOUR A1 - Garrels, Tim A1 - Khodabakhsh, Athar A1 - Renard, Bernhard Y. A1 - Baum, Katharina T1 - LazyFox: fast and parallelized overlapping community detection in large graphs JF - PEERJ Computer Science N2 - The detection of communities in graph datasets provides insight about a graph's underlying structure and is an important tool for various domains such as social sciences, marketing, traffic forecast, and drug discovery. While most existing algorithms provide fast approaches for community detection, their results usually contain strictly separated communities. However, most datasets would semantically allow for or even require overlapping communities that can only be determined at much higher computational cost. We build on an efficient algorithm, FOX, that detects such overlapping communities. FOX measures the closeness of a node to a community by approximating the count of triangles which that node forms with that community. We propose LAZYFOX, a multi-threaded adaptation of the FOX algorithm, which provides even faster detection without an impact on community quality. This allows for the analyses of significantly larger and more complex datasets. LAZYFOX enables overlapping community detection on complex graph datasets with millions of nodes and billions of edges in days instead of weeks. As part of this work, LAZYFOX's implementation was published and is available as a tool under an MIT licence at https://github.com/TimGarrels/LazyFox. KW - Overlapping community detection KW - Large networks KW - Weighted clustering coefficient KW - Heuristic triangle estimation KW - Parallelized algorithm KW - C++ tool KW - Runtime improvement KW - Open source KW - Graph algorithm KW - Community analysis Y1 - 2023 U6 - https://doi.org/10.7717/peerj-cs.1291 SN - 2376-5992 VL - 9 PB - PeerJ Inc. CY - London ER - TY - JOUR A1 - Gärtner, Thomas A1 - Schneider, Juliana A1 - Arnrich, Bert A1 - Konigorski, Stefan T1 - Comparison of Bayesian Networks, G-estimation and linear models to estimate causal treatment effects in aggregated N-of-1 trials with carry-over effects JF - BMC Medical Research Methodology N2 - Background The aggregation of a series of N-of-1 trials presents an innovative and efficient study design, as an alternative to traditional randomized clinical trials. Challenges for the statistical analysis arise when there is carry-over or complex dependencies of the treatment effect of interest. Methods In this study, we evaluate and compare methods for the analysis of aggregated N-of-1 trials in different scenarios with carry-over and complex dependencies of treatment effects on covariates. For this, we simulate data of a series of N-of-1 trials for Chronic Nonspecific Low Back Pain based on assumed causal relationships parameterized by directed acyclic graphs. In addition to existing statistical methods such as regression models, Bayesian Networks, and G-estimation, we introduce a carry-over adjusted parametric model (COAPM). Results The results show that all evaluated existing models have a good performance when there is no carry-over and no treatment dependence. When there is carry-over, COAPM yields unbiased and more efficient estimates while all other methods show some bias in the estimation. When there is known treatment dependence, all approaches that are capable to model it yield unbiased estimates. Finally, the efficiency of all methods decreases slightly when there are missing values, and the bias in the estimates can also increase. Conclusions This study presents a systematic evaluation of existing and novel approaches for the statistical analysis of a series of N-of-1 trials. We derive practical recommendations which methods may be best in which scenarios. KW - N-of-1 trials KW - Randomized clinical trials KW - Bayesian Networks; KW - G-estimation KW - Linear model KW - Simulation study KW - Chronic Nonspecific Low KW - Back Pain Y1 - 2023 U6 - https://doi.org/10.1186/s12874-023-02012-5 SN - 1471-2288 VL - 23 IS - 1 PB - BMC CY - London ER - TY - JOUR A1 - Moontaha, Sidratul A1 - Schumann, Franziska Elisabeth Friederike A1 - Arnrich, Bert T1 - Online learning for wearable EEG-Based emotion classification JF - Sensors N2 - Giving emotional intelligence to machines can facilitate the early detection and prediction of mental diseases and symptoms. Electroencephalography (EEG)-based emotion recognition is widely applied because it measures electrical correlates directly from the brain rather than indirect measurement of other physiological responses initiated by the brain. Therefore, we used non-invasive and portable EEG sensors to develop a real-time emotion classification pipeline. The pipeline trains different binary classifiers for Valence and Arousal dimensions from an incoming EEG data stream achieving a 23.9% (Arousal) and 25.8% (Valence) higher F1-Score on the state-of-art AMIGOS dataset than previous work. Afterward, the pipeline was applied to the curated dataset from 15 participants using two consumer-grade EEG devices while watching 16 short emotional videos in a controlled environment. Mean F1-Scores of 87% (Arousal) and 82% (Valence) were achieved for an immediate label setting. Additionally, the pipeline proved to be fast enough to achieve predictions in real-time in a live scenario with delayed labels while continuously being updated. The significant discrepancy from the readily available labels on the classification scores leads to future work to include more data. Thereafter, the pipeline is ready to be used for real-time applications of emotion classification. KW - online learning KW - real-time KW - emotion classification KW - AMIGOS dataset KW - wearable EEG (muse and neurosity crown) KW - psychopy experiments Y1 - 2023 U6 - https://doi.org/10.3390/s23052387 SN - 1424-8220 VL - 23 IS - 5 PB - MDPI CY - Basel ER - TY - JOUR A1 - Mkaouer, Bessem A1 - Amara, Samiha A1 - Bouguezzi, Raja A1 - Ben Abderrahmen, Abderraouf A1 - Chaabene, Helmi T1 - Validity of a new sport-specific endurance test in artistic gymnastics JF - Frontiers in sports and active living N2 - Introduction General and particularly sport-specific testing is an integral aspect of performance optimization in artistic gymnastics. In artistic gymnastics, however, only non-specific field tests have been used to assess endurance performance (e.g., Multistage Shuttle Run Test; Cooper's Test). Methods This study aimed to examine the validity of a new sport-specific endurance test in artistic gymnastics. Fourteen elite-level gymnasts (i.e., eight males and six females) participated in this study. The newly developed artistic gymnastics-specific endurance test (AGSET) was conducted on two different occasions seven days apart to determine its reliability. To assess the concurrent validity of AGSET, participants performed the multistage shuttle run test (MSRT). Maximum oxygen uptake (VO2max) and respiratory exchange ratio (RER) were directly assessed using a portable gas analyzer system during both protocols. Additionally, the total time maintained (TTM) during the AGSET, maximum heart rate (HRmax), maximal aerobic speed (MAS), and blood lactate concentration (BLa) during the two protocols were collected. Results The main findings indicated that all variables derived from the AGSET (i.e., VO2max, MAS, HRmax, BLa, and RER) displayed very good relative (all intraclass correlation coefficients [ICC] > 0.90) and absolute (all typical errors of measurement [TEM] < 5%) reliability. Further, results showed that the ability of the AGSET to detect small changes in VO2max, MAS, BLa, and RER was good (smallest worthwhile change [SWC0.2] > TEM), except HRmax (SWC0.2 < TEM). Additionally, results showed a nearly perfect association between the VO2max values derived from the AGSET and MSRT (r = 0.985; coefficient of determination [R-2] = 97%) with no statistically significant differences (p>0.05). The mean (bias) +/- 95% limits of agreement between the two protocols were 0.28 +/- 0.55 mlminkg-1. Discussion AGSET seems to present very good reliability and concurrent validity for assessing endurance performance in elite artistic gymnastics. In addition, the newly developed protocol presents a good ability to detect small changes in performance. KW - artistic gymnastics KW - field test KW - aerobic endurance KW - validity KW - reliability KW - assessment KW - physical fitness KW - elite athletes Y1 - 2023 U6 - https://doi.org/10.3389/fspor.2023.1159807 SN - 2624-9367 VL - 5 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Warschburger, Petra A1 - Kamrath, Clemens A1 - Lanzinger, Stefanie A1 - Sengler, Claudia A1 - Wiegand, Susanna A1 - Göldel, Julia Marlen A1 - Weihrauch-Blüher, Susann A1 - Holl, Reinhard A1 - Minden, Kirsten T1 - A prospective analysis of the long-term impact of the COVID-19 pandemic on well-being and health care among children with a chronic condition and their families BT - a study protocol of the KICK-COVID study JF - BMC pediatrics N2 - Background There is consistent evidence that the COVID-19 pandemic is associated with an increased psychosocial burden on children and adolescents and their parents. Relatively little is known about its particular impact on high-risk groups with chronic physical health conditions (CCs). Therefore, the primary aim of the study is to analyze the multiple impacts on health care and psychosocial well-being on these children and adolescents and their parents. Methods We will implement a two-stage approach. In the first step, parents and their underage children from three German patient registries for diabetes, obesity, and rheumatic diseases, are invited to fill out short questionnaires including questions about corona-specific stressors, the health care situation, and psychosocial well-being. In the next step, a more comprehensive, in-depth online survey is carried out in a smaller subsample. Discussion The study will provide insights into the multiple longer-term stressors during the COVID-19 pandemic in families with a child with a CC. The simultaneous consideration of medical and psycho-social endpoints will help to gain a deeper understanding of the complex interactions affecting family functioning, psychological well-being, and health care delivery. KW - Chronic conditions KW - COVID-19 KW - Children and adolescents KW - Parents KW - Risk perception KW - Psychosocial strain KW - Diabetes KW - Rheumatic diseases KW - Obesity Y1 - 2023 U6 - https://doi.org/10.1186/s12887-023-03912-7 SN - 1471-2431 VL - 23 IS - 1 PB - BioMed Central CY - London ER -