GMFilter and SXTestPlate: software tools for improving the SNPlex™ genotyping system

<p>Abstract</p> <p>Background</p> <p>Genotyping of single-nucleotide polymorphisms (SNPs) is a fundamental technology in modern genetics. The SNPlex™ mid-throughput genotyping system (Applied Biosystems, Foster City, CA, USA) enables the multiplexed genotyping of up to 48 SNPs simultaneously in a single DNA sample. The high level of automation and the large amount of data produced in a high-throughput laboratory require advanced software tools for quality control and workflow management.</p> <p>Results</p> <p>We have developed two programs, which address two main aspects of quality control in a SNPlex™ genotyping environment: GMFilter improves the analysis of SNPlex™ plates by removing wells with a low overall signal intensity. It enables scientists to automatically process the raw data in a standardized way before analyzing a plate with the proprietary GeneMapper software from Applied Biosystems. SXTestPlate examines the genotype concordance of a SNPlex™ test plate, which was typed with a control SNP set. This program allows for regular quality control checks of a SNPlex™ genotyping platform. It is compatible to other genotyping methods as well.</p> <p>Conclusion</p> <p>GMFilter and SXTestPlate provide a valuable tool set for laboratories engaged in genotyping based on the SNPlex™ system. The programs enhance the analysis of SNPlex™ plates with the GeneMapper software and enable scientists to evaluate the performance of their genotyping platform.</p

On the Influence of Diurnal and Subdiurnal Signals in the Normal Vector on Large Ring Laser Gyroscope Observations

The ring laser gyroscope (RLG) technique has been investigated for over 20 years as a potential complement to space geodetic techniques in measuring Earth rotation. However, RLGs are also sensitive to changes in their terrestrial orientation. Therefore in this paper, we review how the high-frequency band (i.e. signals shorter than 0.5 cycle per day) of the known phenomena causing site deformation contribute to the RLG observable, the Sagnac frequency. We study the impact of solid Earth tides, ocean tidal loading and non-tidal loading phenomena (atmospheric pressure loading and continental hydrosphere loading). Also, we evaluate the differences between available models of the phenomena and the importance of the Love numbers used in modeling the impact of solid Earth tides. Finally, we compare modeled variations in the instrument orientation with the ones observed with a tiltmeter. Our results prove that at the present accuracy of the RLG technique, solid Earth tides and ocean tidal loading effects have significant effect on RLG measurements, and continental hydrosphere loading can be actually neglected. Regarding the atmospheric loading model, its application might introduce some undesired signals. We also show that discrepancies arising from the use of different models can be neglected, and there is almost no impact arising from the use of different Love numbers. Finally, we discuss differences between data reduced with tiltmeter observations and these reduced with modeled signal, and potential causes of this discrepancies

Audio-based Roughness Sensing and Tactile Feedback for Haptic Perception in Telepresence

Haptic perception is highly important for immersive teleoperation of robots, especially for accomplishing manipulation tasks. We propose a low-cost haptic sensing and rendering system, which is capable of detecting and displaying surface roughness. As the robot fingertip moves across a surface of interest, two microphones capture sound coupled directly through the fingertip and through the air, respectively. A learning-based detector system analyzes the data in real time and gives roughness estimates with both high temporal resolution and low latency. Finally, an audio-based vibrational actuator displays the result to the human operator. We demonstrate the effectiveness of our system through lab experiments and our winning entry in the ANA Avatar XPRIZE competition finals, where briefly trained judges solved a roughness-based selection task even without additional vision feedback. We publish our dataset used for training and evaluation together with our trained models to enable reproducibility of results.Comment: IEEE International Conference on Systems, Man, and Cybernetics (SMC), Honolulu, Hawaii, USA, October 202

Robust Immersive Telepresence and Mobile Telemanipulation: NimbRo wins ANA Avatar XPRIZE Finals

Robotic avatar systems promise to bridge distances and reduce the need for travel. We present the updated NimbRo avatar system, winner of the $5M grand prize at the international ANA Avatar XPRIZE competition, which required participants to build intuitive and immersive robotic telepresence systems that could be operated by briefly trained operators. We describe key improvements for the finals, compared to the system used in the semifinals: To operate without a power- and communications tether, we integrated a battery and a robust redundant wireless communication system. Video and audio data are compressed using low-latency HEVC and Opus codecs. We propose a new locomotion control device with tunable resistance force. To increase flexibility, the robot's upper-body height can be adjusted by the operator. We describe essential monitoring and robustness tools which enabled the success at the competition. Finally, we analyze our performance at the competition finals and discuss lessons learned.Comment: M. Schwarz and C. Lenz contributed equall

Silicon Promotes Exodermal Casparian Band Formation in Si-Accumulating and Si-Excluding Species by Forming Phenol Complexes

We studied the effect of Silicon (Si) on Casparian band (CB) development, chemical composition of the exodermal CB and Si deposition across the root in the Si accumulators rice and maize and the Si non-accumulator onion. Plants were cultivated in nutrient solution with and without Si supply. The CB development was determined in stained root cross-sections. The outer part of the roots containing the exodermis was isolated after enzymatic treatment. The exodermal suberin was transesterified with MeOH/BF3 and the chemical composition was measured using gas chromatography-mass spectroscopy (GC-MS) and flame ionization detector (GC-FID). Laser ablation-inductively coupled plasma-mass spectroscopy (LA-ICP-MS) was used to determine the Si deposition across root cross sections. Si promoted CB formation in the roots of Si-accumulator and Si non-accumulator species. The exodermal suberin was decreased in rice and maize due to decreased amounts of aromatic suberin fractions. Si did not affect the concentration of lignin and lignin-like polymers in the outer part of rice, maize and onion roots. The highest Si depositions were found in the tissues containing CB. These data along with literature were used to suggest a mechanism how Si promotes the CB development by forming complexes with phenols.DFG/SCHR 506/12-