The Effects of Thermonuclear Reaction Rate Variations on Nova Nucleosynthesis: A Sensitivity Study

We investigate the effects of thermonuclear reaction rate uncertainties on nova nucleosynthesis. One-zone nucleosynthesis calculations have been performed by adopting temperature-density-time profiles of the hottest hydrogen-burning zone (i.e., the region in which most of the nucleosynthesis takes place). We obtain our profiles from 7 different, recently published, hydrodynamic nova simulations covering peak temperatures in the range from Tpeak=0.145-0.418 GK. For each of these profiles, we individually varied the rates of 175 reactions within their associated errors and analyzed the resulting abundance changes of 142 isotopes in the mass range below A=40. In total, we performed 7350 nuclear reaction network calculations. We use the most recent thermonuclear reaction rate evaluations for the mass ranges A=1-20 and A=20-40. For the theoretical astrophysicist, our results indicate the extent to which nova nucleosynthesis calculations depend on presently uncertain nuclear physics input, while for the experimental nuclear physicist our results represent at least a qualitative guide for future measurements at stable and radioactive ion beam facilities. We find that present reaction rate estimates are reliable for predictions of Li, Be, C and N abundances in nova nucleosynthesis. However, rate uncertainties of several reactions have to be reduced significantly in order to predict more reliable O, F, Ne, Na, Mg, Al, Si, S, Cl and Ar abundances. Results are presented in tabular form for each adopted nova simulation.Comment: Accepted for publication in The Astrophysical Journal Suppl. Serie

JWST/MIRI Spectroscopy of the Disk of the Young Eruptive Star EX Lup in Quiescence

EX Lup is a low-mass pre-main sequence star that occasionally shows accretion-related outbursts. Here, we present JWST/MIRI medium resolution spectroscopy obtained for EX Lup fourteen years after its powerful outburst. EX Lup is now in quiescence and displays a Class II spectrum. We detect a forest of emission lines from molecules previously identified in infrared spectra of classical T Tauri disks: H2O, OH, H2, HCN, C2H2, and CO2. The detection of organic molecules demonstrates that they are back after disappearing during the large outburst. Spectral lines from water and OH are for the first time de-blended and will provide a much improved characterization of their distribution and density in the inner disk. The spectrum also shows broad emission bands from warm, sub-micron size amorphous silicate grains at 10 and 18 um. During the outburst, in 2008, crystalline forsterite grains were annealed in the inner disk within 1 au, but their spectral signatures in the 10 um silicate band later disappeared. With JWST we re-discovered these crystals via their 19.0, 20.0, and 23.5 um emission, whose strength implies that the particles are at ~3 au from the star. This suggests that crystalline grains formed in 2008 were transported outwards and now approach the water snowline, where they may be incorporated into planetesimals. Containing several key tracers of planetesimal and planet formation, EX Lup is an ideal laboratory to study the effects of variable luminosity on the planet-forming material and may provide explanation for the observed high crystalline fraction in solar system comets.Comment: 9 pages, 4 figures, accepted for publication in ApJL. JWST/MIRI spectrum is available for download at https://tinyurl.com/spexodisksJWS

Time evolution of 1D gapless models from a domain-wall initial state: SLE continued?

We study the time evolution of quantum one-dimensional gapless systems evolving from initial states with a domain-wall. We generalize the path-integral imaginary time approach that together with boundary conformal field theory allows to derive the time and space dependence of general correlation functions. The latter are explicitly obtained for the Ising universality class, and the typical behavior of one- and two-point functions is derived for the general case. Possible connections with the stochastic Loewner evolution are discussed and explicit results for one-point time dependent averages are obtained for generic \kappa for boundary conditions corresponding to SLE. We use this set of results to predict the time evolution of the entanglement entropy and obtain the universal constant shift due to the presence of a domain wall in the initial state.Comment: 27 pages, 10 figure

Viridot: An automated virus plaque (immunofocus) counter for the measurement of serological neutralizing responses with application to dengue virus.

The gold-standard method for quantifying neutralizing antibody responses to many viruses, including dengue virus (DENV), is the plaque reduction neutralization test (PRNT, also called the immunofocus reduction neutralization test). The PRNT conducted on 96-well plates is high-throughput and requires a smaller volume of antiserum than on 6- or 24-well plates, but manual plaque counting is challenging and existing automated plaque counters are expensive or difficult to optimize. We have developed Viridot (Viridot package), a program for R with a user interface in shiny, that counts viral plaques of a variety of phenotypes, estimates neutralizing antibody titers, and performs other calculations of use to virologists. The Viridot plaque counter includes an automatic parameter identification mode (misses <10 plaques/well for 87% of diverse DENV strains [n = 1521]) and a mode that allows the user to fine-tune the parameters used for counting plaques. We compared standardized manual and Viridot plaque counting methods applied to the same wells by two analyses and found that Viridot plaque counts were as similar to the same analyst's manual count (Lin's concordance correlation coefficient, ρc = 0.99 [95% confidence interval: 0.99-1.00]) as manual counts between analysts (ρc = 0.99 [95% CI: 0.98-0.99]). The average ratio of neutralizing antibody titers based on manual counted plaques to Viridot counted plaques was 1.05 (95% CI: 0.98-1.14), similar to the average ratio of antibody titers based on manual plaque counts by the two analysts (1.06 [95% CI: 0.84-1.34]). Across diverse DENV and ZIKV strains (n = 14), manual and Viridot plaque counts were mostly consistent (range of ρc = 0.74 to 1.00) and the average ratio of antibody titers based on manual and Viridot counted plaques was close to 1 (0.94 [0.86-1.02]). Thus, Viridot can be used for plaque counting and neutralizing antibody titer estimation of diverse DENV strains and potentially other viruses on 96-well plates as well as for formalization of plaque-counting rules for standardization across experiments and analysts

The Cuprous-Cupric Complex in Hydrochloric Acid Solution

In the process described by Diehl and Brouns (1) for the direct determination of copper in bronze by electrodeposition from hydrochloric acid solution using hydroxylammonium chloride as anodic depolarizer and controlling the cathode potential automatically (3), the sample of bronze is dissolved in hydrochloric acid by the dropwise addition of nitric acid or of hydrogen peroxide. Subsequently the solution is diluted and electrolyzed, the cathode reaction being· first the reduction of cupric ion to the chlorocuprous ion, CuCl3==, and then the deposition of copper. The time of electrolysis can be materially shortened if the first reduction is effected chemically, by the addition of hydrocxylammonium chloride or of stannous chloride. If the reducing agent be added to the solution before it is diluted, that is, to a fairly concentrated hydrochloric acid solution, the solution turns dark brown or black, the color being due to some material in solution which disappears on dilution. It became of interest to learn more of this dark colored solution, particularly since it was observed that a small amount of antimony did or did not deposit with the copper depending on whether the reduction was made before or after the dilution

An Open-System Quantum Simulator with Trapped Ions

The control of quantum systems is of fundamental scientific interest and promises powerful applications and technologies. Impressive progress has been achieved in isolating the systems from the environment and coherently controlling their dynamics, as demonstrated by the creation and manipulation of entanglement in various physical systems. However, for open quantum systems, engineering the dynamics of many particles by a controlled coupling to an environment remains largely unexplored. Here we report the first realization of a toolbox for simulating an open quantum system with up to five qubits. Using a quantum computing architecture with trapped ions, we combine multi-qubit gates with optical pumping to implement coherent operations and dissipative processes. We illustrate this engineering by the dissipative preparation of entangled states, the simulation of coherent many-body spin interactions and the quantum non-demolition measurement of multi-qubit observables. By adding controlled dissipation to coherent operations, this work offers novel prospects for open-system quantum simulation and computation.Comment: Pre-review submission to Nature. For an updated and final version see publication. Manuscript + Supplementary Informatio

CLO: The cell line ontology

Abstract Background Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions. Construction and content Collaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as ‘cell line’, ‘cell line cell’, ‘cell line culturing’, and ‘mortal’ vs. ‘immortal cell line cell’. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The new hierarchical structure makes it easier to browse, query, and perform automated classification. We have recently added classes representing more than 2,000 cell line cells from the RIKEN BRC Cell Bank to CLO. Overall, the CLO now contains ~38,000 classes of specific cell line cells derived from over 200 in vivo cell types from various organisms. Utility and discussion The CLO has been applied to different biomedical research studies. Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO’s utility goes beyond a catalogue of cell line types. The alignment of the CLO with related ontologies combined with the use of ontological reasoners will support sophisticated inferencing to advance translational informatics development.http://deepblue.lib.umich.edu/bitstream/2027.42/109554/1/13326_2013_Article_185.pd

Multicentric assessment of safety and efficacy of combinatorial adjuvant brain metastasis treatment by intraoperative radiotherapy and immunotherapy

Purpose Following surgical resection of brain metastases (BMs), intraoperative radiation therapy (IORT) provides a promising alternative to adjuvant external beam radiation therapy (EBRT) by enabling superior organ at risk preservation, reduction of in-hospital times and timely admission to subsequent systemic treatments, which increasingly comprise novel targeted immunotherapeutic approaches. We sought to assess safety and efficacy of IORT in combination with immune checkpoint inhibitors (ICIs) and other targeted therapies (TTs). Methods In a multicentric approach incorporating individual patient data from six international IORT centers, all patients with BMs undergoing IORT were retrospectively assessed for combinatorial treatment with ICIs/TTs and evaluated for toxicity and cumulative rates, including wound dehiscence, radiation necrosis (RN), leptomeningeal spread (LMS), local control (LC), distant brain progression (DBP) and estimated overall survival (OS). Results A total of 103 lesions with a median diameter of 34 mm receiving IORT combined with immunomodulatory systemic treatment or other TTs were included. The median follow up was 13.2 (1.2-102.4) months and the median IORT dose was 25 (18-30) Gy prescribed to the applicator surface. There was one grade 3 adverse event related to IORT recorded (2.2%). A 4.9% cumulative RN rate was observed. The 1-year LCR was 98.0% and the 1-year DBP-free rate 60.0%. Median time to DBP was 5.5 (1.0-18.5) months in the subgroup of patients experiencing DBP and the cumulative LMS rate was 4.9%. The median estimated OS was 26 (1.2-not reached) months with a 1-year survival rate of 74.0%. Early initiation of IT/TT was associated with a non-significant trend towards improved DBP rate and OS. Conclusion The combination of ICIs/TT with IORT for resected BMs does not seem to increase toxicity, while yielding encouraging local control outcomes in the difficult-to-treat subgroup of larger BMs. Time gaps between surgery and systemic treatment could be shortened or avoided. The definitive role of IORT in local control after BM resection will be defined in a prospective trial

Signatures of a dissipative phase transition in photon correlation measurements

This work was supported by the Swiss National Science Foundation (SNSF) through the National Centre of Competence in Research - Quantum Science and Technology (NCCR QSIT). A.S., C.S., and S.H. acknowledge support by the State of Bavaria and the DFG within the Project Schn1376/3-1.Understanding and characterizing phase transitions in driven-dissipative systems constitutes a new frontier for many-body physics[1-8]. A generic feature of dissipative phase transitions is a vanishing gap in the Liouvillian spectrum [9], which leads to long-lived deviations from the steady state as the system is driven towards the transition. Here, we show that photon correlation measurements can be used to characterize the corresponding critical slowing down of non-equilibrium dynamics. We focus on the extensively studied phenomenon of optical bistability in GaAs cavity polaritons [10,11], which can be described as a first-order dissipative phase transition [12-14]. Increasing the excitation strength towards the bistable range results in an increasing photon-bunching signal along with a decay time that is prolonged by more than nine orders of magnitude as compared with that of single polaritons. In the limit of strong polariton interactions leading to pronounced quantum fluctuations, the mean-field bistability threshold is washed out. Nevertheless, the functional form with which the Liouvillian gap closes as the thermodynamic limit is approached provides a signature of the emerging dissipative phase transition. Our results establish photon correlation measurements as an invaluable tool for studying dynamical properties of dissipative phase transitions without requiring phase-sensitive interferometric measurements.PostprintPeer reviewe

Thyroid hormone receptor alpha modulates fibrogenesis in hepatic stellate cells

Objective: Progressive hepatic fibrosis can be considered the final stage of chronic liver disease. Hepatic stellate cells (HSC) play a central role in liver fibrogenesis. Thyroid hormones (TH, e.g. thyroxine; T4 and triiodothyronine; T3) significantly affect development, growth, cell differentiation and metabolism through activation of TH receptor α and/or β (TRα/β). Here, we evaluated the influence of TH in hepatic fibrogenesis. Design: Human liver tissue was obtained from explanted livers following transplantation. TRα-deficient (TRα-KO) and wild-type (WT) mice were fed a control or a profibrogenic methionine-choline deficient (MCD) diet. Liver tissue was assessed by qRT-PCR for fibrogenic gene expression. In vitro, HSC were treated with TGFβ in the presence or absence of T3. HSC with stable TRα knockdown and TRα deficient mouse embryonic fibroblasts (MEF) were used to determine receptor-specific function. Activation of HSC and MEF was assessed using the wound healing assay, Western blotting, and qRT-PCR. Results: TRα and TRβ expression is downregulated in the liver during hepatic fibrogenesis in humans and mice. TRα represents the dominant isoform in HSC. In vitro, T3 blunted TGFβ-induced expression of fibrogenic genes in HSC and abrogated wound healing by modulating TGFβ signalling, which depended on TRα presence. In vivo, TRα-KO enhanced MCD diet-induced liver fibrogenesis. Conclusion: These observations indicate that TH action in non-parenchymal cells is highly relevant. The interaction of TRα with TH regulates the phenotype of HSC via the TGFβ signalling pathway. Thus, the TH–TR axis may be a valuable target for future therapy of liver fibrosis.</p