Hochschule Bonn-Rhein-Sieg
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Cost-Effective Next Generation Sequencing-Based STR Typing with Improved Analysis of Minor, Degraded and Inhibitor-Containing DNA Samples
No full textForensic DNA profiles are established by multiplex PCR amplification of a set of highly variable short tandem repeat (STR) loci followed by capillary electrophoresis (CE) as a means to assign alleles to PCR products of differential length. Recently, CE analysis of STR amplicons has been supplemented by high-throughput next generation sequencing (NGS) techniques that are able to detect isoalleles bearing sequence polymorphisms and allow for an improved analysis of degraded DNA. Several such assays have been commercialised and validated for forensic applications. However, these systems are cost-effective only when applied to high numbers of samples. We report here an alternative, cost-efficient shallow-sequence output NGS assay called maSTR assay that, in conjunction with a dedicated bioinformatics pipeline called SNiPSTR, can be implemented with standard NGS instrumentation. In a back-to-back comparison with a CE-based, commercial forensic STR kit, we find that for samples with low DNA content, with mixed DNA from different individuals, or containing PCR inhibitors, the maSTR assay performs equally well, and with degraded DNA is superior to CE-based analysis. Thus, the maSTR assay is a simple, robust and cost-efficient NGS-based STR typing method applicable for human identification in forensic and biomedical contexts
A hybrid skill parameterisation model combining symbolic and subsymbolic elements for introspective robots
No full textIn the design of robot skills, the focus generally lies on increasing the flexibility and reliability of the robot execution process; however, typical skill representations are not designed for analysing execution failures if they occur or for explicitly learning from failures. In this paper, we describe a learning-based hybrid representation for skill parameterisation called an execution model, which considers execution failures to be a natural part of the execution process. We then (i) demonstrate how execution contexts can be included in execution models, (ii) introduce a technique for generalising models between object categories by combining generalisation attempts performed by a robot with knowledge about object similarities represented in an ontology, and (iii) describe a procedure that uses an execution model for identifying a likely hypothesis of a parameterisation failure. The feasibility of the proposed methods is evaluated in multiple experiments performed with a physical robot in the context of handle grasping, object grasping, and object pulling. The experimental results suggest that execution models contribute towards avoiding execution failures, but also represent a first step towards more introspective robots that are able to analyse some of their execution failures in an explicit manner
Stratified Taylor–Green vortex by lattice Boltzmann methods: Influence of stencils, forcing schemes, and collision models
No full textStably stratified Taylor–Green vortex simulations are performed by lattice Boltzmann methods (LBM) and compared to other recent works using Navier–Stokes solvers. The density variation is modeled with a separate distribution function in addition to the particle distribution function modeling the flow physics. Different stencils, forcing schemes, and collision models are tested and assessed. The overall agreement of the lattice Boltzmann solutions with reference solutions from other works is very good, even when no explicit subgrid model is used, but the quality depends on the LBM setup. Although the LBM forcing scheme is not decisive for the quality of the solution, the choice of the collision model and of the stencil are crucial for adequate solutions in underresolved conditions. The LBM simulations confirm the suppression of vertical flow motion for decreasing initial Froude numbers. To gain further insight into buoyancy effects, energy decay, dissipation rates, and flux coefficients are evaluated using the LBM model for various Froude numbers
Vegetables as a vehicle for antimicrobial resistance (vAMR): An agroecosystem exploration from the One Health perspective in India
No full textIntroduction: Antimicrobial resistance (AMR) has emerged as one of the leading threats to public health. AMR possesses a multidimensional challenge that has social, economic, and environmental dimensions that encompass the food production system, influencing human and animal health. The One Health approach highlights the inextricable linkage and interdependence between the health of people, animals, agriculture, and the environment. Antibiotic use in any of these One Health areas can potentially impact the health of other areas. There is a dearth of evidence on AMR from the natural environment, such as the plant-based agriculture sector. Antibiotics, antibiotic-resistant bacteria (ARB), and related AMR genes (ARGs) are assumed to present in the natural environment and disseminate resistance to fresh produce/vegetables and thus to human health upon consumption. Therefore, this study aims to investigate the role of vegetables in the spread of AMR through an agroecosystem exploration from a One Health perspective in Ahmedabad, India.
Protocol: The present study will be executed in Ahmedabad, located in Gujarat state in the Western part of India, by adopting a mixed-method approach. First, a systematic review will be conducted to document the prevalence of ARB and ARGs on fresh produce in South Asia. Second, agriculture farmland surveys will be used to collect the general farming practices and the data on common vegetables consumed raw by the households in Ahmedabad. Third, vegetable and soil samples will be collected from the selected agriculture farms and analyzed for the presence or absence of ARB and ARGs using standard microbiological and molecular methods.
Discussion: The analysis will help to understand the spread of ARB/ARGs through the agroecosystem. This is anticipated to provide an insight into the current state of ARB/ARGs contamination of fresh produce/vegetables and will assist in identifying the relevant strategies for effectively controlling and preventing the spread of AMR
Evaluation of Drift Detection Techniques for Automated Machine Learning Pipelines
No full textMachine learning-based solutions are frequently adapted in several applications that require big data in operations. The performance of a model that is deployed into operations is subject to degradation due to unanticipated changes in the flow of input data. Hence, monitoring data drift becomes essential to maintain the model’s desired performance. Based on the conducted review of the literature on drift detection, statistical hypothesis testing enables to investigate whether incoming data is drifting from training data. Because Maximum Mean Discrepancy (MMD) and Kolmogorov-Smirnov (KS) have shown to be reliable distance measures between multivariate distributions in the literature review, both were selected from several existing techniques for experimentation. For the scope of this work, the image classification use case was experimented with using the Stream-51 dataset. Based on the results from different drift experiments, both MMD and KS showed high Area Under Curve values. However, KS exhibited faster performance than MMD with fewer false positives. Furthermore, the results showed that using the pre-trained ResNet-18 for feature extraction maintained the high performance of the experimented drift detectors. Furthermore, the results showed that the performance of the drift detectors highly depends on the sample sizes of the reference (training) data and the test data that flow into the pipeline’s monitor. Finally, the results also showed that if the test data is a mixture of drifting and non-drifting data, the performance of the drift detectors does not depend on how the drifting data are scattered with the non-drifting ones, but rather their amount in the test se
Real-World Approach for Evaluating Capacity Fading in Lithium-ion Batteries Using Novel Cyclic Testing Methods
No full textBattery lifespan estimation is an essential aspect of battery management systems. It allows end users and original equipment manufacturers to plan for future battery replacements. However, accurately estimating the capacity of a battery is complex due to the different capacity fading phenomenon which are related to different factors such as temperature, charge-discharge rate, rest period duration, etc. A realistic cyclic testing method is needed to evaluate the life span, as it lets the users assess various factors’ impacting battery performance over time. Different cyclic testing methods are proposed in the literature; however, the most efficient approach will depend on the specific application and the testing objectives. A new approach, closer to real-world driving scenarios, is proposed in this work for battery capacity fading evaluation. A deeper comprehension of the results helps develop an empirical relation appropriate to evaluate capacity fading at given testing conditions easily
Decoding Range Variability in Electric Vehicles: Unravelling the Influence of Cell-to-Cell Parameter Variation and Pack Configuration
No full textElectric vehicles (EVs) are rapidly growing in popularity, but range variability has become an important research area with significant implications for EV performance, usability, and overall market adoption. This study aims to unravel the complexities of range variability by examining the contributing factors and offering innovative strategies to mitigate these differences during pack design. Through a detailed analysis of cell parameter deviation, cell connections, battery configuration, battery pack size, and driving behavior, the research illuminates their impact on extractable energy and driving range. The study employed a comprehensive approach and conducted systematic simulation-based experimentation to identify the optimal battery pack configuration based on maximum extractable energy, minimal variability and maximum range. The results reveal insights into the relationship between discharge rate and battery pack performance, and the impact of cell parameter variations on pack energy output. This research advances the understanding of EV performance optimisation, reduces pack-to-pack variability, and extends battery pack lifespan
Integrating Continuous and Teleporting VR Locomotion Into a Seamless 'HyperJump' Paradigm
No full textPharmacological inhibitors of the cystic fibrosis transmembrane conductance regulator exert off-target effects on epithelial cation channels
Get PDFThe cystic fibrosis transmembrane conductance regulator (CFTR) anion channel and the epithelial Na+ channel (ENaC) play essential roles in transepithelial ion and fluid transport in numerous epithelial tissues. Inhibitors of both channels have been important tools for defining their physiological role in vitro. However, two commonly used CFTR inhibitors, CFTRinh-172 and GlyH-101, also inhibit non-CFTR anion channels, indicating they are not CFTR specific. However, the potential off-target effects of these inhibitors on epithelial cation channels has to date not been addressed. Here, we show that both CFTR blockers, at concentrations routinely employed by many researchers, caused a significant inhibition of store-operated calcium entry (SOCE) that was time-dependent, poorly reversible and independent of CFTR. Patch clamp experiments showed that both CFTRinh-172 and GlyH-101 caused a significant block of Orai1-mediated whole cell currents, establishing that they likely reduce SOCE via modulation of this Ca2+ release-activated Ca2+ (CRAC) channel. In addition to off-target effects on calcium channels, both inhibitors significantly reduced human αβγ-ENaC-mediated currents after heterologous expression in Xenopus oocytes, but had differential effects on δβγ-ENaC function. Molecular docking identified two putative binding sites in the extracellular domain of ENaC for both CFTR blockers. Together, our results indicate that caution is needed when using these two CFTR inhibitors to dissect the role of CFTR, and potentially ENaC, in physiological processes