The \u3cem\u3eChlamydomonas\u3c/em\u3e Genome Reveals the Evolution of Key Animal and Plant Functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella

A checklist for using Beals’ index with incomplete floristic monitoring data : reply to Christensen et al. (2021): Problems in using Beals’ index to detect species trends in incomplete floristic monitoring data

Christensen et al. criticized the application of Beals’ index of sociological favourability to adjust for incomplete species lists when comparing repeated surveys. Their main argument was that using Beals’ conditional occurrence probabilities would systematically underestimate biodiversity change compared to using observed frequencies. Although this might be the case for rare species, as we explicitly stated in our original publication, we here use a worked-out example to show that this criticism is unjustified for species that are sufficiently represented in the reference data set. In our opinion, the misconception derives from ignoring one of the key requirements for applying Beal's index, which is the use of a sufficiently large reference data set to derive a reliable co occurrence matrix. We here show how the predicted probability for the occurrence of a species depends on the size of the reference data set and give recommendations on the premises for applying Beals’ approach for monitoring purposes

Soluble receptor for advanced glycation end products (sRAGE) as a biomarker of COPD

BACKGROUND: Soluble receptor for advanced glycation end products (sRAGE) is a proposed emphysema and airflow obstruction biomarker; however, previous publications have shown inconsistent associations and only one study has investigate the association between sRAGE and emphysema. No cohorts have examined the association between sRAGE and progressive decline of lung function. There have also been no evaluation of assay compatibility, receiver operating characteristics, and little examination of the effect of genetic variability in non-white population. This manuscript addresses these deficiencies and introduces novel data from Pittsburgh COPD SCCOR and as well as novel work on airflow obstruction. A meta-analysis is used to quantify sRAGE associations with clinical phenotypes. METHODS: sRAGE was measured in four independent longitudinal cohorts on different analytic assays: COPDGene (n = 1443); SPIROMICS (n = 1623); ECLIPSE (n = 2349); Pittsburgh COPD SCCOR (n = 399). We constructed adjusted linear mixed models to determine associations of sRAGE with baseline and follow up forced expiratory volume at one second (FEV1) and emphysema by quantitative high-resolution CT lung density at the 15th percentile (adjusted for total lung capacity). RESULTS: Lower plasma or serum sRAGE values were associated with a COPD diagnosis (P < 0.001), reduced FEV1 (P < 0.001), and emphysema severity (P < 0.001). In an inverse-variance weighted meta-analysis, one SD lower log10-transformed sRAGE was associated with 105 ± 22 mL lower FEV1 and 4.14 ± 0.55 g/L lower adjusted lung density. After adjusting for covariates, lower sRAGE at baseline was associated with greater FEV1 decline and emphysema progression only in the ECLIPSE cohort. Non-Hispanic white subjects carrying the rs2070600 minor allele (A) and non-Hispanic African Americans carrying the rs2071288 minor allele (A) had lower sRAGE measurements compare to those with the major allele, but their emphysema-sRAGE regression slopes were similar. CONCLUSIONS: Lower blood sRAGE is associated with more severe airflow obstruction and emphysema, but associations with progression are inconsistent in the cohorts analyzed. In these cohorts, genotype influenced sRAGE measurements and strengthened variance modelling. Thus, genotype should be included in sRAGE evaluations

POLICY PREFERENCE FORMATION IN LEGISLATIVE POLITICS:STRUCTURES, ACTORS, AND FOCAL POINTS

This dissertation introduces and tests a model of policy preference formation in legislative politics. Emphasizing a dynamic relationship between structure, agent, and decision-making process, it ties the question of policy choice to the dimensionality of the normative political space and the strategic actions of parliamentary agenda-setters. The model proposes that structural factors, such as ideology, shape policy preferences to the extent that legislative specialists successfully link them to specific policy proposals through the provision of informational focal points. These focal points shift attention toward particular aspects of a legislative proposal, thus shaping the dominant interpretation of its content and consequences and, in turn, individual-level policy preferences. The propositions of the focal point model are tested empirically with data from the European Parliament (EP), using both qualitative (interview data, content analyses of parliamentary debates) and quantitative methods (multinomial logit regression analyses of roll-call votes). The findings have implications for our understanding of politics and law-making in the European Union and for the study of legislative decision-making more generally

The Mass-Luminosity Relation in the L/T Transition:Individual Dynamical Masses for the New J-Band Flux Reversal Binary SDSSJ105213.51+442255.7AB

We have discovered that SDSSJ105213.51+442255.7 (T0.5$\pm$1.0) is a binary in Keck laser guide star adaptive optics imaging, displaying a large J-to-K-band flux reversal ($\Delta$J = -0.45$\pm$0.09 mag, $\Delta$K = 0.52$\pm$0.05 mag). We determine a total dynamical mass from Keck orbital monitoring (88$\pm$5 $M_{\rm Jup}$) and a mass ratio by measuring the photocenter orbit from CFHT/WIRCam absolute astrometry ($M_B/M_A$ = 0.78$\pm$0.07). Combining these provides the first individual dynamical masses for any field L or T dwarfs, 49$\pm$3 $M_{\rm Jup}$ for the L6.5$\pm$1.5 primary and 39$\pm$3 $M_{\rm Jup}$ for the T1.5$\pm$1.0 secondary. Such a low mass ratio for a nearly equal luminosity binary implies a shallow mass$-$luminosity relation over the L/T transition ($\Delta$log$L_{\rm bol}$/$\Delta$log$M = 0.6^{+0.6}_{-0.8}$). This provides the first observational support that cloud dispersal plays a significant role in the luminosity evolution of substellar objects. Fully cloudy models fail our coevality test for this binary, giving ages for the two components that disagree by 0.2 dex (2.0$\sigma$). In contrast, our observed masses and luminosities can be reproduced at a single age by "hybrid" evolutionary tracks where a smooth change from a cloudy to cloudless photosphere around 1300 K causes slowing of luminosity evolution. Remarkably, such models also match our observed JHK flux ratios and colors well. Overall, it seems that the distinguishing features SDSSJ1052+4422AB, like a J-band flux reversal and high-amplitude variability, are normal for a field L/T binary caught during the process of cloud dispersal, given that the age (1.11$^{+0.17}_{-0.20}$ Gyr) and surface gravity (log$g$ = 5.0$-$5.2) of SDSSJ1052+4422AB are typical for field ultracool dwarfs.Comment: Accepted to ApJ; 33 pages, 8 figures, 5 table

Special cases : moons, rings, comets, trojans

Non-planetary bodies provide valuable insight into our current under- standing of planetary formation and evolution. Although these objects are challeng- ing to detect and characterize, the potential information to be drawn from them has motivated various searches through a number of techniques. Here, we briefly review the current status in the search of moons, rings, comets, and trojans in exoplanet systems and suggest what future discoveries may occur in the near future.Comment: Invited review (status August 2017

A review of soil NO transformation: associated processes and possible physiological significance on organisms

NO emissions from soils and ecosystems are of outstanding importance for atmospheric chemistry. Here we review the current knowledge on processes involved in the formation and consumption of NO in soils, the importance of NO for the physiological functioning of different organisms, and for inter- and intra-species signaling and competition, e.g. in the rooting zone between microbes and plants. We also show that prokaryotes and eukaryotes are able to produce NO by multiple pathways and that unspecific enzymo-oxidative mechanisms of NO production are likely to occur in soils. Nitric oxide production in soils is not only linked to NO production by nitrifying and denitrifying microorganisms, but also linked to extracellular enzymes from a wide range of microorganisms. Further investigations are needed to clarify molecular mechanisms of NO production and consumption, its controlling factors, and the significance of NO as a regulator for microbial, animal and plant processes. Such process understanding is required to elucidate the importance of soils as sources (and sinks) for atmospheric NO

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707

Measurement of D*±, D± and Ds± meson production cross sections in pp collisions at √s=7 TeV with the ATLAS detector

The production of D∗±, D± and D±s charmed mesons has been measured with the ATLAS detector in pp collisions at √s= 7 TeV at the LHC, using data corresponding to an integrated luminosity of 280 nb−1. The charmed mesons have been reconstructed in the range of transverse momentum 3.5 <pT(D) <100 GeV and pseudorapidity |η(D)| <2.1. The differential cross sections as a function of transverse momentum and pseudorapidity were measured for D∗± and D± production. The next-to-leading-order QCD predictions are consistent with the data in the visible kinematic region within the large theoretical uncertainties. Using the visible D cross sections and an extrapolation to the full kinematic phase space, the strangeness-suppression factor in charm fragmentation, the fraction of charged non-strange D mesons produced in a vector state, and the total cross section of charm production at √s= 7 TeV were derived