High Temperature Photochemistry in the Atmosphere of HD189733b

Recent infrared spectroscopy of hot exoplanets is beginning to reveal their atmospheric composition. Deep with in the planetary atmosphere, the composition is controlled by thermochemical equilibrium. Photochemistry becomes important higher in the atmosphere, at levels above ~1 bar. These two chemistries compete between ~1-10 bars in hot Jupiter-like atmospheres, depending on the strength of the eddy mixing and temperature. HD189733b provides an excellent laboratory in which to study the consequences of chemistry of hot atmospheres. The recent spectra of HD189733b and HD209458b contain signatures of CH4, CO2, CO and H2O. Here we identify the primary chemical pathways that govern the abundances of CH4, CO2, CO and H2O in the cases of thermochemical equilibrium chemistry, photochemistry, and their combination. Our results suggest that the abundance of these species can be photochemically enhanced above or below the thermochemical equilibrium value, so some caution must be taken when assuming that an atmosphere is in strict thermochemical equilibrium

Simulating chemistry efficiently on fault-tolerant quantum computers

Quantum computers can in principle simulate quantum physics exponentially faster than their classical counterparts, but some technical hurdles remain. Here we consider methods to make proposed chemical simulation algorithms computationally fast on fault-tolerant quantum computers in the circuit model. Fault tolerance constrains the choice of available gates, so that arbitrary gates required for a simulation algorithm must be constructed from sequences of fundamental operations. We examine techniques for constructing arbitrary gates which perform substantially faster than circuits based on the conventional Solovay-Kitaev algorithm [C.M. Dawson and M.A. Nielsen, \emph{Quantum Inf. Comput.}, \textbf{6}:81, 2006]. For a given approximation error $\epsilon$, arbitrary single-qubit gates can be produced fault-tolerantly and using a limited set of gates in time which is $O(\log \epsilon)$ or $O(\log \log \epsilon)$; with sufficient parallel preparation of ancillas, constant average depth is possible using a method we call programmable ancilla rotations. Moreover, we construct and analyze efficient implementations of first- and second-quantized simulation algorithms using the fault-tolerant arbitrary gates and other techniques, such as implementing various subroutines in constant time. A specific example we analyze is the ground-state energy calculation for Lithium hydride.Comment: 33 pages, 18 figure

Exact Results for Hamiltonian Walks from the Solution of the Fully Packed Loop Model on the Honeycomb Lattice

We derive the nested Bethe Ansatz solution of the fully packed O($n$) loop model on the honeycomb lattice. From this solution we derive the bulk free energy per site along with the central charge and geometric scaling dimensions describing the critical behaviour. In the $n=0$ limit we obtain the exact compact exponents $\gamma=1$ and $\nu=1/2$ for Hamiltonian walks, along with the exact value $\kappa^2 = 3 \sqrt 3 /4$ for the connective constant (entropy). Although having sets of scaling dimensions in common, our results indicate that Hamiltonian walks on the honeycomb and Manhattan lattices lie in different universality classes.Comment: 12 pages, RevTeX, 3 figures supplied on request, ANU preprint MRR-050-9

Upper limits for undetected trace species in the stratosphere of Titan

In this paper we describe a first quantitative search for several molecules in Titan's stratosphere in Cassini CIRS infrared spectra. These are: ammonia (NH3), methanol (CH3OH), formaldehyde (H2CO), and acetonitrile (CH3CN), all of which are predicted by photochemical models but only the last of which observed, and not in the infrared. We find non-detections in all cases, but derive upper limits on the abundances from low-noise observations at 25{\deg}S and 75{\deg}N. Comparing these constraints to model predictions, we conclude that CIRS is highly unlikely to see NH3 or CH3OH emissions. However, CH3CN and H2CO are closer to CIRS detectability, and we suggest ways in which the sensitivity threshold may be lowered towards this goal.Comment: 11 pages plus 6 figure file

Thermochemistry and Photochemistry in Cooler Hydrogen Dominated Extrasolar Planets: The Case of GJ436b

We introduce a new thermochemical kinetics and photochemical model. We use high-temperature bidirectional reaction rates for important H, C, O and N reactions (most importantly for CH$_4$ to CO interconversion), allowing us to attain thermochemical equilibrium, deep in an atmosphere, purely kinetically. This allows ab initio chemical modeling of an entire atmosphere, from deep-atmosphere thermochemical equilibrium to the photochemically dominated regime. We use our model to explore the atmospheric chemistry of cooler ($T_{eff} < 10^3$ K) extrasolar giant planets. In particular, we choose to model the nearby hot Neptune GJ436b, the only planet in this temperature regime for which spectroscopic measurements and estimates of chemical abundances now exist. Recent {\it Spitzer} measurements with retrieval have shown that methane is driven strongly out of equilibrium and is deeply depleted on the dayside of GJ 436b, whereas quenched carbon monoxide is abundant. This is surprising because GJ 436b is cooler than many of the heavily irradiated hot Jovians and thermally favorable for CH$_4$, and thus requires an efficient mechanism for destroying it. We include realistic estimates of ultraviolet flux from the parent dM star GJ 436, to bound the direct photolysis and photosensitized depletion of CH$_4$. While our models indicate fairly rich disequilibrium conditions are likely in cooler exoplanets over a range of planetary metallicities, we are unable to generate the conditions for substantial CH$_4$ destruction. One possibility is an anomalous source of abundant H atoms between 0.01-1 bars (which attack CH$_4$), but we cannot as yet identify an efficient means to produce these hot atoms

Angiogenesis inhibitors in clinical development; where are we now and where are we going?

Angiogenesis is crucial for tumour growth and the formation of metastases. Various classes of angiogenesis inhibitors that are each able to inhibit one of the various steps of this complex process can be distinguished. Results from clinical studies with these agents are summarised. In general, it has been shown that most angiogenesis inhibitors can be safely administered, but that tumour regressions are rare. Combining angiogenesis inhibitors with cytotoxic chemotherapy can enhance anticancer activity. Recently, some promising data with regard to clinical efficacy have been presented. While performing clinical studies with angiogenesis inhibitors, defining biological activity is crucial, but thus far no validated techniques are available. It is conceivable that in the near future various classes of angiogenesis inhibitors will be combined in an attempt to further improve antiangiogenic and anticancer activity

Systematic reviews of observational studies of Risk of Thrombosis and Bleeding in General and Gynecologic Surgery (ROTBIGGS) : introduction and methodology

Funding Information: The Risk of Thrombosis and Bleeding in General and Gynecologic Surgery (ROTBIGGS) project was conducted by the Clinical Urology and Epidemiology (CLUE) Working Group and supported by the Academy of Finland (309387, 340957), Sigrid Jusélius Foundation and Competitive Research Funding of the Helsinki University Hospital (TYH2019321; TYH2020248). The sponsors had no role in the analysis and interpretation of the data or the manuscript preparation, review, or approval. Funding Information: KMA received a research grant from Astra Zeneca, and is consultant for Gedeon Richter, and received reimbursement for attending a scientific meeting from GSK (Tesaro Bio). RMT received reimbursement for attending a scientific meeting from Olympus. LIL, GHG, YL, RC, ALL, VJS, IEJK, PJK, RJC, RLA, KA, KMA, IB-L, MHB, JLC, SC, PJG, HAG-P, FZG, HAG, LH, MLI-K, KMJ, PKK, NK, TPK, AJK, TK, HL, AKM, BTN, TPN, CN, SMO, SP, NP, CBBR, ARR, TS, RMT, RWMV, YW, YX, LY, JH, and KAOT have no financial conflicts of interest. GHG and RC were panel members of the European Association of Urology (EAU) ad hoc Guideline on Thromboprophylaxis in Urological Surgery. KAOT was chair of the European Association of Urology (EAU) ad hoc Guideline on Thromboprophylaxis in Urological Surgery and panel member of the American Society of Hematology (ASH) Guideline Panel on Prevention of Venous Thromboembolism (VTE) in Surgical Hospitalized Patients. Publisher Copyright: © 2021, The Author(s).Background Venous thromboembolism (VTE) and bleeding are serious and potentially fatal complications of surgical procedures. Pharmacological thromboprophylaxis decreases the risk of VTE but increases the risk of major post-operative bleeding. The decision to use pharmacologic prophylaxis therefore represents a trade-off that critically depends on the incidence of VTE and bleeding in the absence of prophylaxis. These baseline risks vary widely between procedures, but their magnitude is uncertain. Systematic reviews addressing baseline risks are scarce, needed, and require innovations in methodology. Indeed, systematic summaries of these baseline risk estimates exist neither in general nor gynecologic surgery. We will fill this knowledge gap by performing a series of systematic reviews and meta-analyses of the procedure-specific and patient risk factor stratified risk estimates in general and gynecologic surgeries. Methods We will perform comprehensive literature searches for observational studies in general and gynecologic surgery reporting symptomatic VTE or bleeding estimates. Pairs of methodologically trained reviewers will independently assess the studies for eligibility, evaluate the risk of bias by using an instrument developed for this review, and extract data. We will perform meta-analyses and modeling studies to adjust the reported risk estimates for the use of thromboprophylaxis and length of follow up. We will derive the estimates of risk from the median estimates of studies rated at the lowest risk of bias. The primary outcomes are the risk estimates of symptomatic VTE and major bleeding at 4 weeks post-operatively for each procedure stratified by patient risk factors. We will apply the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach to rate evidence certainty. Discussion This series of systematic reviews, modeling studies, and meta-analyses will inform clinicians and patients regarding the trade-off between VTE prevention and bleeding in general and gynecologic surgeries. Our work advances the standards in systematic reviews of surgical complications, including assessment of risk of bias, criteria for arriving at the best estimates of risk (including modeling of the timing of events and dealing with suboptimal data reporting), dealing with subgroups at higher and lower risk of bias, and use of the GRADE approach. Systematic review registration PROSPERO CRD42021234119Peer reviewe

Wild Type and Mutant 2009 Pandemic Influenza A (H1N1) Viruses Cause More Severe Disease and Higher Mortality in Pregnant BALB/c Mice

BACKGROUND: Pregnant women infected by the pandemic influenza A (H1N1) 2009 virus had more severe disease and higher mortality but its pathogenesis is still unclear. PRINCIPAL FINDINGS: We showed that higher mortality, more severe pneumonitis, higher pulmonary viral load, lower peripheral blood T lymphocytes and antibody responses, higher levels of proinflammatory cytokines and chemokines, and worse fetal development occurred in pregnant mice than non-pregnant controls infected by either wild type (clinical isolate) or mouse-adapted mutant virus with D222G substitution in hemagglutinin. These disease-associated changes and the lower respiratory tract involvement were worse in pregnant mice challenged by mutant virus. Though human placental origin JEG-3 cell line could be infected and proinflammatory cytokines or chemokines were elevated in amniotic fluid of some mice, no placental or fetal involvement by virus were detected by culture, real-time reverse transcription polymerase chain reaction or histopathological changes. Dual immunofluorescent staining of viral nucleoprotein and type II alveolar cell marker SP-C protein suggested that the majority of infected alveolar epithelial cells were type II pneumocytes. CONCLUSION: The adverse effect of this pandemic virus on maternal and fetal outcome is largely related to the severe pulmonary disease and the indirect effect of inflammatory cytokine spillover into the systemic circulation

Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases

The scientific literature represents a rich source for retrieval of knowledge on associations between biomedical concepts such as genes, diseases and cellular processes. A commonly used method to establish relationships between biomedical concepts from literature is co-occurrence. Apart from its use in knowledge retrieval, the co-occurrence method is also well-suited to discover new, hidden relationships between biomedical concepts following a simple ABC-principle, in which A and C have no direct relationship, but are connected via shared B-intermediates. In this paper we describe CoPub Discovery, a tool that mines the literature for new relationships between biomedical concepts. Statistical analysis using ROC curves showed that CoPub Discovery performed well over a wide range of settings and keyword thesauri. We subsequently used CoPub Discovery to search for new relationships between genes, drugs, pathways and diseases. Several of the newly found relationships were validated using independent literature sources. In addition, new predicted relationships between compounds and cell proliferation were validated and confirmed experimentally in an in vitro cell proliferation assay. The results show that CoPub Discovery is able to identify novel associations between genes, drugs, pathways and diseases that have a high probability of being biologically valid. This makes CoPub Discovery a useful tool to unravel the mechanisms behind disease, to find novel drug targets, or to find novel applications for existing drugs