A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia

In resolving the vertebrate tree of life, two fundamental questions remain: 1) what is the phylogenetic position of turtles within amniotes, and 2) what are the relationships between the three major lissamphibian (extant amphibian) groups? These relationships have historically been difficult to resolve, with five different hypotheses proposed for turtle placement, and four proposed branching patterns within Lissamphibia. We compiled a large cDNA/EST dataset for vertebrates (75 genes for 129 taxa) to address these outstanding questions. Gene-specific phylogenetic analyses revealed a great deal of variation in preferred topology, resulting in topologically ambiguous conclusions from the combined dataset. Due to consistent preferences for the same divergent topologies across genes, we suspected systematic phylogenetic error as a cause of some variation. Accordingly, we developed and tested a novel statistical method that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship. After removing putatively biased sites, support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia, with Lissamphibia potentially paraphyletic.Organismic and Evolutionary Biolog

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

<p>Abstract</p> <p>Background</p> <p>The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT) is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes.</p> <p>Results</p> <p>PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function.</p> <p>Conclusion</p> <p>PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any web browser with no client side software setup or installation required. Source code is freely available to researchers interested in setting up a local version of PSAT for analysis of genomes not available through the public server. Access to the public web server and instructions for obtaining source code can be found at <url>http://www.nwrce.org/psat</url>.</p

Topological kink plasmons on magnetic-domain boundaries.

Two-dimensional topological materials bearing time reversal-breaking magnetic fields support protected one-way edge modes. Normally, these edge modes adhere to physical edges where material properties change abruptly. However, even in homogeneous materials, topology still permits a unique form of edge modes - kink modes - residing at the domain boundaries of magnetic fields within the materials. This scenario, despite being predicted in theory, has rarely been demonstrated experimentally. Here, we report our observation of topologically-protected high-frequency kink modes - kink magnetoplasmons (KMPs) - in a GaAs/AlGaAs two-dimensional electron gas (2DEG) system. These KMPs arise at a domain boundary projected from an externally-patterned magnetic field onto a uniform 2DEG. They propagate unidirectionally along the boundary, protected by a difference of gap Chern numbers ([Formula: see text]) in the two domains. They exhibit large tunability under an applied magnetic field or gate voltage, and clear signatures of nonreciprocity even under weak-coupling to evanescent photons

Simultaneous Measurement of the Dissolution Kinetics of Responsive DNA Hydrogels at Multiple Length Scales

Recent years have seen increasing study of stimulus-responsive hydrogels constructed from aptamer-connected DNA building blocks. Presumably due to a lack of simple, quantitative tools with which to measure gel responsiveness, however, the literature describing these materials is largely qualitative. In response we demonstrate here simple, time-resolved, multiscale methods for measuring the response kinetics of these materials. Specifically, by employing trace amounts of fluorophore-quencher labeled crosslinkers and the rheology of entrapped fluorescent particles we simultaneously measure dissolution at molecular, hundred-nanometer, and hundred-micron length-scales. For our test-bed system, an adenine-responsive hydrogel, we find biphasic response kinetics dependent on both effector concentration and depth within the gel and a dissolution pattern uniform at scales longer than a few times the monomer-monomer distance. Likewise, we find that, in agreement with theoretical predictions, dissolution kinetics over the hundred nanometer length scale exhibit a power-law-like dependence on the fraction of disrupted crosslinks before a distinct crossover from solid-like to liquid-like behavio

Effectiveness of Switching Smoking-Cessation Medications Following Relapse

Introduction—Nicotine dependence is a chronic disorder often characterized by multiple failed quit attempts (QAs). Yet, little is known about the sequence of methods used across multiple QAs or how this may impact future ability to abstain from smoking. This prospective cohort study examines the effectiveness of switching smoking-cessation medications (SCMs) across multiple QAs. Methods—Adult smokers (aged ≥ 18 years) participating in International Tobacco Control surveys in the United Kingdom, U.S., Canada, and Australia (N=795) who: (1) completed two consecutive surveys between 2006 and 2011; (2) initiated a QA at least 1 month before each survey; and (3) provided data for the primary predictor (SCM use during most recent QA), outcome (1-month point prevalence abstinence), and relevant covariates. Analyses were conducted in 2016. Results—Five SCM user classifications were identified: (1) non-users (43.5%); (2) early users (SCM used for initial, but not subsequent QA; 11.4%); (3) later users (SCM used for subsequent, but not initial QA; 18.4%); (4) repeaters (same SCM used for both QAs; 10.7%); and (5) switchers (different SCM used for each QA; 14.2%). Abstinence rates were lower for non-users (15.9%, OR=0.48, p=0.002), early users (16.6%, OR=0.27, p=0.03), and repeaters (12.4%, OR=0.36, p=0.004) relative to switchers (28.5%). Conclusions—Findings suggest smokers will be more successful if they use a SCM in QAs and vary the SCM they use across time. That smokers can increase their odds of quitting by switching SCMs is an important message that could be communicated to smokers

An instrument for in situ time-resolved X-ray imaging and diffraction of laser powder bed fusion additive manufacturing processes

In situ X-ray-based measurements of the laser powder bed fusion (LPBF) additive manufacturing process produce unique data for model validation and improved process understanding. Synchrotron X-ray imaging and diffraction provide high resolution, bulk sensitive information with sufficient sampling rates to probe melt pool dynamics as well as phase and microstructure evolution. Here, we describe a laboratory-scale LPBF test bed designed to accommodate diffraction and imaging experiments at a synchrotron X-ray source during LPBF operation. We also present experimental results using Ti-6Al-4V, a widely used aerospace alloy, as a model system. Both imaging and diffraction experiments were carried out at the Stanford Synchrotron Radiation Lightsource. Melt pool dynamics were imaged at frame rates up to 4 kHz with a ∼1.1 μm effective pixel size and revealed the formation of keyhole pores along the melt track due to vapor recoil forces. Diffraction experiments at sampling rates of 1 kHz captured phase evolution and lattice contraction during the rapid cooling present in LPBF within a ∼50 × 100 μm area. We also discuss the utility of these measurements for model validation and process improvement

Annual cycle observations of aerosols capable of ice formation in central Arctic clouds

The Arctic is warming faster than anywhere else on Earth, prompting glacial melt, permafrost thaw, and sea ice decline. These severe consequences induce feedbacks that contribute to amplified warming, affecting weather and climate globally. Aerosols and clouds play a critical role in regulating radiation reaching the Arctic surface. However, the magnitude of their effects is not adequately quantified, especially in the central Arctic where they impact the energy balance over the sea ice. Specifically, aerosols called ice nucleating particles (INPs) remain understudied yet are necessary for cloud ice production and subsequent changes in cloud lifetime, radiative effects, and precipitation. Here, we report observations of INPs in the central Arctic over a full year, spanning the entire sea ice growth and decline cycle. Further, these observations are size-resolved, affording valuable information on INP sources. Our results reveal a strong seasonality of INPs, with lower concentrations in the winter and spring controlled by transport from lower latitudes, to enhanced concentrations of INPs during the summer melt, likely from marine biological production in local open waters. This comprehensive characterization of INPs will ultimately help inform cloud parameterizations in models of all scales

Universal logic with encoded spin qubits in silicon

Qubits encoded in a decoherence-free subsystem and realized in exchange-coupled silicon quantum dots are promising candidates for fault-tolerant quantum computing. Benefits of this approach include excellent coherence, low control crosstalk, and configurable insensitivity to certain error sources. Key difficulties are that encoded entangling gates require a large number of control pulses and high-yielding quantum dot arrays. Here we show a device made using the single-layer etch-defined gate electrode architecture that achieves both the required functional yield needed for full control and the coherence necessary for thousands of calibrated exchange pulses to be applied. We measure an average two-qubit Clifford fidelity of $97.1 \pm 0.2\%$ with randomized benchmarking. We also use interleaved randomized benchmarking to demonstrate the controlled-NOT gate with $96.3 \pm 0.7\%$ fidelity, SWAP with $99.3 \pm 0.5\%$ fidelity, and a specialized entangling gate that limits spreading of leakage with $93.8 \pm 0.7\%$ fidelity

Subsurface Cooling Rates and Microstructural Response during Laser Based Metal Additive Manufacturing

Laser powder bed fusion (LPBF) is a method of additive manufacturing characterized by the rapid scanning of a high powered laser over a thin bed of metallic powder to create a single layer, which may then be built upon to form larger structures. Much of the melting, resolidification, and subsequent cooling take place at much higher rates and with much higher thermal gradients than in traditional metallurgical processes, with much of this occurring below the surface. We have used in situ high speed X-ray diffraction to extract subsurface cooling rates following resolidification from the melt and above the β-transus in titanium alloy Ti-6Al-4V. We observe an inverse relationship with laser power and bulk cooling rates. The measured cooling rates are seen to correlate to the level of residual strain borne by the minority β-Ti phase with increased strain at slower cooling rates. The α-Ti phase shows a lattice contraction which is invariant with cooling rate. We also observe a broadening of the diffraction peaks which is greater for the β-Ti phase at slower cooling rates and a change in the relative phase fraction following LPBF. These results provide a direct measure of the subsurface thermal history and demonstrate its importance to the ultimate quality of additively manufactured materials