Identification of high confidence human poly(A) RNA isoform scaffolds using nanopore sequencing.

Nanopore sequencing devices read individual RNA strands directly. This facilitates identification of exon linkages and nucleotide modifications; however, using conventional methods the 5′ and 3′ ends of poly(A) RNA cannot be identified unambiguously. This is due in part to the architecture of the nanopore/enzyme-motor complex, and in part to RNA degradation in vivo and in vitro that can obscure transcription start and end sites. In this study, we aimed to identify individual full-length human RNA isoform scaffolds among ~4 million nanopore poly(A)-selected RNA reads. First, to identify RNA strands bearing 5′ m7G caps, we exchanged the biological cap for a modified cap attached to a 45-nucleotide oligomer. This oligomer adaptation method improved 5′ end sequencing and ensured correct identification of the 5′ m7G capped ends. Second, among these 5′-capped nanopore reads, we screened for ionic current signatures consistent with a 3′ polyadenylation site. Combining these two steps, we identified 294,107 individual high-confidence full-length RNA scaffolds, most of which (257,721) aligned to protein-coding genes. Of these, 4,876 scaffolds indicated unannotated isoforms that were often internal to longer, previously identified RNA isoforms. Orthogonal data confirmed the validity of these high-confidence RNA scaffolds.

Detecting industrial motor faults with current signatures

Background: A major player in industry is the induction motor. The constant motion and mechanical nature of motors causes much wear and tear, creating a need for frequent maintenance such as changing contact brushes. Unmannered and infrequent monitoring of motors, as is common in the industry, can lead to overexertion and cause major faults. If a motor fault is detected earlier through the use of automated fault monitoring, it could prevent minor faults from developing into major faults, reducing the cost and down-time of production due the motor repairs. There are few available methods to detect three-phase motor faults. One method is to analyze average vibration signals values of V, I, pf, P, Q, S, THD and frequency. Others are to analyze instantaneous signal signatures of V and I frequencies, or V and I trajectory plotting a Lissajous curve. These methods need at least three sensors for current and three for voltage for a three-phase motor detection. Methods: Our proposed method of monitoring faults in three-phase industrial motors uses Hilbert Transform (HT) instantaneous current signature curve only, reducing the number of sensors required. Our system detects fault signatures accurately at any voltage or current levels, whether it is delta or star connected motors. This is due to our system design, which incorporates normalized curves of HT in the fault analysis database. We have conducted this experiment in our campus laboratory for two different three-phase motors with four different fault experiments. Results: The results shown in this paper are a comparison of two methods, the V and I Lissajous trajectory curve and our HT instantaneous current signature curve. Conclusion: We have chosen them as our benchmark as their fault results closely resemble our system results, but our system benefits such as universality and a cost reduction in sensors of 50%.

Azimuthal field signatures associated with magnetosphere-ionosphere coupling in the Jovian magnetosphere: Comparison between Juno observations and theoretical modelling

<p>We present a comparison of magnetic field data collected by the NASA Juno spacecraft, with the magnetosphere-ionosphere (MI) coupling model for the Jovian system developed by the University of Leicester. We study the magnetic field of Jupiter, in the Northern Hemisphere, for Perijoves 1-13. By virtue of the offset of the magnetic field to the rotation axis and the subsequent “wobble” of the Juno trajectory in magnetic coordinates, these northern hemisphere portions of PJs 1-13 see the spacecraft traversing the magnetic field lines connecting to the inner, middle, outer and tail regions of the magnetosphere. As such, even away from the close Perijove period, the observations contain evidence of the expected magnetic field perturbations associated with field-aligned currents associated with this fundamental MI coupling. In this study, therefore, we focus on investigating the nature of the field-aligned current signatures evident in the residual azimuthal field (having subtracted the Connerney et al 2018 JRM09 internal magnetic field model) along the magnetic field lines outside of the close periapsides. We map the residual azimuthal field signatures into the ionosphere, and calculate the corresponding ionospheric Pedersen current on an orbit by orbit basis. We compare the magnitude and distribution of these field-aligned current signatures to those expected from the Leicester model, and consider the observed orbit-by-orbit variation as a function of ionospheric colatitude and longitude. We deduce estimates for the field-aligned current densities on auroral field lines for each observation using the Pedersen currents and their distribution in co-latitude, and compare to the previous work of Kotsiaros et al [2019]. We discuss possible reasons for the variations we see, and present the next steps of our broader analysis.</p>

A contained Mycobacterium tuberculosis mouse infection model predicts active disease and containment in humans

Previous studies have identified whole-blood transcriptional risk and disease signatures for Tuberculosis (TB); however, several lines of evidence suggest that these signatures primarily reflect bacterial burden, which increases prior to symptomatic disease. We found that the peripheral blood transcriptome of mice with contained Mycobacterium tuberculosis infection (CMTB) has striking similarities to that of humans with active TB and that a signature derived from these mice predicts human disease with comparable accuracy to signatures derived directly from humans. A set of genes associated with immune defense are upregulated in CMTB mice but not in humans with active TB suggesting that their upregulation is associated with bacterial containment. A signature comprised of these genes predicts both protection from TB disease and successful treatment at early time points where current signatures are not predictive. These results suggest that detailed study of the CMTB mouse model may enable identification of biomarkers for human TB.

Ultra-Low Noise Amplifier Array System for High Throughput Single Entity Analysis

Electrochemical measurements at the single entity level provide ultra-sensitive tools for precise diagnosis and understanding of basic biological and chemical processes. By decoding current signatures, the single-entity electrochemistry provides abundant...

Identification of high confidence human poly(A) RNA isoform scaffolds using nanopore sequencing

ABSTRACTNanopore sequencing devices read individual RNA strands directly. This facilitates identification of exon linkages and nucleotide modifications; however, using conventional methods the 5′ and 3′ ends of poly(A) RNA cannot be identified unambiguously. This is due in part to the architecture of the nanopore/enzyme-motor complex, and in part to RNA degradation in vivo and in vitro that can obscure transcription start and end sites. In this study, we aimed to identify individual full-length human RNA isoform scaffolds among ∼4 million nanopore poly(A)-selected RNA reads. First, to identify RNA strands bearing 5′ m7G caps, we exchanged the biological cap for a modified cap attached to a 45-nucleotide oligomer. This oligomer adaptation method improved 5′ end sequencing and ensured correct identification of the 5′ m7G capped ends. Second, among these 5′-capped nanopore reads, we screened for ionic current signatures consistent with a 3′ polyadenylation site. Combining these two steps, we identified 294,107 individual high-confidence full-length RNA scaffolds, most of which (257,721) aligned to protein-coding genes. Of these, 4,876 scaffolds indicated unannotated isoforms that were often internal to longer, previously identified RNA isoforms. Orthogonal data confirmed the validity of these high-confidence RNA scaffolds.

A First Comparison Between Ionospheric and Surface Level Magnetic Fields at Mars

<p>With both the Mars Atmosphere and Volatile Evolution (MAVEN) mission and the Interior Exploration using Seismic Investigations, Geodesy and Heat Transport (InSight) mission concurrently operating at Mars, we are able to make two point comparisons of the vector magnetic field at Mars for the first time. During MAVEN overflights of the InSight landing site, we compared deviations in the ionospheric magnetic field to variations in the surface level magnetic field. We find significant orbit to orbit variability in the magnitude and direction of the ionospheric magnetic field as well as significant day to day variability of the surface level magnetic field. We attribute this variability to time varying ionospheric currents. However, when analyzing the ensemble of 16 individual MAVEN overflights of the InSight landing location, we see no clear correlation between the magnitudes or directions of the ionospheric magnetic field and the surface magnetic field as might be expected. If the presumed ionospheric currents have a small scale size, then the ionospheric magnetic field will display increased variability as MAVEN flies through the current structure. Whereas the present analysis is restricted to mostly nightside MAVEN overflights where current are expected to be weak, future analyses should incorporate dayside overflights where current are expected to be stronger and current signatures more clear.</p>