Refine
Year of publication
- 2021 (63) (remove)
Document Type
- Article (44)
- Working Paper (7)
- Doctoral Thesis (6)
- Postprint (2)
- Report (2)
- Master's Thesis (1)
- Sound (1)
Is part of the Bibliography
- yes (63) (remove)
Keywords
- Chlamydomonas (2)
- Forschungsdaten (2)
- Institutionalisierung (2)
- MiSpEx (2)
- SEPE (2)
- acclimation (2)
- behaviour (2)
- composition (2)
- ecophysiology (2)
- football (2)
Institute
- Extern (63) (remove)
The spread of antibiotic-resistant bacteria poses a globally increasing threat to public health care. The excessive use of antibiotics in animal husbandry can develop resistances in the stables. Transmission through direct contact with animals and contamination of food has already been proven. The excrements of the animals combined with a binding material enable a further potential path of spread into the environment, if they are used as organic manure in agricultural landscapes. As most of the airborne bacteria are attached to particulate matter, the focus of the work will be the atmospheric dispersal via the dust fraction.
Field measurements on arable lands in Brandenburg, Germany and wind erosion studies in a wind tunnel were conducted to investigate the risk of a potential atmospheric dust-associated spread of antibiotic-resistant bacteria from poultry manure fertilized agricultural soils. The focus was to (i) characterize the conditions for aerosolization and (ii) qualify and quantify dust emissions during agricultural operations and wind erosion.
PM10 (PM, particulate matter with an aerodynamic diameter smaller than 10 µm) emission factors and bacterial fluxes for poultry manure application and incorporation have not been previously reported before. The contribution to dust emissions depends on the water content of the manure, which is affected by the manure pretreatment (fresh, composted, stored, dried), as well as by the intensity of manure spreading from the manure spreader. During poultry manure application, PM10 emission ranged between 0.05 kg ha-1 and 8.37 kg ha-1. For comparison, the subsequent land preparation contributes to 0.35 – 1.15 kg ha-1 of PM10 emissions. Manure particles were still part of dust emissions but they were accounted to be less than 1% of total PM10 emissions due to the dilution of poultry manure in the soil after manure incorporation. Bacterial emissions of fecal origin were more relevant during manure application than during the subsequent manure incorporation, although PM10 emissions of manure incorporation were larger than PM10 emissions of manure application for the non-dried manure variants.
Wind erosion leads to preferred detachment of manure particles from sandy soils, when poultry manure has been recently incorporated. Sorting effects were determined between the low-density organic particles of manure origin and the soil particles of mineral origin close above the threshold of 7 m s-1. In dependence to the wind speed, potential erosion rates between 101 and 854 kg ha-1 were identified, if 6 t ha-1 of poultry manure were applied. Microbial investigation showed that manure bacteria got detached more easily from the soil surface during wind erosion, due to their attachment on manure particles.
Although antibiotic-resistant bacteria (ESBL-producing E. coli) were still found in the poultry barns, no further contamination could be detected with them in the manure, fertilized soils or in the dust generated by manure application, land preparation or wind erosion. Parallel studies of this project showed that storage of poultry manure for a few days (36 – 72 h) is sufficient to inactivate ESBL-producing E. coli. Further antibiotic-resistant bacteria, i.e. MRSA and VRE, were only found sporadically in the stables and not at all in the dust. Therefore, based on the results of this work, the risk of a potential infection by dust-associated antibiotic-resistant bacteria can be considered as low.
The increasing development of antibiotic resistance in bacteria has been a major problem for years, both in human and veterinary medicine. Prophylactic measures, such as the use of vaccines, are of great importance in reducing the use of antibiotics in livestock. These vaccines are mainly produced based on formaldehyde inactivation. However, the latter damages the recognition elements of the bacterial proteins and thus could reduce the immune response in the animal. An alternative inactivation method developed in this work is based on gentle photodynamic inactivation using carbon nanodots (CNDs) at excitation wavelengths λex > 290 nm. The photodynamic inactivation was characterized on the nonvirulent laboratory strain Escherichia coli K12 using synthesized CNDs. For a gentle inactivation, the CNDs must be absorbed into the cytoplasm of the E. coli cell. Thus, the inactivation through photoinduced formation of reactive oxygen species only takes place inside the bacterium, which means that the outer membrane is neither damaged nor altered. The loading of the CNDs into E. coli was examined using fluorescence microscopy. Complete loading of the bacterial cells could be achieved in less than 10 min. These studies revealed a reversible uptake process allowing the recovery and reuse of the CNDs after irradiation and before the administration of the vaccine. The success of photodynamic inactivation was verified by viability assays on agar. In a homemade flow photoreactor, the fastest successful irradiation of the bacteria could be carried out in 34 s. Therefore, the photodynamic inactivation based on CNDs is very effective. The membrane integrity of the bacteria after irradiation was verified by slide agglutination and atomic force microscopy. The method developed for the laboratory strain E. coli K12 could then be successfully applied to the important avian pathogens Bordetella avium and Ornithobacterium rhinotracheale to aid the development of novel vaccines.
To achieve a sustainable energy economy, it is necessary to turn back on the combustion of fossil fuels as a means of energy production and switch to renewable sources. However, their temporal availability does not match societal consumption needs, meaning that renewably generated energy must be stored in its main generation times and allocated during peak consumption periods. Electrochemical energy storage (EES) in general is well suited due to its infrastructural independence and scalability. The lithium ion battery (LIB) takes a special place, among EES systems due to its energy density and efficiency, but the scarcity and uneven geological occurrence of minerals and ores vital for many cell components, and hence the high and fluctuating costs will decelerate its further distribution.
The sodium ion battery (SIB) is a promising successor to LIB technology, as the fundamental setup and cell chemistry is similar in the two systems. Yet, the most widespread negative electrode material in LIBs, graphite, cannot be used in SIBs, as it cannot store sufficient amounts of sodium at reasonable potentials. Hence, another carbon allotrope, non-graphitizing or hard carbon (HC) is used in SIBs. This material consists of turbostratically disordered, curved graphene layers, forming regions of graphitic stacking and zones of deviating layers, so-called internal or closed pores.
The structural features of HC have a substantial impact of the charge-potential curve exhibited by the carbon when it is used as the negative electrode in an SIB. At defects and edges an adsorption-like mechanism of sodium storage is prevalent, causing a sloping voltage curve, ill-suited for the practical application in SIBs, whereas a constant voltage plateau of relatively high capacities is found immediately after the sloping region, which recent research attributed to the deposition of quasimetallic sodium into the closed pores of HC.
Literature on the general mechanism of sodium storage in HCs and especially the role of the closed pore is abundant, but the influence of the pore geometry and chemical nature of the HC on the low-potential sodium deposition is yet in an early stage. Therefore, the scope of this thesis is to investigate these relationships using suitable synthetic and characterization methods. Materials of precisely known morphology, porosity, and chemical structure are prepared in clear distinction to commonly obtained ones and their impact on the sodium storage characteristics is observed. Electrochemical impedance spectroscopy in combination with distribution of relaxation times analysis is further established as a technique to study the sodium storage process, in addition to classical direct current techniques, and an equivalent circuit model is proposed to qualitatively describe the HC sodiation mechanism, based on the recorded data. The obtained knowledge is used to develop a method for the preparation of closed porous and non-porous materials from open porous ones, proving not only the necessity of closed pores for efficient sodium storage, but also providing a method for effective pore closure and hence the increase of the sodium storage capacity and efficiency of carbon materials.
The insights obtained and methods developed within this work hence not only contribute to the better understanding of the sodium storage mechanism in carbon materials of SIBs, but can also serve as guidance for the design of efficient electrode materials.
Strong as a Hippo’s Heart: Biomechanical Hippo Signaling During Zebrafish Cardiac Development
(2021)
The heart is comprised of multiple tissues that contribute to its physiological functions. During development, the growth of myocardium and endocardium is coupled and morphogenetic processes within these separate tissue layers are integrated. Here, we discuss the roles of mechanosensitive Hippo signaling in growth and morphogenesis of the zebrafish heart. Hippo signaling is involved in defining numbers of cardiac progenitor cells derived from the secondary heart field, in restricting the growth of the epicardium, and in guiding trabeculation and outflow tract formation. Recent work also shows that myocardial chamber dimensions serve as a blueprint for Hippo signaling-dependent growth of the endocardium. Evidently, Hippo pathway components act at the crossroads of various signaling pathways involved in embryonic zebrafish heart development. Elucidating how biomechanical Hippo signaling guides heart morphogenesis has direct implications for our understanding of cardiac physiology and pathophysiology.
“Chunking” spoken language
(2021)
In this introductory paper to the special issue on “Weak cesuras in talk-in-interaction”, we aim to guide the reader into current work on the “chunking” of naturally occurring talk. It is conducted in the methodological frameworks of Conversation Analysis and Interactional Linguistics – two approaches that consider the interactional aspect of humans talking with each other to be a crucial starting point for its analysis. In doing so, we will (1) lay out the background of this special issue (what is problematic about “chunking” talk-in-interaction, the characteristics of the methodological approach chosen by the contributors, the cesura model), (2) highlight what can be gained from such a revised understanding of “chunking” in talk-in-interaction by referring to previous work with this model as well as the findings of the contributions to this special issue, and (3) indicate further directions such work could take starting from papers in this special issue. We hope to induce a fruitful exchange on the phenomena discussed, across methodological divides.
Objective
Insulin regulates mitochondrial function, thereby propagating an efficient metabolism. Conversely, diabetes and insulin resistance are linked to mitochondrial dysfunction with a decreased expression of the mitochondrial chaperone HSP60. The aim of this investigation was to determine the effect of a reduced HSP60 expression on the development of obesity and insulin resistance.
Methods
Control and heterozygous whole-body HSP60 knockout (Hsp60+/−) mice were fed a high-fat diet (HFD, 60% calories from fat) for 16 weeks and subjected to extensive metabolic phenotyping. To understand the effect of HSP60 on white adipose tissue, microarray analysis of gonadal WAT was performed, ex vivo experiments were performed, and a lentiviral knockdown of HSP60 in 3T3-L1 cells was conducted to gain detailed insights into the effect of reduced HSP60 levels on adipocyte homeostasis.
Results
Male Hsp60+/− mice exhibited lower body weight with lower fat mass. These mice exhibited improved insulin sensitivity compared to control, as assessed by Matsuda Index and HOMA-IR. Accordingly, insulin levels were significantly reduced in Hsp60+/− mice in a glucose tolerance test. However, Hsp60+/− mice exhibited an altered adipose tissue metabolism with elevated insulin-independent glucose uptake, adipocyte hyperplasia in the presence of mitochondrial dysfunction, altered autophagy, and local insulin resistance.
Conclusions
We discovered that the reduction of HSP60 in mice predominantly affects adipose tissue homeostasis, leading to beneficial alterations in body weight, body composition, and adipocyte morphology, albeit exhibiting local insulin resistance.
Development of chronic pain after a low back pain episode is associated with increased pain sensitivity, altered pain processing mechanisms and the influence of psychosocial factors. Although there is some evidence that multimodal therapy (such as behavioral or motor control therapy) may be an important therapeutic strategy, its long-term effect on pain reduction and psychosocial load is still unclear. Prospective longitudinal designs providing information about the extent of such possible long-term effects are missing. This study aims to investigate the long-term effects of a homebased uni- and multidisciplinary motor control exercise program on low back pain intensity, disability and psychosocial variables. 14 months after completion of a multicenter study comparing uni- and multidisciplinary exercise interventions, a sample of one study center (n = 154) was assessed once more. Participants filled in questionnaires regarding their low back pain symptoms (characteristic pain intensity and related disability), stress and vital exhaustion (short version of the Maastricht Vital Exhaustion Questionnaire), anxiety and depression experiences (the Hospital and Anxiety Depression Scale), and pain-related cognitions (the Fear Avoidance Beliefs Questionnaire). Repeated measures mixed ANCOVAs were calculated to determine the long-term effects of the interventions on characteristic pain intensity and disability as well as on the psychosocial variables. Fifty four percent of the sub-sample responded to the questionnaires (n = 84). Longitudinal analyses revealed a significant long-term effect of the exercise intervention on pain disability. The multidisciplinary group missed statistical significance yet showed a medium sized long-term effect. The groups did not differ in their changes of the psychosocial variables of interest. There was evidence of long-term effects of the interventions on pain-related disability, but there was no effect on the other variables of interest. This may be partially explained by participant's low comorbidities at baseline. Results are important regarding costless homebased alternatives for back pain patients and prevention tasks. Furthermore, this study closes the gap of missing long-term effect analysis in this field.
Emotions are a complex concept and they are present in our everyday life. Persons on the autism spectrum are said to have difficulties in social interactions, showing deficits in emotion recognition in comparison to neurotypically developed persons. But social-emotional skills are believed to be positively augmented by training. A new adaptive social cognition training tool “E.V.A.” is introduced which teaches emotion recognition from face, voice and body language. One cross-sectional and one longitudinal study with adult neurotypical and autistic participants were conducted. The aim of the cross-sectional study was to characterize the two groups and see if differences in their social-emotional skills exist. The longitudinal study, on the other hand, aimed for detecting possible training effects following training with the new training tool. In addition, in both studies usability assessments were conducted to investigate the perceived usability of the new tool for neurotypical as well as autistic participants. Differences were found between autistic and neurotypical participants in their social-emotional and emotion recognition abilities. Training effects for neurotypical participants in an emotion recognition task were found after two weeks of home training. Similar perceived usability was found for the neurotypical and autistic participants. The current findings suggest that persons with ASC do not have a general deficit in emotion recognition, but are in need for more time to correctly recognize emotions. In addition, findings suggest that training emotion recognition abilities is possible. Further studies are needed to verify if the training effects found for neurotypical participants also manifest in a larger ASC sample.
Computation of the instantaneous phase and amplitude via the Hilbert Transform is a powerful tool of data analysis. This approach finds many applications in various science and engineering branches but is not proper for causal estimation because it requires knowledge of the signal’s past and future. However, several problems require real-time estimation of phase and amplitude; an illustrative example is phase-locked or amplitude-dependent stimulation in neuroscience. In this paper, we discuss and compare three causal algorithms that do not rely on the Hilbert Transform but exploit well-known physical phenomena, the synchronization and the resonance. After testing the algorithms on a synthetic data set, we illustrate their performance computing phase and amplitude for the accelerometer tremor measurements and a Parkinsonian patient’s beta-band brain activity.
We study the probability density function (PDF) of the first-reaction times between a diffusive ligand and a membrane-bound, immobile imperfect target region in a restricted 'onion-shell' geometry bounded by two nested membranes of arbitrary shapes. For such a setting, encountered in diverse molecular signal transduction pathways or in the narrow escape problem with additional steric constraints, we derive an exact spectral form of the PDF, as well as present its approximate form calculated by help of the so-called self-consistent approximation. For a particular case when the nested domains are concentric spheres, we get a fully explicit form of the approximated PDF, assess the accuracy of this approximation, and discuss various facets of the obtained distributions. Our results can be straightforwardly applied to describe the PDF of the terminal reaction event in multi-stage signal transduction processes.
Quantitative geomorphic research depends on accurate topographic data often collected via remote sensing. Lidar, and photogrammetric methods like structure-from-motion, provide the highest quality data for generating digital elevation models (DEMs). Unfortunately, these data are restricted to relatively small areas, and may be expensive or time-consuming to collect. Global and near-global DEMs with 1 arcsec (∼30 m) ground sampling from spaceborne radar and optical sensors offer an alternative gridded, continuous surface at the cost of resolution and accuracy. Accuracy is typically defined with respect to external datasets, often, but not always, in the form of point or profile measurements from sources like differential Global Navigation Satellite System (GNSS), spaceborne lidar (e.g., ICESat), and other geodetic measurements. Vertical point or profile accuracy metrics can miss the pixel-to-pixel variability (sometimes called DEM noise) that is unrelated to true topographic signal, but rather sensor-, orbital-, and/or processing-related artifacts. This is most concerning in selecting a DEM for geomorphic analysis, as this variability can affect derivatives of elevation (e.g., slope and curvature) and impact flow routing. We use (near) global DEMs at 1 arcsec resolution (SRTM, ASTER, ALOS, TanDEM-X, and the recently released Copernicus) and develop new internal accuracy metrics to assess inter-pixel variability without reference data. Our study area is in the arid, steep Central Andes, and is nearly vegetation-free, creating ideal conditions for remote sensing of the bare-earth surface. We use a novel hillshade-filtering approach to detrend long-wavelength topographic signals and accentuate short-wavelength variability. Fourier transformations of the spatial signal to the frequency domain allows us to quantify: 1) artifacts in the un-projected 1 arcsec DEMs at wavelengths greater than the Nyquist (twice the nominal resolution, so > 2 arcsec); and 2) the relative variance of adjacent pixels in DEMs resampled to 30-m resolution (UTM projected). We translate results into their impact on hillslope and channel slope calculations, and we highlight the quality of the five DEMs. We find that the Copernicus DEM, which is based on a carefully edited commercial version of the TanDEM-X, provides the highest quality landscape representation, and should become the preferred DEM for topographic analysis in areas without sufficient coverage of higher-quality local DEMs.
Background:
Research into the application of virtual reality technology in the health care sector has rapidly increased, resulting in a large body of research that is difficult to keep up with.
Objective:
We will provide an overview of the annual publication numbers in this field and the most productive and influential countries, journals, and authors, as well as the most used, most co-occurring, and most recent keywords.
Methods:
Based on a data set of 356 publications and 20,363 citations derived from Web of Science, we conducted a bibliometric analysis using BibExcel, HistCite, and VOSviewer.
Results:
The strongest growth in publications occurred in 2020, accounting for 29.49% of all publications so far. The most productive countries are the United States, the United Kingdom, and Spain; the most influential countries are the United States, Canada, and the United Kingdom. The most productive journals are the Journal of Medical Internet Research (JMIR), JMIR Serious Games, and the Games for Health Journal; the most influential journals are Patient Education and Counselling, Medical Education, and Quality of Life Research. The most productive authors are Riva, del Piccolo, and Schwebel; the most influential authors are Finset, del Piccolo, and Eide. The most frequently occurring keywords other than “virtual” and “reality” are “training,” “trial,” and “patients.” The most relevant research themes are communication, education, and novel treatments; the most recent research trends are fitness and exergames.
Conclusions:
The analysis shows that the field has left its infant state and its specialization is advancing, with a clear focus on patient usability.
Research on problem solving offers insights into how humans process task-related information and which strategies they use (Newell and Simon, 1972; Öllinger et al., 2014). Problem solving can be defined as the search for possible changes in one's mind (Kahneman, 2003). In a recent study, Adams et al. (2021) assessed whether the predominant problem solving strategy when making changes involves adding or subtracting elements. In order to do this, they used several examples of simple problems, such as editing text or making visual patterns symmetrical, either in naturalistic settings or on-line. The essence of the authors' findings is a strong preference to add rather than subtract elements across a diverse range of problems, including the stabilizing of artifacts, creating symmetrical patterns, or editing texts. More specifically, they succeeded in demonstrating that “participants were less likely to identify advantageous subtractive changes when the task did not (vs. did) cue them to consider subtraction, when they had only one opportunity (vs. several) to recognize the shortcomings of an additive search strategy or when they were under a higher (vs. lower) cognitive load” (Adams et al., 2021, p. 258).
Addition and subtraction are generally defined as de-contextualized mathematical operations using abstract symbols (Russell, 1903/1938). Nevertheless, understanding of both symbols and operations is informed by everyday activities, such as making or breaking objects (Lakoff and Núñez, 2000; Fischer and Shaki, 2018). The universal attribution of “addition bias” or “subtraction neglect” to problem solving activities is perhaps a convenient shorthand but it overlooks influential framing effects beyond those already acknowledged in the report and the accompanying commentary (Meyvis and Yoon, 2021).
Most importantly, while Adams et al.'s study addresses an important issue, their very method of verbally instructing participants, together with lack of control over several known biases, might render their findings less than conclusive. Below, we discuss our concerns that emerged from the identified biases, namely those regarding the instructions and the experimental materials. Moreover, we refer to research from mathematical cognition that provides new insights into Adams et al.'s findings.
The large literature that aims to find evidence of climate migration delivers mixed findings. This meta-regression analysis i) summarizes direct links between adverse climatic events and migration, ii) maps patterns of climate migration, and iii) explains the variation in outcomes. Using a set of limited dependent variable models, we meta-analyze thus-far the most comprehensive sample of 3,625 estimates from 116 original studies and produce novel insights on climate migration. We find that extremely high temperatures and drying conditions increase migration. We do not find a significant effect of sudden-onset events. Climate migration is most likely to emerge due to contemporaneous events, to originate in rural areas and to take place in middle-income countries, internally, to cities. The likelihood to become trapped in affected areas is higher for women and in low-income countries, particularly in Africa. We uniquely quantify how pitfalls typical for the broader empirical climate impact literature affect climate migration findings. We also find evidence of different publication biases.
While a growing body of literature finds positive impacts of Start-Up Subsidies (SUS) on labor market outcomes of participants, little is known about how the design of these programs shapes their effectiveness and hence how to improve policy. As experimental variation in program design is unavailable, we exploit the 2011 reform of the current German SUS program for the unemployed which strengthened case-workers’ discretionary power, increased entry requirements and reduced monetary support. We estimate the impact of the reform on the program’s effectiveness using samples of participants and non-participants from before and after the reform. To control for time-constant unobserved heterogeneity as well as differential selection patterns based on observable characteristics over time, we combine Difference-in-Differences with inverse probability weighting using covariate balancing propensity scores. Holding participants’ observed characteristics as well as macroeconomic conditions constant, the results suggest that the reform was successful in raising employment effects on average. As these findings may be contaminated by changes in selection patterns based on unobserved characteristics, we assess our results using simulation-based sensitivity analyses and find that our estimates are highly robust to changes in unobserved characteristics. Hence, the reform most likely had a positive impact on the effectiveness of the program, suggesting that increasing entry requirements and reducing support in-creased the program’s impacts while reducing the cost per participant.
Im Projekt „Forschungsdatenmanagement in Brandenburg (FDM-BB)“ wurden grundlegende Erkenntnisse bezüglich der Anforderungen und des Status Quo im Bereich Forschungsdatenmanagement (FDM) an den acht brandenburgischen Hochschulen generiert mit dem Ziel, daraus konkrete Handlungs- und Implementierungsempfehlungen für Brandenburg abzuleiten.
Mit Hilfe von spezifischen Umfragen (FactSheets, FDM-Palette) an den Hochschulen und Interviews mit den anderen geförderten FDM-Bundeslandinitiativen konnte eine Priorisierung der nächsten Schritte auf dem Weg hin zu einem institutionellen und nachhaltigen Forschungsdatenmanagement identifiziert werden, die jeweils in den Verantwortungsbereichen der folgenden drei Akteursgruppen liegen: Ministerium für Wirtschaft, Forschung und Kultur in Brandenburg (MWFK), die einzelne Hochschule und für gemeinsame Maßnahmen die kooperative Umsetzung durch (fast) alle Hochschulen.
Zusätzlich wurden Implementierungsempfehlungen erarbeitet, wie der lokale Kompetenzaufbau an den einzelnen Hochschulen in Brandenburg, die kooperative Bereitstellung landesweit relevanter IT-Dienste und Dienstleistungen sowie die Koordinierung FDM-BB.
Ziel ist auch, für Brandenburg gemeinsam eine Forschungsdatenstrategie zu formulieren, die alle brandenburgischen Einrichtungen einbezieht und mit Hilfe von kooperativ verteilten Verantwortlichkeiten dem (noch) sehr dynamischen Thema Forschungsdatenmanagement gerecht werden kann.
Infants show impressive speech decoding abilities and detect acoustic regularities that highlight the syntactic relations of a language, often coded via non-adjacent dependencies (NADs, e.g., is singing). It has been claimed that infants learn NADs implicitly and associatively through passive listening and that there is a shift from effortless associative learning to a more controlled learning of NADs after the age of 2 years, potentially driven by the maturation of the prefrontal cortex. To investigate if older children are able to learn NADs, Lammertink et al. (2019) recently developed a word-monitoring serial reaction time (SRT) task and could show that 6–11-year-old children learned the NADs, as their reaction times (RTs) increased then they were presented with violated NADs. In the current study we adapted their experimental paradigm and tested NAD learning in a younger group of 52 children between the age of 4–8 years in a remote, web-based, game-like setting (whack-a-mole). Children were exposed to Italian phrases containing NADs and had to monitor the occurrence of a target syllable, which was the second element of the NAD. After exposure, children did a “Stem Completion” task in which they were presented with the first element of the NAD and had to choose the second element of the NAD to complete the stimuli. Our findings show that, despite large variability in the data, children aged 4–8 years are sensitive to NADs; they show the expected differences in r RTs in the SRT task and could transfer the NAD-rule in the Stem Completion task. We discuss these results with respect to the development of NAD dependency learning in childhood and the practical impact and limitations of collecting these data in a web-based setting.
Comprior
(2021)
Background
Reproducible benchmarking is important for assessing the effectiveness of novel feature selection approaches applied on gene expression data, especially for prior knowledge approaches that incorporate biological information from online knowledge bases. However, no full-fledged benchmarking system exists that is extensible, provides built-in feature selection approaches, and a comprehensive result assessment encompassing classification performance, robustness, and biological relevance. Moreover, the particular needs of prior knowledge feature selection approaches, i.e. uniform access to knowledge bases, are not addressed. As a consequence, prior knowledge approaches are not evaluated amongst each other, leaving open questions regarding their effectiveness.
Results
We present the Comprior benchmark tool, which facilitates the rapid development and effortless benchmarking of feature selection approaches, with a special focus on prior knowledge approaches. Comprior is extensible by custom approaches, offers built-in standard feature selection approaches, enables uniform access to multiple knowledge bases, and provides a customizable evaluation infrastructure to compare multiple feature selection approaches regarding their classification performance, robustness, runtime, and biological relevance.
Conclusion
Comprior allows reproducible benchmarking especially of prior knowledge approaches, which facilitates their applicability and for the first time enables a comprehensive assessment of their effectiveness
Transitory starch plays a central role in the life cycle of plants. Many aspects of this important metabolism remain unknown; however, starch granules provide insight into this persistent metabolic process. Therefore, monitoring alterations in starch granules with high temporal resolution provides one significant avenue to improve understanding. Here, a previously established method that combines LCSM and safranin-O staining for in vivo imaging of transitory starch granules in leaves of Arabidopsis thaliana was employed to demonstrate, for the first time, the alterations in starch granule size and morphology that occur both throughout the day and during leaf aging. Several starch-related mutants were included, which revealed differences among the generated granules. In ptst2 and sex1-8, the starch granules in old leaves were much larger than those in young leaves; however, the typical flattened discoid morphology was maintained. In ss4 and dpe2/phs1/ss4, the morphology of starch granules in young leaves was altered, with a more rounded shape observed. With leaf development, the starch granules became spherical exclusively in dpe2/phs1/ss4. Thus, the presented data provide new insights to contribute to the understanding of starch granule morphogenesis.