Differential ratio amplicons (Ramp) for the evaluation of RNA integrity extracted from complex environmental samples

Reliability and reproducibility of transcriptomics‐based studies are dependent on RNA integrity. In microbial ecology, microfluidics‐based techniques, such as the Ribosomal Integrity Number (RIN), targeting rRNA are currently the only approaches to evaluate RNA integrity. However, the relationship between rRNA and mRNA integrity is unknown. Here we present an integrity index, the Ratio Amplicon, Ramp, adapted from human clinical studies, to directly monitor mRNA integrity from complex environmental samples. We show, in a suite of experimental degradations of RNA extracted from sediment, that while the RIN generally reflected the degradation status of RNA the Ramp mapped mRNA degradation better. Furthermore, we examined the effect of degradation on transcript community structure by amplicon sequencing of 16S rRNA, amoA and glnA transcripts. We successfully sequenced transcripts for all three targets even from highly‐degraded RNA samples. While RNA degradation changed the community structure of the mRNA profiles, no changes were observed for the 16S rRNA transcript profiles. Since both RT‐Q‐PCR and sequencing results were obtained, even from highly degraded samples, we strongly recommend evaluating RNA integrity prior to downstream processing to ensure meaningful results. For this both the RIN and Ramp are useful, with the Ramp better evaluating mRNA integrity in this study

ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS based metabolomics

We present ProbMetab, an R package which promotes substantial improvement in automatic probabilistic LC-MS based metabolome annotation. The inference engine core is based on a Bayesian model implemented to: (i) allow diverse source of experimental data and metadata to be systematically incorporated into the model with alternative ways to calculate the likelihood function and; (ii) allow sensitive selection of biologically meaningful biochemical reactions databases as Dirichlet-categorical prior distribution. Additionally, to ensure result interpretation by system biologists, we display the annotation in a network where observed mass peaks are connected if their candidate metabolites are substrate/product of known biochemical reactions. This graph can be overlaid with other graph-based analysis, such as partial correlation networks, in a visualization scheme exported to Cytoscape, with web and stand alone versions. ProbMetab was implemented in a modular fashion to fit together with established upstream (xcms, CAMERA, AStream, mzMatch.R, etc) and downstream R package tools (GeneNet, RCytoscape, DiffCorr, etc). ProbMetab, along with extensive documentation and case studies, is freely available under GNU license at: http://labpib.fmrp.usp.br/methods/probmetab/.Comment: Manuscript to be submitted very soon. 7 pages, 3 color figures. There is a companion material, the two case studies, which are going to be posted here together with the main text in next updated versio

Two-flow magnetohydrodynamical jets around young stellar objects

We present the first-ever simulations of non-ideal magnetohydrodynamical (MHD) stellar winds coupled with disc-driven jets where the resistive and viscous accretion disc is self-consistently described. The transmagnetosonic, collimated MHD outflows are investigated numerically using the VAC code. Our simulations show that the inner outflow is accelerated from the central object hot corona thanks to both the thermal pressure and the Lorentz force. In our framework, the thermal acceleration is sustained by the heating produced by the dissipated magnetic energy due to the turbulence. Conversely, the outflow launched from the resistive accretion disc is mainly accelerated by the magneto-centrifugal force. We also show that when a dense inner stellar wind occurs, the resulting disc-driven jet have a different structure, namely a magnetic structure where poloidal magnetic field lines are more inclined because of the pressure caused by the stellar wind. This modification leads to both an enhanced mass ejection rate in the disc-driven jet and a larger radial extension which is in better agreement with the observations besides being more consistent.Comment: Accepted for publication in Astrophysics & Space Science. Referred proceeding of the fifth Mont Stromlo Symposium Dec. 1-8 2006, Canberra, Australia. 5 pages, 3 figures. For high resolution version of the paper, please click here http://www.apc.univ-paris7.fr/~fcasse/publications.htm

Oxygen vacancy engineering of TaOx-based resistive memories by Zr doping for improved variability and synaptic behavior

Resistive switching devices are promising emerging non-volatile memories. However, one of the biggest challenges for resistive switching (RS) memory applications is the device-to-device (D2D) variability which is related to the intrinsic stochastic formation and configuration of oxygen vacancy (VO) conductive filaments. In order to reduce D2D variability, the control of oxygen vacancy formation and configuration is paramount. We report in this study Zr doping of TaOx-based RS devices prepared by pulsed laser deposition (PLD) as an efficient mean to reduce VO formation energy and increase conductive filament (CF) confinement, thus reducing D2D variability. Such findings were supported by X-ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry (SE) and electronic transport analysis. Zr doped films presented increased VO concentration, and more localized VO thanks to the interaction with Zr. According to DC and pulse mode electrical characterization, D2D variability was decreased by a factor of 7, resistance window was doubled and a more gradual and monotonic long-term potentiation/depression (LTP/LTD) in pulse switching was achieved in forming-free Zr:TaOx devices thus displaying promising performance for artificial synapse applications.Comment: 19 pages, 10 figure

Limit laws of entrance times for low complexity Cantor minimal systems

This paper is devoted to the study of limit laws of entrance times to cylinder sets for Cantor minimal systems of zero entropy using their representation by means of ordered Bratteli diagrams. We study in detail substitution subshifts and we prove these limit laws are piecewise linear functions. The same kind of results is obtained for classical low complexity systems given by non stationary ordered Bratteli diagrams

Glueballs, gluon condensate, and pure glue QCD below T_c

A quasiparticle description of pure glue QCD thermodynamics at T<T_c is proposed and compared to recent lattice data. Given that a gas of glueballs with constant mass cannot quantitatively reproduce the early stages of the deconfinement phase transition, the problem is to identify a relevant mechanism leading to the observed sudden increase of the pressure, trace anomaly, etc. It is shown that the strong decrease of the gluon condensate near T_c combined with the increasing thermal width of the lightest glueballs might be the trigger of the phase transition.Comment: 5 pages, 5 figures; analysis refined in v2, explanations added; v3 to appear in EPJ

Comparison of total ankle replacement and ankle arthrodesis in patients with haemophilia using gait analysis : two case reports

BACKGROUND: Severe hemophilia is an inherited, lifelong bleeding disorder characterized by spontaneous bleeding, which results in painful joint deformities. Currently two surgical treatments are available to treat haemophilia-related ankle joint destruction: ankle arthrodesis and total ankle replacement. The aim of the present study was to compare these two surgical procedures in haemophiliac subjects. CASE PRESENTATION: Kinematic and dynamic parameters were quantified using a three-dimensional gait-analysis system in two similar clinical cases. In Caucasian case 1, ankle arthrodesis was chosen because of a kinematic ankle flexion defect and lack of dynamic power regeneration. The defect in energy absorption was compensated for by the contralateral side. Total ankle replacement in Caucasian case 2 allowed sparing the ipsilateral knee (maximum 0.27 preoperatively vs. 0.71 W/kg postoperatively) and hip joints powers (maximum 0.43 preoperatively vs. 1.25 W/kg postoperatively) because of the small ankle dorsiflexion motion. CONCLUSIONS: Total ankle replacement is recommended for haemophiliac patients who present with a preserved ankle range of motion

Performance Testing of a Large-Format Reflection Grating Prototype for a Suborbital Rocket Payload

The soft X-ray grating spectrometer on board the Off-plane Grating Rocket Experiment (OGRE) hopes to achieve the highest resolution soft X-ray spectrum of an astrophysical object when it is launched via suborbital rocket. Paramount to the success of the spectrometer are the performance of the $>250$ reflection gratings populating its reflection grating assembly. To test current grating fabrication capabilities, a grating prototype for the payload was fabricated via electron-beam lithography at The Pennsylvania State University's Materials Research Institute and was subsequently tested for performance at Max Planck Institute for Extraterrestrial Physics' PANTER X-ray Test Facility. Bayesian modeling of the resulting data via Markov chain Monte Carlo (MCMC) sampling indicated that the grating achieved the OGRE single-grating resolution requirement of $R_{g}(\lambda/\Delta\lambda)>4500$ at the 94% confidence level. The resulting $R_g$ posterior probability distribution suggests that this confidence level is likely a conservative estimate though, since only a finite $R_g$ parameter space was sampled and the model could not constrain the upper bound of $R_g$ to less than infinity. Raytrace simulations of the system found that the observed data can be reproduced with a grating performing at $R_g=\infty$. It is therefore postulated that the behavior of the obtained $R_g$ posterior probability distribution can be explained by a finite measurement limit of the system and not a finite limit on $R_g$. Implications of these results and improvements to the test setup are discussed.Comment: 25 pages, 16 figures, preprint of an article accepted for publication in the Journal of Astronomical Instrumentation \copyright 2020 [copyright World Scientific Publishing Company] [https://www.worldscientific.com/worldscinet/jai

Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France

Exploring differences in nitrification within adjacent sedimentary structures of ridges and runnels on the Brouage mudflat, France, we quantified Potential Nitrification Rates (PNR) alongside amoA genes and transcripts. PNR was lower in ridges (≈1.7 fold-lower) than runnels, despite higher (≈1.8 fold-higher) ammonia-oxidizing bacteria (AOB) abundance. However, AOB were more transcriptionally active in runnels (≈1.9 fold-higher). Sequencing of amoA genes and transcripts revealed starkly contrasting profiles with transcripts from ridges and runnels dominated (≈91 % in ridges and ≈98 % in runnels) by low abundant (≈4.6 % of the DNA community in runnels and ≈0.8 % in ridges) but highly active phylotypes. The higher PNR in runnels was explained by higher abundance of this group, an uncharacterised Nitrosomonas sp. cluster. This cluster is phylogenetically similar to other active ammonia-oxidizers with worldwide distribution in coastal environments indicating its potential, but previously overlooked, contribution to ammonia oxidation globally. In contrast DNA profiles were dominated by highly abundant but low-activity clusters phylogenetically distinct from known Nitrosomonas (Nm) and Nitrosospira (Ns). This cluster is also globally distributed in coastal sediments, primarily detected as DNA, and often classified as Nitrosospira or Nitrosomonas. We therefore propose to classify this cluster as Ns/Nm. Our work indicates that low abundant but highly active AOB could be responsible for the nitrification globally, while the abundant AOB Ns/Nm may not be transcriptionally active, and as such account for the lack of correlation between rate processes and gene abundances often reported in the literature. It also raises the question as to what this seemingly inactive group is doing

Autonomous Medical Needle Steering In Vivo

The use of needles to access sites within organs is fundamental to many interventional medical procedures both for diagnosis and treatment. Safe and accurate navigation of a needle through living tissue to an intra-tissue target is currently often challenging or infeasible due to the presence of anatomical obstacles in the tissue, high levels of uncertainty, and natural tissue motion (e.g., due to breathing). Medical robots capable of automating needle-based procedures in vivo have the potential to overcome these challenges and enable an enhanced level of patient care and safety. In this paper, we show the first medical robot that autonomously navigates a needle inside living tissue around anatomical obstacles to an intra-tissue target. Our system leverages an aiming device and a laser-patterned highly flexible steerable needle, a type of needle capable of maneuvering along curvilinear trajectories to avoid obstacles. The autonomous robot accounts for anatomical obstacles and uncertainty in living tissue/needle interaction with replanning and control and accounts for respiratory motion by defining safe insertion time windows during the breathing cycle. We apply the system to lung biopsy, which is critical in the diagnosis of lung cancer, the leading cause of cancer-related death in the United States. We demonstrate successful performance of our system in multiple in vivo porcine studies and also demonstrate that our approach leveraging autonomous needle steering outperforms a standard manual clinical technique for lung nodule access.Comment: 22 pages, 6 figure