Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.

In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation. Using selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) and covariation analysis, we explore the structural features of the third genome segment of cucumber mosaic virus (CMV), RNA3 (2216 nt), both in vitro and in plant cell lysates. Comparing SHAPE-Seq and covariation analysis results revealed multiple SEs in the coat protein open reading frame and 3' untranslated region. Four of these SEs were mutated and serially passaged in Nicotiana tabacum plants to identify biologically selected changes to the original mutated sequences. After passaging, loop mutants showed partial reversion to their wild-type sequence and SEs that were structurally disrupted by mutations were restored to wild-type-like structures via synonymous mutations in planta. These results support the existence and selection of virus open reading frame SEs in the host organism and provide a framework for further studies on the role of RNA structure in viral infection. Additionally, this work demonstrates the applicability of high-throughput chemical probing in plant cell lysates and presents a new method for calculating SHAPE reactivities from overlapping reverse transcriptase priming sites

Road Safety in Great Britain: An Exploratory Data Analysis

Great Britain has one of the safest road networks in the world. However, the consequences of any death or serious injury are devastating for loved ones, as well as for those who help the severely injured. This paper aims to analyse Great Britain's road safety situation and show the response measures for areas where the total damage caused by accidents can be significantly and quickly reduced. For the past 30 years, the UK has had a good record in reducing fatalities over the past 30 years, there is still a considerable number of road deaths. The government continues to scale back road deaths empowering responsible road users by identifying and prosecuting the parameters that make the roads less safe. This study represents an exploratory analysis with deep insights which could provide policy makers with invaluable insights into how accidents happen and how they can be mitigated. We use STATS19 data published by the UK government. Since we need more information about locations which is not provided in STATA19, we first expand the features of the dataset using OpenStreetMap and Visual Crossing. This paper also provides a discussion regarding new road safety methods

Tunneling Study of the Charge-Ordering Gap on the Surface of La0.350_{0.350}Pr0.275_{0.275}Ca0.375_{0.375}MnO3_3 Thin Films

Variable temperature scanning tunneling microscopy/spectroscopy studies on (110) oriented epitaxial thin films of La$_{0.350}$Pr$_{0.275}$Ca$_{0.375}$MnO$_3$ are reported in the temperature range of 77 to 340 K. The films, grown on lattice matched NdGaO$_3$ substrates, show a hysteretic metal-insulator transition in resistivity at 170 K. The topographic STM images show step-terrace morphology while the conductance images display a nearly homogeneous surface. The normalized conductance spectra at low temperatures (T$<$150 K) show an energy gap of 0.5 eV while for T$\geq$180 K a gap of 0.16 eV is found from the activated behavior of the zero bias conductance. The presence of energy gap and the absence of phase separation on the surface over more than 2 $\mu$m$\times$2 $\mu$m area contradicts the metallic behavior seen in resistivity measurements at low temperatures. We discuss the measured energy gap in terms of the stabilization of the insulating CO phase at the film surface.Comment: 5 pages, 5 figures To appear in Phys. Rev.

Fibronectin and Cyclic Strain Improve Cardiac Progenitor Cell Regenerative Potential In Vitro.

Cardiac progenitor cells (CPCs) have rapidly advanced to clinical trials, yet little is known regarding their interaction with the microenvironment. Signaling cues present in the microenvironment change with development and disease. This work aims to assess the influence of two distinct signaling moieties on CPCs: cyclic biaxial strain and extracellular matrix. We evaluate four endpoints for improving CPC therapy: paracrine signaling, proliferation, connexin43 expression, and alignment. Vascular endothelial growth factor A (about 900 pg/mL) was secreted by CPCs cultured on fibronectin and collagen I. The application of mechanical strain increased vascular endothelial growth factor A secretion 2-4-fold for CPCs cultured on poly-L-lysine, laminin, or a naturally derived cardiac extracellular matrix. CPC proliferation was at least 25% higher on fibronectin than that on other matrices, especially for lower strain magnitudes. At 5% strain, connexin43 expression was highest on fibronectin. With increasing strain magnitude, connexin43 expression decreased by as much as 60% in CPCs cultured on collagen I and a naturally derived cardiac extracellular matrix. Cyclic mechanical strain induced the strongest CPC alignment when cultured on fibronectin or collagen I. This study demonstrates that culturing CPCs on fibronectin with 5% strain magnitude is optimal for their vascular endothelial growth factor A secretion, proliferation, connexin43 expression, and alignment

Inhibitory effects of tibial nerve stimulation on bladder neurophysiology in rats

Tibial nerve stimulation (TNS) is a form of peripheral neuromodulation which has been found effective in treating overactive bladder symptoms, with lesser side effects than first line pharmacotherapy. Despite its widespread clinical use, the underlying mechanism of action is not fully understood. Our aim was to study its effect on the bladder neurophysiology and the trigger mechanism of voiding in the overactive detrusor, simulated by acetic acid (AA) instillation. In urethane anaesthetized male Wistar rats, the tibial nerve was stimulated for 30 min at 5 Hz, pulse width 200 µs and amplitude approximately three times the threshold to induce a slight toe movement. The pressure at which a voiding contraction was triggered (pthres) did not change significantly between the pre- and post-TNS measurements in AA induced detrusor overactivity. It was found that TNS significantly reversed the effects of AA irritation by increasing the bladder compliance and the bladder volume at pthres, as well as suppressed the threshold afferent nerve activity. The slope of the linear relationship between pressure and the afferent activity increased after AA instillation and decreased significantly after stimulation. In addition to its well-known central inhibitory mechanisms, this study has demonstrated that TNS improves bladder storage capacity by delaying the onset of voiding, via an inhibitory effect on the bladder afferent signaling at the peripheral level

Generic effective source for scalar self-force calculations

A leading approach to the modelling of extreme mass ratio inspirals involves the treatment of the smaller mass as a point particle and the computation of a regularized self-force acting on that particle. In turn, this computation requires knowledge of the regularized retarded field generated by the particle. A direct calculation of this regularized field may be achieved by replacing the point particle with an effective source and solving directly a wave equation for the regularized field. This has the advantage that all quantities are finite and require no further regularization. In this work, we present a method for computing an effective source which is finite and continuous everywhere, and which is valid for a scalar point particle in arbitrary geodesic motion in an arbitrary background spacetime. We explain in detail various technical and practical considerations that underlie its use in several numerical self-force calculations. We consider as examples the cases of a particle in a circular orbit about Schwarzschild and Kerr black holes, and also the case of a particle following a generic time-like geodesic about a highly spinning Kerr black hole. We provide numerical C code for computing an effective source for various orbital configurations about Schwarzschild and Kerr black holes.Comment: 24 pages, 7 figures, final published versio

Chemical constituents of Eremomastax speciosa (Hochst.) Cufod leaves and its cytotoxic potential on NIH-3T3 cells

This study aimed at assessing the cytotoxicity of Eremomastax speciosa crude extract on NIH-3T3 fibroblast cell lines and reporting the chemical constituents in the extract. The MTT assay on NIH-3T3 cells showed a significantly lower (p &lt; 0.05) inhibition from E. speciosa (IC50 &gt; 30 µg/mL) compared to cyclohexamide (IC50 &gt; 0.8 µg/mL). This result validates the non-toxicity observed with the use of E. speciosa on normal cells at low to moderate doses. Four compounds were isolated and identified from their EIMS as well as 1D and 2D NMR spectroscopic data namely hydroxyandrographolide (1), stigmasterol glucoside (2), (Z)-4-coumaric acid 4-O-β-D-apiofuranosyl-(1’’→2’)-O-β-D-glucopyranoside (3) and 5-methoxy-4,4′-di-O-methyl- secolariciresinol-9′-monoacetate (4). These compounds are isolated from this species for the first time. Thirteen volatile constituents were detected in the extract using gas chromatography mass spectrometry (GC-MS). Besides 6,10,14-trimethy-2-pentadecanone (12.63%), mostly fatty acid esters were detected in high amounts notably ethyl hexadecanoate (16.00%), ethyl-9,12,15-octadecatrienoate (11.51%) and 9,12-octadecadienoic acid ethyl ester (8.05%). This study revealed many unsaturated fatty acid esters in E. speciosa and is noteworthy that ω-3 and ω-6 fatty acid esters were predominant, hence an added nutritional value to this plant. &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; KEY WORDS: Eremomastax speciosa, Secondary metabolites, NIH-3T3 cytotoxicity, NMR, GC-MS &nbsp; Bull. Chem. Soc. Ethiop. 2020, 34(3), 633-640. DOI: https://dx.doi.org/10.4314/bcse.v34i3.1