FAST: FAST Analysis of Sequences Toolbox.

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought

On the emergence of the Λ{\bf\Lambda}CDM model from self-interacting Brans-Dicke theory in d=5{\bf d= 5}

We investigate whether a self-interacting Brans-Dicke theory in $d=5$ without matter and with a time-dependent metric can describe, after dimensional reduction to $d=4$, the FLRW model with accelerated expansion and non-relativistic matter. By rewriting the effective 4-dimensional theory as an autonomous three-dimensional dynamical system and studying its critical points, we show that the $\Lambda$CDM cosmology cannot emerge from such a model. This result suggests that a richer structure in $d=5$ may be needed to obtain the accelerated expansion as well as the matter content of the 4-dimensional universe.Comment: 7 pages, 7 figure

RNA Sequencing Reveals Novel Transcripts from Sympathetic Stellate Ganglia During Cardiac Sympathetic Hyperactivity.

Cardiovascular disease is the most prevalent age-related illness worldwide, causing approximately 15 million deaths every year. Hypertension is central in determining cardiovascular risk and is a strong predictive indicator of morbidity and mortality; however, there remains an unmet clinical need for disease-modifying and prophylactic interventions. Enhanced sympathetic activity is a well-established contributor to the pathophysiology of hypertension, however the cellular and molecular changes that increase sympathetic neurotransmission are not known. The aim of this study was to identify key changes in the transcriptome in normotensive and spontaneously hypertensive rats. We validated 15 of our top-scoring genes using qRT-PCR, and network and enrichment analyses suggest that glutamatergic signalling plays a key role in modulating Ca2+ balance within these ganglia. Additionally, phosphodiesterase activity was found to be altered in stellates obtained from the hypertensive rat, suggesting that impaired cyclic nucleotide signalling may contribute to disturbed Ca2+ homeostasis and sympathetic hyperactivity in hypertension. We have also confirmed the presence of these transcripts in human donor stellate samples, suggesting that key genes coupled to neurotransmission are conserved. The data described here may provide novel targets for future interventions aimed at treating sympathetic hyperactivity associated with cardiovascular disease and other dysautonomias

Lifshitz-Slyozov Scaling For Late-Stage Coarsening With An Order-Parameter-Dependent Mobility

The coarsening dynamics of the Cahn-Hilliard equation with order-parameter dependent mobility, $\lambda(\phi) \propto (1-\phi^2)^\alpha$, is addressed at zero temperature in the Lifshitz-Slyozov limit where the minority phase occupies a vanishingly small volume fraction. Despite the absence of bulk diffusion for $\alpha>0$, the mean domain size is found to grow as $\propto t^{1/(3+\alpha)}$, due to subdiffusive transport of the order parameter through the majority phase. The domain-size distribution is determined explicitly for the physically relevant case $\alpha = 1$.Comment: 4 pages, Revtex, no figure

Defect and solute properties in dilute Fe-Cr-Ni austenitic alloys from first principles

We present results of an extensive set of first-principles density functional theory calculations of point defect formation, binding and clustering energies in austenitic Fe with dilute concentrations of Cr and Ni solutes.Comment: 24 pages, 10 figures, published in Phys. Rev.

A Single Cell Transcriptomics Map of Paracrine Networks in the Intrinsic Cardiac Nervous System

We developed a spatially-tracked single neuron transcriptomics map of an intrinsic cardiac ganglion, the right atrial ganglionic plexus (RAGP) that is a critical mediator of sinoatrial node (SAN) activity. This 3D representation of RAGP used neuronal tracing to extensively map the spatial distribution of the subset of neurons that project to the SAN. RNA-seq of laser capture microdissected neurons revealed a distinct composition of RAGP neurons compared to the central nervous system and a surprising finding that cholinergic and catecholaminergic markers are coexpressed, suggesting multipotential phenotypes that can drive neuroplasticity within RAGP. High-throughput qPCR of hundreds of laser capture microdissected single neurons confirmed these findings and revealed a high dimensionality of neuromodulatory factors that contribute to dynamic control of the heart. Neuropeptide-receptor coexpression analysis revealed a combinatorial paracrine neuromodulatory network within RAGP informing follow-on studies on the vagal control of RAGP to regulate cardiac function in health and disease

Thinking the unthinkable: Imagining an ‘un-American,’ Girl-friendly, Women- and Trans-Inclusive Alternative for Baseball

The purpose of this article is twofold: to capture the injustice inherent in the gendered bifurcation of baseball and softball via the prism of critical feminist sport studies; and to begin to imagine a girl-friendly/women-and trans-inclusive future for baseball that is less fertile for cooptation into post-911 United States security state discourses. In this article I link the "unthinkability" of the occupational segregation of baseball in North America to the dominance of the ideology of the two sex system and European disasporic morality. To illustrate the extent of this occupational segregation via the gendered bifurcation of baseball and softball, I draw on feminist sport studies to examine the exemplars or "texts" of three Canadian brother/sister baseball softball duos: Jason Bay and Lauren Bay Regula; Brett and Danielle Lawrie; and Mathew and Katie Reyes

Change of tRNA identity leads to a divergent orthogonal histidyl-tRNA synthetase/tRNAHis pair

Mature tRNAHis has at its 5′-terminus an extra guanylate, designated as G−1. This is the major recognition element for histidyl-tRNA synthetase (HisRS) to permit acylation of tRNAHis with histidine. However, it was reported that tRNAHis of a subgroup of α-proteobacteria, including Caulobacter crescentus, lacks the critical G−1 residue. Here we show that recombinant C. crescentus HisRS allowed complete histidylation of a C. crescentus tRNAHis transcript (lacking G−1). The addition of G−1 did not improve aminoacylation by C. crescentus HisRS. However, mutations in the tRNAHis anticodon caused a drastic loss of in vitro histidylation, and mutations of bases A73 and U72 also reduced charging. Thus, the major recognition elements in C. crescentus tRNAHis are the anticodon, the discriminator base and U72, which are recognized by the divergent (based on sequence similarity) C. crescentus HisRS. Transplantation of these recognition elements into an Escherichia coli tRNAHis template, together with addition of base U20a, created a competent substrate for C. crescentus HisRS. These results illustrate how a conserved tRNA recognition pattern changed during evolution. The data also uncovered a divergent orthogonal HisRS/tRNAHis pair

Spinal neuromodulation mitigates myocardial ischemia-induced sympathoexcitation by suppressing the intermediolateral nucleus hyperactivity and spinal neural synchrony

IntroductionMyocardial ischemia disrupts the cardio-spinal neural network that controls the cardiac sympathetic preganglionic neurons, leading to sympathoexcitation and ventricular tachyarrhythmias (VTs). Spinal cord stimulation (SCS) is capable of suppressing the sympathoexcitation caused by myocardial ischemia. However, how SCS modulates the spinal neural network is not fully known.MethodsIn this pre-clinical study, we investigated the impact of SCS on the spinal neural network in mitigating myocardial ischemia-induced sympathoexcitation and arrhythmogenicity. Ten Yorkshire pigs with left circumflex coronary artery (LCX) occlusion-induced chronic myocardial infarction (MI) were anesthetized and underwent laminectomy and a sternotomy at 4−5 weeks post-MI. The activation recovery interval (ARI) and dispersion of repolarization (DOR) were analyzed to evaluate the extent of sympathoexcitation and arrhythmogenicity during the left anterior descending coronary artery (LAD) ischemia. Extracellular in vivo and in situ spinal dorsal horn (DH) and intermediolateral column (IML) neural recordings were performed using a multichannel microelectrode array inserted at the T2-T3 segment of the spinal cord. SCS was performed for 30 min at 1 kHz, 0.03 ms, 90% motor threshold. LAD ischemia was induced pre- and 1 min post-SCS to investigate how SCS modulates spinal neural network processing of myocardial ischemia. DH and IML neural interactions, including neuronal synchrony as well as cardiac sympathoexcitation and arrhythmogenicity markers were evaluated during myocardial ischemia pre- vs. post-SCS.ResultsARI shortening in the ischemic region and global DOR augmentation due to LAD ischemia was mitigated by SCS. Neural firing response of ischemia-sensitive neurons during LAD ischemia and reperfusion was blunted by SCS. Further, SCS showed a similar effect in suppressing the firing response of IML and DH neurons during LAD ischemia. SCS exhibited a similar suppressive impact on the mechanical, nociceptive and multimodal ischemia sensitive neurons. The LAD ischemia and reperfusion-induced augmentation in neuronal synchrony between DH-DH and DH-IML pairs of neurons were mitigated by the SCS.DiscussionThese results suggest that SCS is decreasing the sympathoexcitation and arrhythmogenicity by suppressing the interactions between the spinal DH and IML neurons and activity of IML preganglionic sympathetic neurons

Searches for exclusive Higgs and Z boson decays into J/ψγ,ψ(2S)γ,and Υ(nS)γ at √s=13 TeV with the ATLAS detector

Searches for the exclusive decays of the Higgs and Z bosons into a J/ψ,ψ(2S), or Υ(nS)(n=1,2,3) meson and a photon are performed with a pp collision data sample corresponding to an integrated luminosity of 36.1 fb −1 collected at √s =13 TeV with the ATLAS detector at the CERN Large Hadron Collider. No significant excess of events is observed above the expected backgrounds, and 95% confidence-level upper limits on the branching fractions of the Higgs boson decays to J/ψγ, ψ(2S)γ,and Υ(nS)γ of 3.5×10 −4, 2.0×10−3,and(4.9,5.9,5.7)×10 −4,respectively, are obtained assuming Standard Model production. The corresponding 95% confidence-level upper limits for the branching fractions of the Z boson decays are 2.3×10 −6, 4.5×10 −6 and (2.8,1.7,4.8)×10 −6, respectively