Understanding different dominance patterns in western Amazonian forests

Dominance of neotropical tree communities by a few species is widely documented, but dominant trees show a variety of distributional patterns still poorly understood. Here, we used 503 forest inventory plots (93,719 individuals ≥2.5 cm diameter, 2609 species) to explore the relationships between local abundance, regional frequency and spatial aggregation of dominant species in four main habitat types in western Amazonia. Although the abundance-occupancy relationship is positive for the full dataset, we found that among dominant Amazonian tree species, there is a strong negative relationship between local abundance and regional frequency and/or spatial aggregation across habitat types. Our findings suggest an ecological trade-off whereby dominant species can be locally abundant (local dominants) or regionally widespread (widespread dominants), but rarely both (oligarchs). Given the importance of dominant species as drivers of diversity and ecosystem functioning, unravelling different dominance patterns is a research priority to direct conservation efforts in Amazonian forests.Publisher PDFPeer reviewe

Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, individuals with clonal mosaic events (clonal mosaicism for chromosome alterations and/or loss of chromosome Y) showed an increased risk of COVID-19 lethality

Search for eccentric black hole coalescences during the third observing run of LIGO and Virgo

Despite the growing number of confident binary black hole coalescences observed through gravitational waves so far, the astrophysical origin of these binaries remains uncertain. Orbital eccentricity is one of the clearest tracers of binary formation channels. Identifying binary eccentricity, however, remains challenging due to the limited availability of gravitational waveforms that include effects of eccentricity. Here, we present observational results for a waveform-independent search sensitive to eccentric black hole coalescences, covering the third observing run (O3) of the LIGO and Virgo detectors. We identified no new high-significance candidates beyond those that were already identified with searches focusing on quasi-circular binaries. We determine the sensitivity of our search to high-mass (total mass M>70 M⊙) binaries covering eccentricities up to 0.3 at 15 Hz orbital frequency, and use this to compare model predictions to search results. Assuming all detections are indeed quasi-circular, for our fiducial population model, we place an upper limit for the merger rate density of high-mass binaries with eccentricities 0<e≤0.3 at 0.33 Gpc−3 yr−1 at 90\% confidence level

Ultralight vector dark matter search using data from the KAGRA O3GK run

Among the various candidates for dark matter (DM), ultralight vector DM can be probed by laser interferometric gravitational wave detectors through the measurement of oscillating length changes in the arm cavities. In this context, KAGRA has a unique feature due to differing compositions of its mirrors, enhancing the signal of vector DM in the length change in the auxiliary channels. Here we present the result of a search for U(1)B−L gauge boson DM using the KAGRA data from auxiliary length channels during the first joint observation run together with GEO600. By applying our search pipeline, which takes into account the stochastic nature of ultralight DM, upper bounds on the coupling strength between the U(1)B−L gauge boson and ordinary matter are obtained for a range of DM masses. While our constraints are less stringent than those derived from previous experiments, this study demonstrates the applicability of our method to the lower-mass vector DM search, which is made difficult in this measurement by the short observation time compared to the auto-correlation time scale of DM

Risk of deep vein thrombosis in patients undergoing knee arthroscopy

Background In this report we attempt to estimate the incidence of deep vein thrombosis in patients undergoing low-complexity knee arthroscopy and explore possible indications for anti-embolic prophylaxis according to the calculated probability of deep vein thrombosis. Methods This is a prospective cohort study. Subjects were adult patients undergoing low-complexity knee arthroscopy between September 2001 and November 2004. Patients with a diagnosis of deep vein thrombosis before the procedure and those who were receiving anticoagulant medications were excluded. Doppler ultrasound was performed 8 and 30 days after the procedure. Multivariate logistic regression model was used to calculate the probabilities of deep vein thrombosis depending on the presence or absence of risk factors. One hundred and four patients were included. Results The estimated incidence of deep vein thrombosis was 8.6% [95% confidence interval (CI) 3% to 14%]. Bivariate analysis showed an association between tourniquet duration time longer than 40 minutes and deep vein thrombosis (P = 0.019). Multivariate logistic regression analysis confirmed that association (OR = 14.7, 95% CI 1.4-157, P = 0.02) and showed a trend towards significance for the association between hormonal therapy and deep vein thrombosis (OR = 10.9, 95% CI 0.6187, P = 0.09). According to the logistic regression model, seven different clinical scenarios showed a high probability of deep vein thrombosis. Conclusions The risk of deep vein thrombosis in patients undergoing lowcomplexity knee arthroscopy may be high enough to justify antiembolic prophylaxis depending on the absence or presence of risk factors. Prolonged tourniquet duration time is associated with deep vein thrombosis. Level of Evidence Level II (prognostic study with patient enrollment at the same time in their disease process and completed follow-up for more than 80% of the patients)

Understanding different dominance patterns in western Amazonian forests

<p><span>Dominance of neotropical tree communities by a few species is widely documented, but dominant trees show a variety of distributional patterns still poorly understood. Here, we used 503 forest inventory plots (93,719 individuals ≥ 2.5 cm diameter, 2,609 species) to explore the relationships between local abundance, regional frequency, and spatial aggregation of dominant species in four main habitat types in western Amazonia. Contrary to the widely supported positive abundance-occupancy relationship in ecology, we found that among dominant Amazonian tree species, there is a strong negative relationship between local abundance and regional frequency and/or spatial aggregation across habitat types. Our findings suggest an ecological trade-off whereby dominant species can be locally abundant (local dominants) or regionally widespread (widespread dominants), but rarely both (oligarchs). Given the importance of dominant species as drivers of diversity and ecosystem functioning, unraveling different dominance patterns is a research priority to direct conservation efforts in Amazonian forests.</span></p><p>Funding provided by: Ministry of Economy, Industry and Competitiveness<br>Crossref Funder Registry ID: https://ror.org/034900433<br>Award Number: CGL2016–75414–P</p><p>Funding provided by: Ministerio de Ciencia e Innovación<br>Crossref Funder Registry ID: https://ror.org/05r0vyz12<br>Award Number: PID2019-105064GB-I00</p><p>Funding provided by: Ministry of Economy, Industry and Competitiveness<br>Crossref Funder Registry ID: https://ror.org/034900433<br>Award Number: CGL2015-72431-EXP</p><p><span>We used data from 503 forest inventory plots spread across western Amazonia, from Colombia to Bolivia. A total of 363 plots had an area of 0.1 ha, 134 plots were smaller than 0.1 ha (range from 0.025 to 0.08 ha), and 6 plots were larger (range from 0.128 to 0.213 ha). Plots are included in the RedGentry network</span><span>. </span><span>Across all plots, we measured stems with a diameter at breast height ≥ 2.5 cm within the plot limits. <span>Plots covered the main four habitat types in western Amazonia: 383 in terra firme (76%), 54 in floodplain (11%), 35 in swamp (7%) and 31 in white sand (6%) forests.</span></span></p> <p><span>We excluded all individuals not identified to species level (mean 14% of individuals per plot), since plot data came from different projects and morphospecies were not cross-checked. We also excluded individuals from doubtful identifications, e.g. 'cf.' and 'aff.' (mean 3% of individuals per plot). To the remaining individuals, we checked species names for synonym and spelling mistakes, using the R package 'Taxonstand'</span><span>. Identifications that were difficult to designate to a species were considered morphospecies and were also removed. Finally, we cross-checked our species names list against the most recent checklists of Amazonian species</span><span>. Species not found in these checklists (635 species) were compared with collection records in the Tropicos database, and were excluded because: 572 species of them were growth forms not consistently included in all datasets (epiphytes, lianas, herbs and ferns), 25 were illegitimate Amazonian species with ranges outside of our region and 38 species were considered wrong identifications because they do not have recorded collection since their descriptions. After these filters, </span><span>2,609 </span><span>species and </span><span>93,719 </span><span>individuals remained available for our analyses.</span></p> <p><span>Since plot size varied among datasets, we transformed abundances into relative abundances (i.e., number of individuals per species/total individuals per plot). Then, we defined dominant species as those species that together accounted for 50% of the total relative abundance of all individual trees in each habitat</span><span>. We analyzed separately dominant species by habitat type.</span></p> <p><span>Since our plots are not evenly distributed in space, identifying dominant species considering all plots in each habitat type could favor the selection of spatially clumped species. To explore the effect of this potential bias, we divided our study area into equal 100 x 100 km squares, and we extracted 100 random subsamples from the complete set of plots in each habitat type drawing one plot from each square each time. We identified dominant species in the complete dataset and each subsample.</span></p> <p><span>To test the relationship between local abundance and regional frequency of dominant species by habitat type, we built beta regression models with a logit link function. We used the mean local relative abundance of each dominant species as the dependent variable and both the regional relative frequency and the habitat type as predictors.</span><span> </span>We built species-level rank abundance distribution graphs within each habitat type to explore if local abundance in each plot of each dominant species gave similar information that their mean local abundance. We<span><span> conducted these analyses for: i) the complete dataset, including all plots of each habitat type; and ii) for the 100 subsamples. We further wanted to explore how the tendency changed adding sequentially rarer species. Therefore, we conducted the same analyses for species that account for 60%, 70%, 80%, 85%, 90%, 92.5%, 95%, 97.2% and 100% of the total relative abun</span></span><span><span>dance.</span> </span>To study the relative spatial aggregation of species, we analyzed the co-dominance of each species at each spatial extent and habitat. To do so, we calculated the F index related to each geographical distance between plots to all species and relativized these values to the community-level aggregation curve. </p&gt

Understanding different dominance patterns in western Amazonian forests (all versions - software)

Dominance of neotropical tree communities by a few species is widely documented, yet the different pathways that Amazonian plants follow to achieve dominance remain poorly understood. Here, we used 503 forest inventory plots (93,719 individuals ≥ 2.5 cm diameter, 2,609 species) to explore the relationships between local abundance, regional frequency, and spatial aggregation of dominant species across habitats in western Amazonia. Contrary to the well-supported abundance-occupancy relationship, we found that among dominant Amazonian tree species, there is a strong negative relationship between local abundance and regional frequency/spatial aggregation across habitat types. Our findings suggest an ecological trade-off whereby dominant species can allocate resources to being locally abundant (local dominants) or regionally widespread (widespread dominants), but rarely both (oligarchs). Given the importance of dominant species as drivers of diversity and ecosystem functioning, unraveling different modes of dominance is a research priority to direct conservation efforts in Amazonian forests

Understanding different dominance patterns in western Amazonian forests

Dominance of neotropical tree communities by a few species is widely documented, but dominant trees show a variety of distributional patterns still poorly understood. Here, we used 503 forest inventory plots (93,719 individuals ≥ 2.5 cm diameter, 2,609 species) to explore the relationships between local abundance, regional frequency, and spatial aggregation of dominant species in four main habitat types in western Amazonia. Contrary to the widely supported positive abundance-occupancy relationship in ecology, we found that among dominant Amazonian tree species, there is a strong negative relationship between local abundance and regional frequency and/or spatial aggregation across habitat types. Our findings suggest an ecological trade-off whereby dominant species can be locally abundant (local dominants) or regionally widespread (widespread dominants), but rarely both (oligarchs). Given the importance of dominant species as drivers of diversity and ecosystem functioning, unraveling different dominance patterns is a research priority to direct conservation efforts in Amazonian forests

Efficacy and safety of the CVnCoV SARS-CoV-2 mRNA vaccine candidate in ten countries in Europe and Latin America (HERALD): a randomised, observer-blinded, placebo-controlled, phase 2b/3 trial

Background: Additional safe and efficacious vaccines are needed to control the COVID-19 pandemic. We aimed to analyse the efficacy and safety of the CVnCoV SARS-CoV-2 mRNA vaccine candidate. Methods: HERALD is a randomised, observer-blinded, placebo-controlled, phase 2b/3 clinical trial conducted in 47 centres in ten countries in Europe and Latin America. By use of an interactive web response system and stratification by country and age group (18–60 years and ≥61 years), adults with no history of virologically confirmed COVID-19 were randomly assigned (1:1) to receive intramuscularly either two 0·6 mL doses of CVnCoV containing 12 μg of mRNA or two 0·6 mL doses of 0·9% NaCl (placebo) on days 1 and 29. The primary efficacy endpoint was the occurrence of a first episode of virologically confirmed symptomatic COVID-19 of any severity and caused by any strain from 15 days after the second dose. For the primary endpoint, the trial was considered successful if the lower limit of the CI was greater than 30%. Key secondary endpoints were the occurrence of a first episode of virologically confirmed moderate-to-severe COVID-19, severe COVID-19, and COVID-19 of any severity by age group. Primary safety outcomes were solicited local and systemic adverse events within 7 days after each dose and unsolicited adverse events within 28 days after each dose in phase 2b participants, and serious adverse events and adverse events of special interest up to 1 year after the second dose in phase 2b and phase 3 participants. Here, we report data up to June 18, 2021. The study is registered at ClinicalTrials.gov, NCT04652102, and EudraCT, 2020–003998–22, and is ongoing. Findings: Between Dec 11, 2020, and April 12, 2021, 39 680 participants were enrolled and randomly assigned to receive either CVnCoV (n=19 846) or placebo (n=19 834), of whom 19 783 received at least one dose of CVnCoV and 19 746 received at least one dose of placebo. After a mean observation period of 48·2 days (SE 0·2), 83 cases of COVID-19 occurred in the CVnCoV group (n=12 851) in 1735·29 person-years and 145 cases occurred in the placebo group (n=12 211) in 1569·87 person-years, resulting in an overall vaccine efficacy against symptomatic COVID-19 of 48·2% (95·826% CI 31·0–61·4; p=0·016). Vaccine efficacy against moderate-to-severe COVID-19 was 70·7% (95% CI 42·5–86·1; CVnCoV 12 cases in 1735·29 person-years, placebo 37 cases in 1569·87 person-years). In participants aged 18–60 years, vaccine efficacy against symptomatic disease was 52·5% (95% CI 36·2–64·8; CVnCoV 71 cases in 1591·47 person-years, placebo, 136 cases in 1449·23 person-years). Too few cases occurred in participants aged 61 years or older (CVnCoV 12, placebo nine) to allow meaningful assessment of vaccine efficacy. Solicited adverse events, which were mostly systemic, were more common in CVnCoV recipients (1933 [96·5%] of 2003) than in placebo recipients (1344 [67·9%] of 1978), with 542 (27·1%) CVnCoV recipients and 61 (3·1%) placebo recipients reporting grade 3 solicited adverse events. The most frequently reported local reaction after any dose in the CVnCoV group was injection-site pain (1678 [83·6%] of 2007), with 22 grade 3 reactions, and the most frequently reported systematic reactions were fatigue (1603 [80·0%] of 2003) and headache (1541 [76·9%] of 2003). 82 (0·4%) of 19 783 CVnCoV recipients reported 100 serious adverse events and 66 (0·3%) of 19 746 placebo recipients reported 76 serious adverse events. Eight serious adverse events in five CVnCoV recipients and two serious adverse events in two placebo recipients were considered vaccination-related. None of the fatal serious adverse events reported (eight in the CVnCoV group and six in the placebo group) were considered to be related to study vaccination. Adverse events of special interest were reported for 38 (0·2%) participants in the CVnCoV group and 31 (0·2%) participants in the placebo group. These events were considered to be related to the trial vaccine for 14 (<0·1%) participants in the CVnCoV group and for five (<0·1%) participants in the placebo group. Interpretation: CVnCoV was efficacious in the prevention of COVID-19 of any severity and had an acceptable safety profile. Taking into account the changing environment, including the emergence of SARS-CoV-2 variants, and timelines for further development, the decision has been made to cease activities on the CVnCoV candidate and to focus efforts on the development of next-generation vaccine candidates. Funding: German Federal Ministry of Education and Research and CureVac