Parameters and Predictions for the Long-Period Transiting Planet HD 17156b

We report high-cadence time-series photometry of the recently-discovered transiting exoplanet system HD 17156, spanning the time of transit on UT 2007 October 1, from three separate observatories. We present a joint analysis of our photometry, previously published radial velocity measurements, and times of transit center for 3 additional events. Adopting the spectroscopically-determined values and uncertainties for the stellar mass and radius, we estimate a planet radius of Rp = 1.01 +/- 0.09 RJup and an inclination of i = 86.5 +1.1 -0.7 degrees. We find a time of transit center of Tc = 2454374.8338 +/- 0.0020 HJD and an orbital period of P = 21.21691 +/- 0.00071 days, and note that the 4 transits reported to date show no sign of timing variations that would indicate the presence of a third body in the system. Our results do not preclude the existence of a secondary eclipse, but imply there is only a 9.2% chance for this to be present, and an even lower probability (6.9%) that the secondary eclipse would be a non-grazing event. Due to its eccentric orbit and long period, HD 17156b is a fascinating object for the study of the dynamics of exoplanet atmospheres. To aid such future studies, we present theoretical light curves for the variable infrared emission from the visible hemisphere of the planet throughout its orbit.Comment: 8 pages, 4 figures, 1 table, emulateapj format. v2: accepted for publication in ApJ, minor changes. Changed to emulateapj to save the rainforest

Single-nucleus RNA sequencing of pre-malignant liver reveals disease-associated hepatocyte state with HCC prognostic potential

Current approaches to staging chronic liver diseases have limited utility for predicting liver cancer risk. Here, we employed single-nucleus RNA sequencing (snRNA-seq) to characterize the cellular microenvironment of healthy and pre-malignant livers using two distinct mouse models. Downstream analyses unraveled a previously uncharacterized disease-associated hepatocyte (daHep) transcriptional state. These cells were absent in healthy livers but increasingly prevalent as chronic liver disease progressed. Copy number variation (CNV) analysis of microdissected tissue demonstrated that daHep-enriched regions are riddled with structural variants, suggesting these cells represent a pre-malignant intermediary. Integrated analysis of three recent human snRNA-seq datasets confirmed the presence of a similar phenotype in human chronic liver disease and further supported its enhanced mutational burden. Importantly, we show that high daHep levels precede carcinogenesis and predict a higher risk of hepatocellular carcinoma development. These findings may change the way chronic liver disease patients are staged, surveilled, and risk stratified

Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

<p>Abstract</p> <p>Background</p> <p>Cucumber, <it>Cucumis sativus </it>L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line '9930' and the North American pickling type inbred line 'Gy14'. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber.</p> <p>Results</p> <p>A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The <it>in silico </it>PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newly-discovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available.</p> <p>Conclusions</p> <p>The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.</p

Preliminary Confinement Studies during ECRH in TCV

Within the range of plasma shapes and plasma currents investigated, the electron confinement time, Tau_E increases with density, elongation and negative triangularity (-0.4<delta<+0.4), similar to Ohmic heating (in these low density discharges). In addition, TauEe increases with q_a up to q_a~5 after which it decreases. There is little dependence of TauEe on the heating location provided it is inside the q= I surface. As the heating location is moved outside the q=l surface, TauEe decreases. This may be the explanation of the observed decrease in TauEe at high q_a. The power-induced degradation exponent found is generally as expected: alpaha_P = -0.5

EFFECT OF LOCALISED ELECTRON CYCLOTRON HEATING ON ENERGY CONFINEMENT AND MHD IN TCV

Within the range of plasma shapes and plasma currents investigated, the electron confinement time, tau_Ee, increases with safety factor, density and negative triangularity similar to the Ohmic heating case. There is little dependence of tau_Ee on the heating location provided power deposition occurs inside the q=1 surface; as power deposition moves out of the inversion surface, tau_Ee decreases. The power-induced energy confinement degradation exponent (tau_Ee~PaP) is as usual: alpha_P ~-0.5. As a general trend, central relaxations decrease in amplitude with increasing qa, P_EC, or negative delta, in a situation where the confinement time increases

The Murchison Widefield Array: The Square Kilometre Array Precursor at Low Radio Frequencies

The Murchison Widefield Array (MWA) is one of three Square Kilometre Array Precursor telescopes and is located at the Murchison Radio-astronomy Observatory in the Murchison Shire of the mid-west of Western Australia, a location chosen for its extremely low levels of radio frequency interference. The MWA operates at low radio frequencies, 80–300 MHz, with a processed bandwidth of 30.72 MHz for both linear polarisations, and consists of 128 aperture arrays (known as tiles) distributed over a ~3-km diameter area. Novel hybrid hardware/software correlation and a real-time imaging and calibration systems comprise the MWA signal processing backend. In this paper, the as-built MWA is described both at a system and sub-system level, the expected performance of the array is presented, and the science goals of the instrument are summarised

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant