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Metabolic engineering of microalgae offers a promising solution for sustainable biofuel production, and rational design of engineering strategies can be improved by employing metabolic models that integrate enzyme turnover numbers. However, the coverage of turnover numbers for Chlamydomonas reinhardtii, a model eukaryotic microalga accessible to metabolic engineering, is 17-fold smaller compared to the heterotrophic cell factory Saccharomyces cerevisiae. Here we generate quantitative protein abundance data of Chlamydomonas covering 2337 to 3708 proteins in various growth conditions to estimate in vivo maximum apparent turnover numbers. Using constrained-based modeling we provide proxies for in vivo turnover numbers of 568 reactions, representing a 10-fold increase over the in vitro data for Chlamydomonas. Integration of the in vivo estimates instead of in vitro values in a metabolic model of Chlamydomonas improved the accuracy of enzyme usage predictions. Our results help in extending the knowledge on uncharacterized enzymes and improve biotechnological applications of Chlamydomonas.
PyFin-sentiment
(2023)
Responding to the poor performance of generic automated sentiment analysis solutions on domain-specific texts, we collect a dataset of 10,000 tweets discussing the topics of finance and investing. We manually assign each tweet its market sentiment, i.e., the investor’s anticipation of a stock’s future return. Using this data, we show that all existing sentiment models trained on adjacent domains struggle with accurate market sentiment analysis due to the task’s specialized vocabulary. Consequently, we design, train, and deploy our own sentiment model. It outperforms all previous models (VADER, NTUSD-Fin, FinBERT, TwitterRoBERTa) when evaluated on Twitter posts. On posts from a different platform, our model performs on par with BERT-based large language models. We achieve this result at a fraction of the training and inference costs due to the model’s simple design. We publish the artifact as a python library to facilitate its use by future researchers and practitioners.
Knowledge on the response of sediment export to recent climate change in glacierized areas in the European Alps is limited, primarily because long-term records of suspended sediment concentrations (SSCs) are scarce. Here we tested the estimation of sediment export of the past five decades using quantile regression forest (QRF), a nonparametric, multivariate regression based on random forest. The regression builds on short-term records of SSCs and long records of the most important hydroclimatic drivers (discharge, precipitation and air temperature - QPT). We trained independent models for two nested and partially glacier-covered catchments, Vent (98 km(2)) and Vernagt (11.4 km(2)), in the upper otztal in Tyrol, Austria (1891 to 3772 m a.s.l.), where available QPT records start in 1967 and 1975. To assess temporal extrapolation ability, we used two 2-year SSC datasets at gauge Vernagt, which are almost 20 years apart, for a validation. For Vent, we performed a five-fold cross-validation on the 15 years of SSC measurements. Further, we quantified the number of days where predictors exceeded the range represented in the training dataset, as the inability to extrapolate beyond this range is a known limitation of QRF. Finally, we compared QRF performance to sediment rating curves (SRCs). We analyzed the modeled sediment export time series, the predictors and glacier mass balance data for trends (Mann-Kendall test and Sen's slope estimator) and step-like changes (using the widely applied Pettitt test and a complementary Bayesian approach).Our validation at gauge Vernagt demonstrated that QRF performs well in estimating past daily sediment export (Nash-Sutcliffe efficiency (NSE) of 0.73) and satisfactorily for SSCs (NSE of 0.51), despite the small training dataset. The temporal extrapolation ability of QRF was superior to SRCs, especially in periods with high-SSC events, which demonstrated the ability of QRF to model threshold effects. Days with high SSCs tended to be underestimated, but the effect on annual yields was small. Days with predictor exceedances were rare, indicating a good representativity of the training dataset. Finally, the QRF reconstruction models outperformed SRCs by about 20 percent points of the explained variance.Significant positive trends in the reconstructed annual suspended sediment yields were found at both gauges, with distinct step-like increases around 1981. This was linked to increased glacier melt, which became apparent through step-like increases in discharge at both gauges as well as change points in mass balances of the two largest glaciers in the Vent catchment. We identified exceptionally high July temperatures in 1982 and 1983 as a likely cause. In contrast, we did not find coinciding change points in precipitation. Opposing trends at the two gauges after 1981 suggest different timings of "peak sediment". We conclude that, given large-enough training datasets, the presented QRF approach is a promising tool with the ability to deepen our understanding of the response of high-alpine areas to decadal climate change.
Progressive habitat fragmentation threatens plant species with narrow habitat requirements. While local environmental conditions define population growth rates and recruitment success at the patch level, dispersal is critical for population viability at the landscape scale. Identifying the dynamics of plant meta-populations is often confounded by the uncertainty about soil-stored population compartments. We combined a landscape-scale assessment of an amphibious plant's population structure with measurements of dispersal complexity in time to track dispersal and putative shifts in functional connectivity. Using 13 microsatellite markers, we analyzed the genetic structure of extant Oenanthe aquatica populations and their soil seed banks in a kettle hole system to uncover hidden connectivity among populations in time and space. Considerable spatial genetic structure and isolation-by-distance suggest limited gene flow between sites. Spatial isolation and patch size showed minor effects on genetic diversity. Genetic similarity found among extant populations and their seed banks suggests increased local recruitment, despite some evidence of migration and recent colonization. Results indicate stepping-stone dispersal across adjacent populations. Among permanent and ephemeral demes the resulting meta-population demography could be determined by source-sink dynamics. Overall, these spatiotemporal connectivity patterns support mainland-island dynamics in our system, highlighting the importance of persistent seed banks as enduring sources of genetic diversity.
Background: Following the rapid increase of asylum seekers arriving in the European Union in 2015/16, policymakers have invested heavily in improving their foresight and forecasting capabilities. A common method to elicit expert predictions are Delphi surveys. This approach has attracted concern in the literature, given the high uncertainty in experts’ predictions. However, there exists limited guidance on specific design choices for future-related Delphi surveys.
Objective: We test whether or not small adjustments to the Delphi survey can increase certainty (i.e., reduce variation) in expert predictions on immigration to the EU in 2030.
Methods: Based on a two-round Delphi survey with 178 migration experts, we compare variation and subjective confidence in expert predictions and assess whether additional context information (type of migration flow, sociopolitical context) promotes convergence among experts (i.e., less variation) and confidence in their own estimates.
Results: We find that additional context information does not reduce variation and does not increase confidence in expert predictions on migration.
Conclusions: The results reaffirm recent concerns regarding the limited scope for reducing uncertainty by manipulating the survey setup. Persistent uncertainty may be a result of the complexity of migration processes and limited agreement among migration experts regarding key drivers.
Contribution: We caution policymakers and academics on the use of Delphi surveys for eliciting expert predictions on immigration, even when conducted based on a large pool of experts and using specific scenarios. The potential of alternative approaches such as prediction markets should be further explored.
Perception of peripersonal space (PPS) and interpersonal distance (IPD) has been shown to be modified by external factors such as perceived danger, the use of tools, and social factors. Especially in times of social distancing in the context of the COVID-19 pandemic, it is vital to study factors that modify PPS and IPD. The present work addresses the question of whether wearing a face mask as a protection tool and social interaction impact the perception of IPD. We tested estimated IPD in pictures at three distances: 50 cm, 90 cm, and 150 cm in both social interaction (shaking hands) and without interaction and when the two people in the pictures wore a face mask or not. Data from 60 subjects were analyzed in a linear mixed model (on both difference in distance estimation to the depicted distance and in absolute distance estimation) and in a 3 (distance: 50, 90, 150) x 2 (interaction: no interaction, shake hands), x 2 face mask (no mask, mask) rmANOVA on distance estimation difference. All analyses showed that at a distance of 50 and 90 cm, participants generally underestimated the IPD while at an IPD of 150 cm, participants overestimated the distance. This could be grounded in perceived danger and avoidance behavior at closer distances, while the wider distance between persons was not perceived as dangerous. Our findings at an IPD of 90 cm show that social interaction has the largest effect at the border of our PPS, while the face mask did not affect social interaction at either distance. In addition, the ANOVA results indicate that when no social interaction was displayed, participants felt less unsafe when depicted persons wore a face mask at distances of 90 and 150 cm. This shows that participants are on the one hand aware of the given safety measures and internalized them; on the other hand, that refraining from physical social interaction helps to get close to other persons.
Many widely used observational data sets are comprised of several overlapping instrument records. While data inter-calibration techniques often yield continuous and reliable data for trend analysis, less attention is generally paid to maintaining higher-order statistics such as variance and autocorrelation. A growing body of work uses these metrics to quantify the stability or resilience of a system under study and potentially to anticipate an approaching critical transition in the system. Exploring the degree to which changes in resilience indicators such as the variance or autocorrelation can be attributed to non-stationary characteristics of the measurement process – rather than actual changes in the dynamical properties of the system – is important in this context. In this work we use both synthetic and empirical data to explore how changes in the noise structure of a data set are propagated into the commonly used resilience metrics lag-one autocorrelation and variance. We focus on examples from remotely sensed vegetation indicators such as vegetation optical depth and the normalized difference vegetation index from different satellite sources. We find that time series resulting from mixing signals from sensors with varied uncertainties and covering overlapping time spans can lead to biases in inferred resilience changes. These biases are typically more pronounced when resilience metrics are aggregated (for example, by land-cover type or region), whereas estimates for individual time series remain reliable at reasonable sensor signal-to-noise ratios. Our work provides guidelines for the treatment and aggregation of multi-instrument data in studies of critical transitions and resilience.
Reliability of the active knee joint position sense test and influence of limb dominance and sex
(2023)
The output of a sensorimotor performance can be measured with the joint position sense (JPS) test. However, investigations of leg dominance, sex and quality measures on this test are limited. Therefore, these potential influencing factors as well as reliability and consistency measures were evaluated for angular reproduction performance and neuromuscular activity during the active knee JPS test in healthy participants. Twenty healthy participants (10 males; 10 females; age 29 +/- 8 years; height 165 +/- 39 cm; body mass 69 +/- 13 kg) performed a seated knee JPS test with a target angle of 50 degrees. Measurements were conducted in two sessions separated by two weeks and consisted of two blocks of continuous angular reproduction (three minutes each block). The difference between reproduced and target angle was identified as angular error measured by an electrogoniometer. During reproduction, the neuromuscular activity of the quadriceps muscle was assessed by surface electromyography. Neuromuscular activity was normalized to submaximal voluntary contraction (subMVC) and displayed per muscle and movement phase. Differences between leg dominance and sex were calculated using Friedman-test (alpha = 0.05). Reliability measures including intraclass correlation coefficient (ICC), Bland-Altman analysis (bias +/- limits of agreement (LoA)) and minimal detectable change (MDC) were analysed. No significant differences between leg dominance and sex were found in angular error and neuromuscular activity. Angular error demonstrated inter-session ICC scores of 0.424 with a bias of 2.4 degrees (+/- 2.4 degrees LoA) as well as MDC of 6.8 degrees and moderate intra-session ICC (0.723) with a bias of 1.4 degrees (+/- 1.65 degrees LoA) as well as MDC of 4.7 degrees. Neuromuscular activity for all muscles and movement phases illustrated inter-session ICC ranging from 0.432 to 0.809 with biases between - 2.5 and 13.6% subMVC and MDC from 13.4 to 63.9% subMVC. Intra-session ICC ranged from 0.705 to 0.987 with biases of - 7.7 to 2.4% subMVC and MDC of 2.7 to 46.5% subMVC. Leg dominance and sex seem not to influence angular reproduction performance and neuromuscular activity. Poor to excellent relative reliability paired with an acceptable consistency confirm findings of previous studies. Comparisons to pathological populations should be conducted with caution.
The Adaptive Force (AF) reflects the neuromuscular capacity to adapt to external loads during holding muscle actions and is similar to motions in real life and sports. The maximal isometric AF (AFisoₘₐₓ) was considered to be the most relevant parameter and was assumed to have major importance regarding injury mechanisms and the development of musculoskeletal pain. The aim of this study was to investigate the behavior of different torque parameters over the course of 30 repeated maximal AF trials. In addition, maximal holding vs. maximal pushing isometric muscle actions were compared. A side consideration was the behavior of torques in the course of repeated AF actions when comparing strength and endurance athletes. The elbow flexors of n = 12 males (six strength/six endurance athletes, non-professionals) were measured 30 times (120 s rest) using a pneumatic device. Maximal voluntary isometric contraction (MVIC) was measured pre and post. MVIC, AFisoₘₐₓ, and AFₘₐₓ (maximal torque of one AF measurement) were evaluated regarding different considerations and statistical tests. AFₘₐₓ and AFisoₘₐₓ declined in the course of 30 trials [slope regression (mean ± standard deviation): AFₘₐₓ = −0.323 ± 0.263; AFisoₘₐₓ = −0.45 ± 0.45]. The decline from start to end amounted to −12.8% ± 8.3% (p < 0.001) for AFₘₐₓ and −25.41% ± 26.40% (p < 0.001) for AFisoₘₐₓ. AF parameters declined more in strength vs. endurance athletes. Thereby, strength athletes showed a rather stable decline for AFmax and a plateau formation for AFisoₘₐₓ after 15 trials. In contrast, endurance athletes reduced their AFₘₐₓ, especially after the first five trials, and remained on a rather similar level for AFisomax. The maximum of AFisoₘₐₓ of all 30 trials amounted 67.67% ± 13.60% of MVIC (p < 0.001, n = 12), supporting the hypothesis of two types of isometric muscle action (holding vs. pushing). The findings provided the first data on the behavior of torque parameters after repeated isometric–eccentric actions and revealed further insights into neuromuscular control strategies. Additionally, they highlight the importance of investigating AF parameters in athletes based on the different behaviors compared to MVIC. This is assumed to be especially relevant regarding injury mechanisms.
Reply and Counter-Reply
(2023)