Differential transcriptomic responses to heat stress in surface and subterranean diving beetles

Subterranean habitats are generally very stable environments, and as such evolutionary transitions of organisms from surface to subterranean lifestyles may cause considerable shifts in physiology, particularly with respect to thermal tolerance. In this study we compared responses to heat shock at the molecular level in a geographically widespread, surface-dwelling water beetle to a congeneric subterranean species restricted to a single aquifer (Dytiscidae: Hydroporinae). The obligate subterranean beetle Paroster macrosturtensis is known to have a lower thermal tolerance compared to surface lineages (CTmax 38 °C cf. 42–46 °C), but the genetic basis of this physiological diference has not been characterized. We experimentally manipulated the thermal environment of 24 individuals to demonstrate that both species can mount a heat shock response at high temperatures (35 °C), as determined by comparative transcriptomics. However, genes involved in these responses difer between species and a far greater number were diferentially expressed in the surface taxon, suggesting it can mount a more robust heat shock response; these data may underpin its higher thermal tolerance compared to subterranean relatives. In contrast, the subterranean species examined not only diferentially expressed fewer genes in response to increasing temperatures, but also in the presence of the experimental setup employed here alone. Our results suggest P. macrosturtensis may be comparatively poorly equipped to respond to both thermally induced stress and environmental disturbances more broadly. The molecular fndings presented here have conservation implications for P. macrosturtensis and contribute to a growing narrative concerning weakened thermal tolerances in obligate subterranean organisms at the molecular level.Perry G. Beasley-Hall, Terry Bertozzi, Tessa M. Bradford, Charles S. P. Foster, Karl Jones, Simon M.Tierney, William F. Humphreys, Andrew D.Austin, Steven J. B. Coope

Production of Lambda and Sigma^0 hyperons in proton-proton collisions

This paper reports results on simultaneous measurements of the reaction channels pp -> pK+\Lambda and pp -> pK+\Sigma^0 at excess energies of 204, 239, and 284 MeV (\Lambda) and 127, 162, and 207 MeV (\Sigma^0). Total and differential cross sections are given for both reactions. It is concluded from the measured total cross sections that the high energy limit of the cross section ratio is almost reached at an excess energy of only about 200 MeV. From the differential distributions observed in the overall CMS as well as in the Jackson and helicity frames, a significant contribution of interfering nucleon resonances to the \Lambda production mechanism is concluded while resonant \Sigma^0-production seems to be of lesser importance and takes place only through specific partial waves of the entrance channel. The data also indicate that kaon exchange plays a minor role in the case of \Lambda- but an important role for \Sigma^0-production. Thus the peculiar energy dependence of the \Lambda-to-\Sigma^0 cross section ratio appears in a new light as its explanation requires more than mere differences between the p\Lambda and the p\Sigma^0 final state interaction. The data provide a benchmark for theoretical models already available or yet to come.Comment: 18 pages, 10 figures; accepted by The European Physical Journal A (EPJ A

P-wave excited baryons from pion- and photo-induced hyperon production

We report evidence for $N(1710)P_{11}$, $N(1875)P_{11}$, $N(1900)P_{13}$, $\Delta(1600)P_{33}$, $\Delta(1910)P_{31}$, and $\Delta(1920)P_{33}$, and find indications that $N(1900)P_{13}$ might have a companion state at 1970\,MeV. The controversial $\Delta(1750)P_{31}$ is not seen. The evidence is derived from a study of data on pion- and photo-induced hyperon production, but other data are included as well. Most of the resonances reported here were found in the Karlsruhe-Helsinki (KH84) and the Carnegie-Mellon (CM) analyses but were challenged recently by the Data Analysis Center at GWU. Our analysis is constrained by the energy independent $\pi N$ scattering amplitudes from either KH84 or GWU. The two $\pi N$ amplitudes from KH84 or GWU, respectively, lead to slightly different $\pi N$ branching ratios of contributing resonances but the debated resonances are required in both series of fits.Comment: 22 pages, 28 figures. Some additional sets of data are adde

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Nucleon resonances in the fourth resonance region

Nucleon and $\Delta$ resonances in the fourth resonance region are studied in a multichannel partial-wave analysis which includes nearly all available data on pion- and photo-induced reactions off protons. In the high-mass range, above 1850\,MeV, several alternative solutions yield a good description of the data. For these solutions, masses, widths, pole residues and photo-couplings are given. In particular, we find evidence for nucleon resonances with spin-parities $J^P=1/2^+...7/2^+$. For one set of solutions, there are four resonances forming naturally a spin-quartet of resonances with orbital angular momentum L=2 and spin S=3/2 coupling to $J=1/2,...,7/2$. Just below 1.9\,GeV we find a spin doublet of resonances with $J^P=1/2^-$ and $3/2^-$. Since a spin partner with $J^P=5/2^-$ is missing at this mass, the two resonances form a spin doublet which must have a symmetric orbital-angular-momentum wave function with L=1. For another set of solutions, the four positive-parity resonances are accompanied by mass-degenerate negative-parity partners -- as suggested by the conjecture of chiral symmetry restoration. The possibility of a $J^P=1/2^+, 3/2^+$ spin doublet at 1900\,MeV belonging to a 20-plet is discussed.Comment: 16 page

Properties of baryon resonances from a multichannel partial wave analysis

Properties of nucleon and $\Delta$ resonances are derived from a multichannel partial wave analysis. The statistical significance of pion and photo-induced inelastic reactions off protons are studied in a multichannel partial-wave analysis.Comment: 12 pages, 8 Table

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy