Achieving Brazil's deforestation target will reduce fire and deliver air quality and public health benefits

Climate, deforestation, and forest fires are closely coupled in the Amazon, but models of fire that include these interactions are lacking. We trained machine learning models on temperature, rainfall, deforestation, land-use, and fire data to show that spatial and temporal patterns of fire in the Amazon are strongly modified by deforestation. We find that fire count across the Brazilian Amazon increases by 0.44 percentage points for each percentage point increase in deforestation rate. We used the model to predict that the increased deforestation rate in the Brazilian Amazon from 2013 to 2020 caused a 42% increase in fire counts in 2020. We predict that if Brazil had achieved the deforestation target under the National Policy on Climate Change, there would have been 32% fewer fire counts across the Brazilian Amazon in 2020. Using a regional chemistry-climate model and exposure-response associations, we estimate that the improved air quality due to reduced smoke emission under this scenario would have resulted in 2300 fewer deaths due to reduced exposure to fine particulate matter. Our analysis demonstrates the air quality and public health benefits that would accrue from reducing deforestation in the Brazilian Amazon

X-ray Fluorescence Analysis of Feldspars and Silicate Glass: Effects of Melting Time on Fused Bead Consistency and Volatilisation

Reproducible preparation of lithium tetraborate fused beads for XRF analysis of glass and mineral samples is of paramount importance for analytical repeatability. However, as with all glass melting processes, losses due to volatilisation must be taken into account and their effects are not negligible. Here the effects of fused bead melting time have been studied for four Certified Reference Materials (CRM’s: three feldspars, one silicate glass), in terms of their effects on analytical variability and volatilisation losses arising from fused bead preparation. At melting temperatures of 1065 °C, and for feldspar samples, fused bead melting times shorter than approximately 25 min generally gave rise to a greater deviation of the XRF-analysed composition from the certified composition. This variation might be due to incomplete fusion and/or fused bead inhomogeneity but further research is needed. In contrast, the shortest fused bead melting time for the silicate glass CRM gave an XRF-analysed composition closer to the certified values than longer melting times. This may suggest a faster rate of glass-in-glass dissolution and homogenization during fused bead preparation. For all samples, longer melting times gave rise to greater volatilisation losses (including sulphates and halides) during fusion. This was demonstrated by a linear relationship between SO3 mass loss and time1/2, as predicted by a simple diffusion-based model. Iodine volatilisation displays a more complex relationship, suggestive of diffusion plus additional mechanisms. This conclusion may have implications for vitrification of iodine-bearing radioactive wastes. Our research demonstrates that the nature of the sample material impacts on the most appropriate fusion times. For feldspars no less than ~25 min and no more than ~60 min of fusion at 1065 °C, using Li2B4O7 as the fusion medium and in the context of feldspar samples and the automatic fusion equipment used here, strikes an acceptable (albeit non-ideal) balance between the competing factors of fused bead quality, analytical consistency and mitigating volatilisation losses. Conversely, for the silicate glass sample, shorter fusion times of less than ~30 min under the same conditions provided more accurate analyses whilst limiting volatile losses

Optimising medication data collection in a large-scale clinical trial

© 2019 Lockery et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Objective: Pharmaceuticals play an important role in clinical care. However, in community-based research, medication data are commonly collected as unstructured free-text, which is prohibitively expensive to code for large-scale studies. The ASPirin in Reducing Events in the Elderly (ASPREE) study developed a two-pronged framework to collect structured medication data for 19,114 individuals. ASPREE provides an opportunity to determine whether medication data can be cost-effectively collected and coded, en masse from the community using this framework. Methods: The ASPREE framework of type-to-search box with automated coding and linked free text entry was compared to traditional method of free-text only collection and post hoc coding. Reported medications were classified according to their method of collection and analysed by Anatomical Therapeutic Chemical (ATC) group. Relative cost of collecting medications was determined by calculating the time required for database set up and medication coding. Results Overall, 122,910 participant structured medication reports were entered using the type-tosearch box and 5,983 were entered as free-text. Free-text data contributed 211 unique medications not present in the type-to-search box. Spelling errors and unnecessary provision of additional information were among the top reasons why medications were reported as freetext. The cost per medication using the ASPREE method was approximately USD $0.03 compared with USD$0.20 per medication for the traditional method. Conclusion Implementation of this two-pronged framework is a cost-effective alternative to free-text only data collection in community-based research. Higher initial set-up costs of this combined method are justified by long term cost effectiveness and the scientific potential for analysis and discovery gained through collection of detailed, structured medication data

Overfishing Drives Over One-Third of All Sharks and Rays Toward a Global Extinction Crisis

The scale and drivers of marine biodiversity loss are being revealed by the International Union for Conservation of Nature (IUCN) Red List assessment process. We present the first global reassessment of 1,199 species in Class Chondrichthyes-sharks, rays, and chimeras. The first global assessment (in 2014) concluded that one-quarter (24%) of species were threatened. Now, 391 (32.6%) species are threatened with extinction. When this percentage of threat is applied to Data Deficient species, more than one-third (37.5%) of chondrichthyans are estimated to be threatened, with much of this change resulting from new information. Three species are Critically Endangered (Possibly Extinct), representing possibly the first global marine fish extinctions due to overfishing. Consequently, the chondrichthyan extinction rate is potentially 25 extinctions per million species years, comparable to that of terrestrial vertebrates. Overfishing is the universal threat affecting all 391 threatened species and is the sole threat for 67.3% of species and interacts with three other threats for the remaining third: loss and degradation of habitat (31.2% of threatened species), climate change (10.2%), and pollution (6.9%). Species are disproportionately threatened in tropical and subtropical coastal waters. Science-based limits on fishing, effective marine protected areas, and approaches that reduce or eliminate fishing mortality are urgently needed to minimize mortality of threatened species and ensure sustainable catch and trade of others. Immediate action is essential to prevent further extinctions and protect the potential for food security and ecosystem functions provided by this iconic lineage of predators

Morphological Properties of z~0.5 Absorption-Selected Galaxies: The Role of Galaxy Inclination

We have used GIM2D to quantify the morphological properties of 40 intermediate redshift MgII absorption-selected galaxies (0.03<Wr(2796)<2.9 Ang), imaged with WFPC-2/HST, and compared them to the halo gas properties measured form HIRES/Keck and UVES/VLT quasar spectra. We find that as the quasar-galaxy separation, D, increases the MgII equivalent decreases with large scatter, implying that D is not the only physical parameter affecting the distribution and quantity of halo gas. Our main result shows that inclination correlates with MgII absorption properties after normalizing out the relationship (and scatter) between the absorption properties and D. We find a 4.3 sigma correlation between Wr(2796) and galaxy inclination, normalized by impact parameter, i/D. Other measures of absorption optical depth also correlate with i/D at greater than 3.2 sigma significance. Overall, this result suggests that MgII gas has a co-planer geometry, not necessarily disk-like, that is coupled to the galaxy inclination. It is plausible that the absorbing gas arises from tidal streams, satellites, filaments, etc., which tend to have somewhat co-planer distributions. This result does not support a picture in which MgII absorbers with Wr(2796)<1A are predominantly produced by star-formation driven winds. We further find that; (1) MgII host galaxies have quantitatively similar bulge and disk scale length distribution to field galaxies at similar redshifts and have a mean disk and bulge scale length of 3.8kpc and 2.5kpc, respectively; (2) Galaxy color and luminosity do not correlate strongly with absorption properties, implying a lack of a connection between host galaxy star formation rates and absorption strength; (3) Parameters such as scale lengths and bulge-to-total ratios do not significantly correlate with the absorption parameters, suggesting that the absorption is independent of galaxy size or mass.Comment: 21 pages, 7 figures, 7 tables. Accepted for publication in MNRAS. Revised v3 updates Table 5 columns 8 and 11. ArXiv copy includes full version of Fig. 1 (additional 6 pages

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Cold cap glass-melt migration for radioactive waste vitrification at the Hanford site

With public and environmental pressure to clean-up the 200,000 m3 of radioactive wastes at the Hanford site, WA, USA, in a timely manner, many pathways to efficient processing of the wastes are being explored. One avenue, rife for exploration, is the waste feed-to-glass transition that occurs within a “cold cap” layer inside the melters, used to vitrify the wastes into stable glass wasteforms, for long-term immobilisation of the radioactive isotopes. Foaming beneath the cold cap, caused by the trapping of evolving gases in the glass-forming melt, can restrict heat-transfer from the glass melt to the reacting feed, thus reducing the efficiency of the melters, and the clean-up project. For a high-foaming, high-iron waste feed, HLW-NG-Fe2, a series of laboratory-scale representations of the cold cap were examined for the original feed, a reduced iron raw material (FeC2O4·2H2O), as well as added sucrose, graphite, coke, formic acid and HEDTA. The FeC2O4·2H2O raw material reduced foaming by 50 ± 2%, with minimal change to the final glass structure. Graphite and coke were most effective additives in foam reduction, reducing foaming by 51 ± 3 and 54 ± 3%, respectively. The effect of the reductants on the redox behaviour of Fe, Cr, Mn and Ce with temperature was explored, as well as the contribution to O2 evolution. Manipulation of the structure of the iron in the melt influenced the level of precipitation of Fe, Mn, Cr and Ni -bearing spinel crystals. The final graphite and coke glasses had Fe2+ content above the contract limit, and a structural change identified in most of the glasses, requiring further examination, appears to influence the chemical durability and glass transition temperature. Evidence is presented to suggest adoption of the reductants is feasible for mitigation of excessive foaming, pending further optimisation, although thus far, there is no indication that they offer improved melting rates

Dysregulated Notch signaling in the airway epithelium of children with wheeze

The airway epithelium of children with wheeze is characterized by defective repair that contributes to disease pathobiology. Dysregulation of developmental processes controlled by Notch has been identified in chronic asthma. However, its role in airway epithelial cells of young children with wheeze, particularly during repair, is yet to be determined. We hypothesized that Notch is dysregulated in primary airway epithelial cells (pAEC) of children with wheeze contributing to defective repair. This study investigated transcriptional and protein expression and function of Notch in pAEC isolated from children with and without wheeze. Primary AEC of children with and without wheeze were found to express all known Notch receptors and ligands, although pAEC from children with wheeze expressed significantly lower NOTCH2 (10-fold, p = 0.004) and higher JAG1 (3.5-fold, p = 0.002) mRNA levels. These dysregulations were maintained in vitro and cultures from children with wheeze displayed altered kinetics of both NOTCH2 and JAG1 expression during repair. Following Notch signaling inhibition, pAEC from children without wheeze failed to repair (wound closure rate of 76.9 ± 3.2%). Overexpression of NOTCH2 in pAEC from children with wheeze failed to rescue epithelial repair following wounding. This study illustrates the involvement of the Notch pathway in airway epithelial wound repair in health and disease, where its dysregulation may contribute to asthma development