@article{KleinpeterHeydenreichShainyan2021,
  author    = {Kleinpeter, Erich and Heydenreich, Matthias and Shainyan, Bagrat A.},
  title     = {At the experimental limit of the NMR conformational analysis},
  series = {Organic letters},
  volume    = {23},
  journal   = {Organic letters},
  number    = {2},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1523-7060},
  doi       = {10.1021/acs.orglett.0c03878},
  pages     = {405 -- 409},
  year      = {2021},
  abstract  = {The low temperature (95 K) NMR study of 1-Ph-1-t-Bu-silacyclohexane (1) showed the conformational equilibrium to be extremely one-sided toward thePh(ax),t-Bueq conformer. The barrier to interconversion has been measured (4.2-4.6 kcal/mol) and the conformational equilibrium [Delta nu = 1990.64 ppm (Si-29), 618.9 ppm (C-13), 1-Ph-ax:1-Pheq = (95.6-96.6\%):(3.4-4.4\%), K = 25 +/- 3, Delta G degrees = -RT ln K = 0.58-0.63 kcal/mol] analyzed. The assignment and quantification of the NMR signals is supported by MP2 and DFT calculations.},
  language  = {en}
}
@article{KahlKappelJoshietal.2021,
  author    = {Kahl, Sandra and Kappel, Christian and Joshi, Jasmin Radha and Lenhard, Michael},
  title     = {Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions},
  series = {Ecology and Evolution},
  volume    = {11},
  journal   = {Ecology and Evolution},
  number    = {20},
  publisher = {John Wiley \& Sons, Inc.},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.8103},
  pages     = {13986 -- 14002},
  year      = {2021},
  abstract  = {To predict how widely distributed species will perform under future climate change, it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate change scenario for central Europe and revealed the population structure through whole-genome sequencing. Plants were grown under two temperatures (18°C and 21°C) and three precipitation regimes (65, 75, and 90 mm) to measure their response in biomass and fecundity-related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole-genome approach. We found three major genetic clusters in S. vulgaris from Europe: one cluster comprising Southern European populations, one cluster of Western European populations, and another cluster containing central European populations. Population genetic diversity decreased with increasing latitude, and a Mantel test revealed significant correlations between FST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species S. vulgaris and its intraspecific genetic lineages.},
  language  = {en}
}
@misc{KonakWegnerArnrich2021,
  author    = {Konak, Orhan and Wegner, Pit and Arnrich, Bert},
  title     = {IMU-Based Movement Trajectory Heatmaps for Human Activity Recognition},
  series = {Postprints der Universit{\"a}t Potsdam : Reihe der Digital Engineering Fakult{\"a}t},
  journal   = {Postprints der Universit{\"a}t Potsdam : Reihe der Digital Engineering Fakult{\"a}t},
  number    = {4},
  doi       = {10.25932/publishup-48779},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-487799},
  pages     = {17},
  year      = {2021},
  abstract  = {Recent trends in ubiquitous computing have led to a proliferation of studies that focus on human activity recognition (HAR) utilizing inertial sensor data that consist of acceleration, orientation and angular velocity. However, the performances of such approaches are limited by the amount of annotated training data, especially in fields where annotating data is highly time-consuming and requires specialized professionals, such as in healthcare. In image classification, this limitation has been mitigated by powerful oversampling techniques such as data augmentation. Using this technique, this work evaluates to what extent transforming inertial sensor data into movement trajectories and into 2D heatmap images can be advantageous for HAR when data are scarce. A convolutional long short-term memory (ConvLSTM) network that incorporates spatiotemporal correlations was used to classify the heatmap images. Evaluation was carried out on Deep Inertial Poser (DIP), a known dataset composed of inertial sensor data. The results obtained suggest that for datasets with large numbers of subjects, using state-of-the-art methods remains the best alternative. However, a performance advantage was achieved for small datasets, which is usually the case in healthcare. Moreover, movement trajectories provide a visual representation of human activities, which can help researchers to better interpret and analyze motion patterns.},
  language  = {en}
}
@phdthesis{Wochatz2021,
  author    = {Wochatz, Monique},
  title     = {Influence of different loading conditions on scapular movement and scapular muscle activation patterns},
  school      = {Universit{\"a}t Potsdam},
  pages     = {iv, 129, xiv},
  year      = {2021},
  abstract  = {The scapula plays a significant role in efficient shoulder movement. Thus, alterations from typical scapular motion during upper limb movements are thought to be associated with shoulder pathologies. However, a clear understanding of the relationship is not yet obtained.. Scapular alterations may only represent physiological variability as their occurrence can appear equally as frequent in individuals with and without shoulder disorders. Evaluation of scapular motion during increased load might be a beneficial approach to detect clinically relevant alterations. However, functional motion adaptations in response to maximum effort upper extremity loading has not been established yet. Therefore, the overall purpose of this research project was to give further insight in physiological adaptations of scapular kinematics and their underlying scapular muscle activity in response to high demanding shoulder movements in healthy asymptomatic individuals. Prior to the investigation of the effect of various load situation, the reproducibility of scapular kinematics and scapular muscle activity were evaluated under maximum effort arm movements. Healthy asymptomatic adults performed unloaded and maximal loaded concentric and eccentric isokinetic shoulder flexion and extension movements in the scapular plane while scapular kinematics and scapular muscle activity were simultaneously assessed. A 3D motion capture system (infra-red cameras \& reflective markers) was utilized to track scapular and humerus motion in relation to the thorax. 3D scapular position angles were given for arm raising and lowering between humerus positions of 20° and 120° flexion. To further characterize the scapular pattern, the scapular motion extent and scapulohumeral rhythm (ratio of scapular and humerus motion extent) were determined. Muscle activity of the upper and lower trapezius and the serratus anterior were assessed with surface electromyography. Amplitudes were calculated for the whole ROM and four equidistant movement phases. Reliability was characterized by overall moderate to good reproducibility across the load conditions. Irrespective of applied load, scapular kinematics followed a motion pattern of continuous upward rotation, posterior tilt and external rotation during arm elevation and a continuous downward rotation, anterior tilt and internal rotation during arm lowering. However, kinematics were altered between maximal loaded and unloaded conditions showing increased upward rotation, reduced posterior tilt and external rotation. Further, the scapulohumeral rhythm was decreased and scapular motion extent increased under maximal loaded movements. Muscle activity during maximum effort were of greater magnitude and differed in their pattern in comparison to the continuous increase and decrease of activity during unloaded shoulder flexion and extension. Relationships between scapular kinematics and their underlying scapular muscle activity could only be identified for a few isolated combinations, whereas the majority showed no associations. Scapular kinematics and scapular muscle activity pattern alter according to the applied load. Alterations between the load conditions comply in magnitude and partially in direction with differences seen between symptomatic and asymptomatic individuals. Even though long-term effects of identified adaptations in response to maximum load are so far unclear, deviations from typical scapular motion or muscle activation should not per se be seen as indicators of shoulder impairment. However, evaluation of alterations in scapular motion and activation in response to maximum effort may have the potential to identify individuals that are unable to cope with increased upper limb demands. Findings further challenge the understanding of scapular motion and stabilization by the trapezius and serratus anterior muscles, as clear relationships between the underlying scapular muscle activity and scapular kinematics were neither observed during unloaded nor maximal loaded shoulder movements.},
  language  = {en}
}
@article{TrautmannZhouBrahmsetal.2021,
  author    = {Trautmann, Justin and Zhou, Lin and Brahms, Clemens Markus and Tunca, Can and Ersoy, Cem and Granacher, Urs and Arnrich, Bert},
  title     = {TRIPOD},
  series = {Data : open access ʻData in scienceʼ journal},
  volume    = {6},
  journal   = {Data : open access ʻData in scienceʼ journal},
  number    = {9},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2306-5729},
  doi       = {10.3390/data6090095},
  pages     = {19},
  year      = {2021},
  abstract  = {Inertial measurement units (IMUs) enable easy to operate and low-cost data recording for gait analysis. When combined with treadmill walking, a large number of steps can be collected in a controlled environment without the need of a dedicated gait analysis laboratory. In order to evaluate existing and novel IMU-based gait analysis algorithms for treadmill walking, a reference dataset that includes IMU data as well as reliable ground truth measurements for multiple participants and walking speeds is needed. This article provides a reference dataset consisting of 15 healthy young adults who walked on a treadmill at three different speeds. Data were acquired using seven IMUs placed on the lower body, two different reference systems (Zebris FDMT-HQ and OptoGait), and two RGB cameras. Additionally, in order to validate an existing IMU-based gait analysis algorithm using the dataset, an adaptable modular data analysis pipeline was built. Our results show agreement between the pressure-sensitive Zebris and the photoelectric OptoGait system (r = 0.99), demonstrating the quality of our reference data. As a use case, the performance of an algorithm originally designed for overground walking was tested on treadmill data using the data pipeline. The accuracy of stride length and stride time estimations was comparable to that reported in other studies with overground data, indicating that the algorithm is equally applicable to treadmill data. The Python source code of the data pipeline is publicly available, and the dataset will be provided by the authors upon request, enabling future evaluations of IMU gait analysis algorithms without the need of recording new data.},
  language  = {en}
}
@misc{TrautmannZhouBrahmsetal.2021,
  author    = {Trautmann, Justin and Zhou, Lin and Brahms, Clemens Markus and Tunca, Can and Ersoy, Cem and Granacher, Urs and Arnrich, Bert},
  title     = {TRIPOD - A Treadmill Walking Dataset with IMU, Pressure-distribution and Photoelectric Data for Gait Analysis},
  series = {Postprints der Universit{\"a}t Potsdam : Reihe der Digital Engineering Fakult{\"a}t},
  journal   = {Postprints der Universit{\"a}t Potsdam : Reihe der Digital Engineering Fakult{\"a}t},
  number    = {6},
  doi       = {10.25932/publishup-52202},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-522027},
  pages     = {21},
  year      = {2021},
  abstract  = {Inertial measurement units (IMUs) enable easy to operate and low-cost data recording for gait analysis. When combined with treadmill walking, a large number of steps can be collected in a controlled environment without the need of a dedicated gait analysis laboratory. In order to evaluate existing and novel IMU-based gait analysis algorithms for treadmill walking, a reference dataset that includes IMU data as well as reliable ground truth measurements for multiple participants and walking speeds is needed. This article provides a reference dataset consisting of 15 healthy young adults who walked on a treadmill at three different speeds. Data were acquired using seven IMUs placed on the lower body, two different reference systems (Zebris FDMT-HQ and OptoGait), and two RGB cameras. Additionally, in order to validate an existing IMU-based gait analysis algorithm using the dataset, an adaptable modular data analysis pipeline was built. Our results show agreement between the pressure-sensitive Zebris and the photoelectric OptoGait system (r = 0.99), demonstrating the quality of our reference data. As a use case, the performance of an algorithm originally designed for overground walking was tested on treadmill data using the data pipeline. The accuracy of stride length and stride time estimations was comparable to that reported in other studies with overground data, indicating that the algorithm is equally applicable to treadmill data. The Python source code of the data pipeline is publicly available, and the dataset will be provided by the authors upon request, enabling future evaluations of IMU gait analysis algorithms without the need of recording new data.},
  language  = {en}
}
@phdthesis{MorenoCurtidor2021,
  author    = {Moreno Curtidor, Catalina},
  title     = {Elucidating the molecular basis of enhanced growth in the Arabidopsis thaliana accession Bur-0},
  doi       = {10.25932/publishup-52681},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-526814},
  school      = {Universit{\"a}t Potsdam},
  pages     = {136},
  year      = {2021},
  abstract  = {The life cycle of flowering plants is a dynamic process that involves successful passing through several developmental phases and tremendous progress has been made to reveal cellular and molecular regulatory mechanisms underlying these phases, morphogenesis, and growth. Although several key regulators of plant growth or developmental phase transitions have been identified in Arabidopsis, little is known about factors that become active during embryogenesis, seed development and also during further postembryonic growth. Much less is known about accession-specific factors that determine plant architecture and organ size. Bur-0 has been reported as a natural Arabidopsis thaliana accession with exceptionally big seeds and a large rosette; its phenotype makes it an interesting candidate to study growth and developmental aspects in plants, however, the molecular basis underlying this big phenotype remains to be elucidated. Thus, the general aim of this PhD project was to investigate and unravel the molecular mechanisms underlying the big phenotype in Bur-0. Several natural Arabidopsis accessions and late flowering mutant lines were analysed in this study, including Bur-0. Phenotypes were characterized by determining rosette size, seed size, flowering time, SAM size and growth in different photoperiods, during embryonic and postembryonic development. Our results demonstrate that Bur-0 stands out as an interesting accession with simultaneously larger rosettes, larger SAM, later flowering phenotype and larger seeds, but also larger embryos. Interestingly, inter-accession crosses (F1) resulted in bigger seeds than the parental self-crossed accessions, particularly when Bur-0 was used as the female parental genotype, suggesting parental effects on seed size that might be maternally controlled. Furthermore, developmental stage-based comparisons revealed that the large embryo size of Bur-0 is achieved during late embryogenesis and the large rosette size is achieved during late postembryonic growth. Interestingly, developmental phase progression analyses revealed that from germination onwards, the length of developmental phases during postembryonic growth is delayed in Bur-0, suggesting that in general, the mechanisms that regulate developmental phase progression are shared across developmental phases. On the other hand, a detailed physiological characterization in different tissues at different developmental stages revealed accession-specific physiological and metabolic traits that underlie accession-specific phenotypes and in particular, more carbon resources during embryonic and postembryonic development were found in Bur-0, suggesting an important role of carbohydrates in determination of the bigger Bur-0 phenotype. Additionally, differences in the cellular organization, nuclei DNA content, as well as ploidy level were analyzed in different tissues/cell types and we found that the large organ size in Bur-0 can be mainly attributed to its larger cells and also to higher cell proliferation in the SAM, but not to a different ploidy level. Furthermore, RNA-seq analysis of embryos at torpedo and mature stage, as well as SAMs at vegetative and floral transition stage from Bur-0 and Col-0 was conducted to identify accession-specific genetic determinants of plant phenotypes, shared across tissues and developmental stages during embryonic and postembryonic growth. Potential candidate genes were identified and further validation of transcriptome data by expression analyses of candidate genes as well as known key regulators of organ size and growth during embryonic and postembryonic development confirmed that the high confidence transcriptome datasets generated in this study are reliable for elucidation of molecular mechanisms regulating plant growth and accession-specific phenotypes in Arabidopsis. Taken together, this PhD project contributes to the plant development research field providing a detailed analysis of mechanisms underlying plant growth and development at different levels of biological organization, focusing on Arabidopsis accessions with remarkable phenotypical differences. For this, the natural accession Bur-0 was an ideal outlier candidate and different mechanisms at organ and tissue level, cell level, metabolism, transcript and gene expression level were identified, providing a better understanding of different factors involved in plant growth regulation and mechanisms underlying different growth patterns in nature.},
  language  = {en}
}
@phdthesis{Kaptur2021,
  author    = {Kaptur, Joanna Alexandra},
  title     = {The LEUNIG regulatory complex},
  school      = {Universit{\"a}t Potsdam},
  year      = {2021},
  abstract  = {Patterning along the apical-basal (A-B) axis is a crucial step during the early stages of plant embryogenesis and leads to the establishment of two poles of which each will develop their own stem cell niches. The activity of these meristems is responsible for post-embryonic growth, with the shoot apical meristem (SAM) generating the above-ground organs and the root apical meristem (RAM) producing the subterranean structures of the plant. While several transcriptional regulators governing A-B patterning have been identified, precisely how their regulatory function is orchestrated remains elusive. This study focuses on transcriptional co-regulators LEUNIG (LUG) and closely related LEUNIG_HOMOLOG (LUH) and their role in the formation of A-B patterning during embryogenesis as well as their post-embryonic maintenance. A link between the LUG regulatory complex and SAM formation and maintenance comes from the observation that lug mutants heterozygous for the luh allele (lug luh+/-) often have enlarged SAMs resulting from misregulated cell divisions. A more severe phenotype is observed in lug luh double mutants which are embryonically lethal. In this study, a detailed characterisation of lug luh embryo phenotype reveals that these mutants display aberrant cell divisions along the A-B axis, which correlates with defects in auxin distribution, complete loss of apical identity, and altered expression of transcription factors determining basal fate. Like other co-regulators, LUG and LUH lack intrinsic DNA-binding domains and instead must interact with DNA-binding cofactors to ensure recruitment to regulatory elements of target genes. This either involves direct contact between the co-regulators and transcription factors (TFs) or the formation of higher-order complexes with adaptor proteins such as SEUSS (SEU) or related SEUSS-LIKEs (SLKs), which facilitate binding to specific TFs. Results presented in this study provide insight into the molecular framework for the LUG regulatory complex activity during embryogenesis. Both yeast and in planta assays showed that LUG/LUH and SEU/SLKs physically associate with a variety of WUSCHEL-RELATED HOMEOBOX (WOX) TFs including members of the WOX2-module. Furthermore, genetic interactions between members of the WOX2-module and the LUG regulatory complex, support their mutual action during embryogenesis. Based on the reduced activity of HOMEODOMAIN LEUCINE-ZIPPER CLASS III (HD-ZIPIII) promoters in lug luh embryos, a model is proposed in which the LUG regulatory complex functions together with WOX2-module to promote apical identity and subsequent SAM initiation through regulation of the HD-ZIPIIIs. The activity of the LUG complex in promoting basal embryo identity through positive regulation of microRNA165/166 suggests that this complex also has functions that are independent of the WOX2-module. Preliminary work reported in this study further uncovered the role of the LUG regulatory complex in post-embryonic development. While the fasciated inflorescence meristems of lug luh+/- plants displayed defects in auxin transport and altered activity of stem cell markers, embryonically rescued lug luh mutants formed flat and differentiated SAMs. In addition, rescued lug luh mutants exhibited severely disorganised RAM and defects in quiescent center (QC) specification, supporting the involvement of the LUG complex in post-embryonic RAM maintenance.},
  language  = {en}
}
@article{ChromikPirlBeilharzetal.2021,
  author    = {Chromik, Jonas and Pirl, Lukas and Beilharz, Jossekin Jakob and Arnrich, Bert and Polze, Andreas},
  title     = {Certainty in QRS detection with artificial neural networks},
  series = {Biomedical signal processing and control},
  volume    = {68},
  journal   = {Biomedical signal processing and control},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {1746-8094},
  doi       = {10.1016/j.bspc.2021.102628},
  pages     = {12},
  year      = {2021},
  abstract  = {Detection of the QRS complex is a long-standing topic in the context of electrocardiography and many algorithms build upon the knowledge of the QRS positions. Although the first solutions to this problem were proposed in the 1970s and 1980s, there is still potential for improvements. Advancements in neural network technology made in recent years also lead to the emergence of enhanced QRS detectors based on artificial neural networks. In this work, we propose a method for assessing the certainty that is in each of the detected QRS complexes, i.e. how confident the QRS detector is that there is, in fact, a QRS complex in the position where it was detected. We further show how this metric can be utilised to distinguish correctly detected QRS complexes from false detections.},
  language  = {en}
}
@article{OberkoflerPratxBaeurle2021,
  author    = {Oberkofler, Vicky and Pratx, Loris and B{\"a}urle, Isabel},
  title     = {Epigenetic regulation of abiotic stress memory},
  series = {Current opinion in plant biology},
  volume    = {61},
  journal   = {Current opinion in plant biology},
  publisher = {Elsevier},
  address   = {London},
  issn      = {1369-5266},
  doi       = {10.1016/j.pbi.2021.102007},
  pages     = {7},
  year      = {2021},
  abstract  = {As sessile organisms, plants have evolved sophisticated ways to constantly gauge and adapt to changing environmental conditions including extremes that may be harmful to their growth and development and are thus perceived as stress. In nature, stressful events are often chronic or recurring and thus an initial stress may prime a plant to respond more efficiently to a subsequent stress event. An epigenetic basis of such stress memory was long postulated and in recent years it has been shown that this is indeed the case. High temperature stress has proven an excellent system to unpick the molecular basis of somatic stress memory, which includes histone modifications and nucleosome occupancy. This review discusses recent findings and pinpoints open questions in the field.},
  language  = {en}
}