Quality control and correction method for air temperature data from a citizen science weather station network in Leuven, Belgium

The growing trend toward urbanisation and the increasingly frequent occurrence of extreme weather events emphasise the need for further monitoring and understanding of weather in cities. In order to gain information on these intra-urban weather patterns, dense high-quality atmospheric measurements are needed. Crowdsourced weather stations (CWSs) could be a promising solution to realise such monitoring networks in a cost-efficient way. However, due to their nontraditional measuring equipment and installation settings, the quality of datasets from these networks remains an issue. This paper presents crowdsourced data from the “Leuven.cool” network, a citizen science network of around 100 low-cost weather stations (Fine Offset WH2600) distributed across Leuven, Belgium (50∘52′ N, 4∘42′ E). The dataset is accompanied by a newly developed station-specific temperature quality control (QC) and correction procedure. The procedure consists of three levels that remove implausible measurements while also correcting for inter-station (between-station) and intra-station (station-specific) temperature biases by means of a random forest approach. The QC method is evaluated using data from four WH2600 stations installed next to official weather stations belonging to the Royal Meteorological Institute of Belgium (RMI). A positive temperature bias with a strong relation to the incoming solar radiation was found between the CWS data and the official data. The QC method is able to reduce this bias from 0.15 ± 0.56 to 0.00 ± 0.28 K. After evaluation, the QC method is applied to the data of the Leuven.cool network, making it a very suitable dataset to study local weather phenomena, such as the urban heat island (UHI) effect, in detail. (https://doi.org/10.48804/SSRN3F, Beele et al., 2022).</p

The domestication of the probiotic bacterium Lactobacillus acidophilus

Lactobacillus acidophilus is a Gram-positive lactic acid bacterium that has had widespread historical use in the dairy industry and more recently as a probiotic. Although L. acidophilus has been designated as safe for human consumption, increasing commercial regulation and clinical demands for probiotic validation has resulted in a need to understand its genetic diversity. By drawing on large, well-characterised collections of lactic acid bacteria, we examined L. acidophilus isolates spanning 92 years and including multiple strains in current commercial use. Analysis of the whole genome sequence data set (34 isolate genomes) demonstrated L. acidophilus was a low diversity, monophyletic species with commercial isolates essentially identical at the sequence level. Our results indicate that commercial use has domesticated L. acidophilus with genetically stable, invariant strains being consumed globally by the human population

Modulation of gluteus medius activity reflects the potential of the muscle to meet the mechanical demands during perturbed walking

Mediolateral stability during walking can be controlled by adjustment of foot placement. Reactive activity of gluteus medius (GM) is modulated during the gait cycle. However, the mechanisms behind the modulation are yet unclear. We measured reactive GM activity and kinematics in response to a mediolateral platform translation during different phases of the gait cycle. Forward simulations of perturbed walking were used to evaluate the isolated effect of the perturbation and the GM response on gait stability. We showed that the potential of GM to adjust lateral foot placement and prevent collisions during swing varies during the gait cycle and explains the observed modulation. The observed increase in stance, swing or combined GM activity causes an outward foot placement and therefore compensates for the loss of stability caused by a perturbation early in the gait cycle. GM activity of the swing leg in response to a platform translation late in the gait cycle counteracts foot placement, but prevents collision of the swing foot with the stance leg. This study provides insights in the neuromechanics of reactive control of gait stability and proposes a novel method to distinguish between the effect of perturbation force and reactive muscle activity on gait stability

Interactive visualization of cell expansion process performance

As cell-based technologies are rapidly evolving beyond the laboratory scale, the demand for mass production of high quality cells is increasing. Unfortunately, only limited amounts of cells can be sourced from (human) donors. Therefore sequences of cell expansion steps are required to multiply the original number of cells taken from the donor biopsy to the amounts required for clinical application. Currently a large variety of expansion processes are used and described in literature. However, it is extremely difficult to compare them as many mesenchymal stem cell (MSC) subtypes are used in different culture vessels, with different medium compositions, etc. Moreover, adding to this variation in expansion strategies, within one process there can be significant fluctuations in outcome due to process variability and inherent donor-to-donor related variability. The aim of this work was to analyze the performance of a range of expansion processes for large-scale MSC expansion. Therefore a literature-based study was performed, currently resulting in a database of 73 individual cell expansion processes in 5 different types of culture vessels (microcarrier, (layered) flasks, hollow fiber-, multiplate-, and packed bed-bioreactor), 6 different types of MSCs and many different media compositions. The scale of the processes in terms of final cell numbers ranged between 7.5x106 and 1.1x1010 cells. An interactive process map was created where the scale, efficiency, cell type, culture method and load on downstream processing can be explored (see figure below). This interactive visualization tool provides an integrated perspective on the different culture processes and is able to increase the understanding on process comparability, attainable cell yield, scale-up strategies and the effect of certain critical process parameters on the expansion result. Please click Additional Files below to see the full abstract

The type and concentration of inoculum and substrate as well as the presence of oxygen impact the water kefir fermentation process

Eleven series of water kefir fermentation processes differing in the presence of oxygen and the type and concentration of inoculum and substrate, were followed as a function of time to quantify the impact of these parameters on the kinetics of this process via a modeling approach. Increasing concentrations of the water kefir grain inoculum increased the water kefir fermentation rate, so that the metabolic activity during water kefir fermentation was mainly associated with the grains. Water kefir liquor could also be used as an alternative means of inoculation, but the resulting fermentation process progressed slower than the one inoculated with water kefir grains, and the production of water kefir grain mass was absent. Substitution of sucrose with glucose and/or fructose reduced the water kefir grain growth, whereby glucose was fermented faster than fructose. Lacticaseibacillus paracasei (formerly known as Lactobacillus paracasei), Lentilactobacillus hilgardii (formerly known as Lactobacillus hilgardii), Liquorilactobacillus nagelii (formerly known as Lactobacillus nagelii), Saccharomyces cerevisiae, and Dekkera bruxellensis were the main microorganisms present. Acetic acid bacteria were present in low abundances under anaerobic conditions and only proliferated under aerobic conditions. Visualization of the water kefir grains through scanning electron microscopy revealed that the majority of the microorganisms was attached onto their surface. Lactic acid bacteria and yeasts were predominantly associated with the grains, whereas acetic acid bacteria were predominantly associated with the liquor

Introducing SPeDE : high-throughput dereplication and accurate determination of microbial diversity from matrix-assisted laser desorption-ionization time of flight mass spectrometry data

The isolation of microorganisms from microbial community samples often yields a large number of conspecific isolates. Increasing the diversity covered by an isolate collection entails the implementation of methods and protocols to minimize the number of redundant isolates. Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry methods are ideally suited to this dereplication problem because of their low cost and high throughput. However, the available software tools are cumbersome and rely either on the prior development of reference databases or on global similarity analyses, which are inconvenient and offer low taxonomic resolution. We introduce SPeDE, a user-friendly spectral data analysis tool for the dereplication of MALDI-TOF mass spectra. Rather than relying on global similarity approaches to classify spectra, SPeDE determines the number of unique spectral features by a mix of global and local peak comparisons. This approach allows the identification of a set of nonredundant spectra linked to operational isolation units. We evaluated SPeDE on a data set of 5,228 spectra representing 167 bacterial strains belonging to 132 genera across six phyla and on a data set of 312 spectra of 78 strains measured before and after lyophilization and subculturing. SPeDE was able to dereplicate with high efficiency by identifying redundant spectra while retrieving reference spectra for all strains in a sample. SPeDE can identify distinguishing features between spectra, and its performance exceeds that of established methods in speed and precision. SPeDE is open source under the MIT license and is available from https://github.com/LM-UGent/SPeDE. IMPORTANCE Estimation of the operational isolation units present in a MALDI-TOF mass spectral data set involves an essential dereplication step to identify redundant spectra in a rapid manner and without sacrificing biological resolution. We describe SPeDE, a new algorithm which facilitates culture-dependent clinical or environmental studies. SPeDE enables the rapid analysis and dereplication of isolates, a critical feature when long-term storage of cultures is limited or not feasible. We show that SPeDE can efficiently identify sets of similar spectra at the level of the species or strain, exceeding the taxonomic resolution of other methods. The high-throughput capacity, speed, and low cost of MALDI-TOF mass spectrometry and SPeDE dereplication over traditional gene marker-based sequencing approaches should facilitate adoption of the culturomics approach to bacterial isolation campaigns

Mechanistic insight into RET kinase inhibitors targeting the DFG-out conformation in RET-rearranged cancer

Oncogenic fusion events have been identified in a broad range of tumors. Among them, RET rearrangements represent distinct and potentially druggable targets that are recurrently found in lung adenocarcinomas. Here, we provide further evidence that current anti-RET drugs may not be potent enough to induce durable responses in such tumors. We report that potent inhibitors such as AD80 or ponatinib that stably bind in the DFG-out conformation of RET may overcome these limitations and selectively kill RET-rearranged tumors. Using chemical genomics in conjunction with phosphoproteomic analyses in RET-rearranged cells we identify the CCDC6-RETI788N mutation and drug-induced MAPK pathway reactivation as possible mechanisms, by which tumors may escape the activity of RET inhibitors. Our data provide mechanistic insight into the druggability of RET kinase fusions that may be of help for the development of effective therapies targeting such tumors