Calibration Methodology for the Scripps 13C/12C and 18O/16O stable Isotope program 1992-2018

This report details calibration method for measurements of 13C/12C and 18O/16O ratios of atmospheric CO2 by the Scripps CO2 program from 1992-2018.  The method depends principally on repeat analysis of CO2 derived from a suite of high-pressure gas cylinders filled with compressed natural air pumped at La Jolla.  The first set of three cylinders were given isotopic assignments in 1994 based on comparisons with material artifacts NBS16, NBS17, and NBS19.  Six cylinders subsequently brought into service were assigned values by comparing directly or indirectly with this first set.  A tenth cylinder with natural CO2 in air was obtained from MPI Jena.  Aliquots of CO2 from these cylinders, which serve as secondary standards, were extracted into heat-sealed glass ampoules (“flame-off tubes”) before introduction into the mass spectrometer.  Some of these ampoules have been stored for many years before analysis, allowing long-term isotopic drift of the cylinders to be quantified.  All secondary standards contain natural levels of N2O.  The method corrects for any detected drift, while also applying corrections for N2O interference, for isobaric interferences (“Craig correction”) and for an inter-lab offset identified in early comparisons with the isotope lab at the University of Groningen.  The Jena cylinder was found to be drifting upwards in δ18O at a rate of +0.10 ‰ per decade.  Five of the other nine cylinders were found to be drifting downwards in δ18O, δ13C, or both, at rates of up to -0.11‰ per decade.  The secondary standards were applied uniformly across a transition to a new mass spectrometer in 2000, thereby establishing continuity across this transition.  Results are presented also for instrumental precision based on replicate analyses of standards.  Drift-corrected analyses of the Jena cylinder establishes offsets of +0.037 ‰ in δ13C and +0.041 ‰ in δ18O between the Scripps and JRAS isotopic scales (Scripps more positive)

Lack of Fire Has Limited Physiological Impact on Old-Growth Ponderosa Pine in Dry Montane Forests of North-Central Idaho

Reduced frequency of fire in historically fire-adapted ecosystems may have adverse effects on ecosystem structure, function, and resilience. Lack of fire increases stand density and promotes successional replacement of seral dominant trees by late-successional, more shade-tolerant species. These changes are thought to increase competition for limited resources among trees and to increase physiological stress of dominant, fire-adapted species. However, there has been little effort to directly investigate effects of lack of fire on the physiological status of old trees, especially in unlogged, protected forests. At four remote sites in the Selway-Bitterroot region of Idaho, we tested whether the physiological status of dominant old-growth ponderosa pine trees in repeatedly burned stands (three to four 20th-century wildfires at roughly historical fire frequency) differs from trees in paired stands not burned for at least 70 years. We hypothesized that trees in relatively unburned stands would exhibit signs of physiological stress due to increased competition for resources in higher-density stands. Needle chemistry and morphological variables, fine root production, mycorrhizal infection rates, depth of soil water resources, and recent basal area growth rates were measured as indictors of competition-induced stress. Contrary to predictions, needle carbon isotopic ratio (δ13C) and fine root production, variables related to water stress, were slightly higher in repeatedly burned stands driven by site-specific responses, and there were no significant biological differences between trees in repeatedly burned stands vs. stands unburned for at least 70 years in the remaining variables. Our results raise the possibility that dominant ponderosa pine trees in uneven-aged forests may be more resilient to increased stand density associated with the lack of fire than previously thought. If so, our results have implications for the management of uneven-aged, old-growth forests

Interactive Effects of Historical Logging and Fire Exclusion on Ponderosa Pine Forest Structure in the Northern Rockies

Increased forest density resulting from decades of fire exclusion is often perceived as the leading cause of historically aberrant, severe, contemporary wildfires and insect outbreaks documented in some fire-prone forests of the western United States. Based on this notion, current U. S. forest policy directs managers to reduce stand density and restore historical conditions in fire-excluded forests to help minimize high-severity disturbances. Historical logging, however, has also caused widespread change in forest vegetation conditions, but its long-term effects on vegetation structure and composition have never been adequately quantified. We document that fire-excluded ponderosa pine forests of the northern Rocky Mountains logged prior to 1960 have much higher average stand density, greater homogeneity of stand structure, more standing dead trees and increased abundance of fire-intolerant trees than paired fire-excluded, unlogged counterparts. Notably, the magnitude of the interactive effect of fire exclusion and historical logging substantially exceeds the effects of fire exclusion alone. These differences suggest that historically logged sites are more prone to severe wildfires and insect outbreaks than unlogged, fire-excluded forests and should be considered a high priority for fuels reduction treatments. Furthermore, we propose that ponderosa pine forests with these distinct management histories likely require distinct restoration approaches. We also highlight potential long-term risks of mechanical stand manipulation in unlogged forests and emphasize the need for a long-term view of fuels management

Absence of Evidence of Rift Valley Fever Infection in Eulemur fulvus (Brown Lemur) in Mayotte During an Interepidemic Period.

The potential role of Eulemur fulvus (brown lemur) in the epidemiology of Rift Valley fever (RVF) in Mayotte, during an interepidemic period, was explored. In February and March 2016, 72 animals were blood sampled and tested for RVF. No evidence of RVF genome or antibodies was found in the samples. The role of other wild mammals on the island should, however, be further investigated

Divergent genomic trajectories predate the origin of animals and fungi

22 pages, 4 figures, supplementary information https://doi.org/10.1038/s41586-022-05110-4.-- Data availability: The raw sequence data and assembled genomes generated in this study have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB52884 (https://www.ebi.ac.uk/ena/browser/view/PRJEB52884). The genome assemblies are also available in figshare (https://doi.org/10.6084/m9.figshare.19895962.v1). Protein sequences of the species used in this study were downloaded from the GenBank public databases (https://www.ncbi.nlm.nih.gov/protein/), Uniprot (https://www.uniprot.org/), JGI genome database (https://genome.jgi.doe.gov/portal/) and Ensembl genomes (https://www.ensembl.org). The following specific databases were also used in this study: Pfam A v29 (https://pfam.xfam.org/), EggNOG emapperdb-4.5.1 (http://eggnog5.embl.de) and UniProt reference proteomes release 2016_02 (https://www.uniprot.org/). The supporting data files of this study are available in the following repository: https://doi.org/10.6084/m9.figshare.13140191.v1.-- Code availability: The most relevant custom code developed for this study (the MAPBOS pipeline and the machine learning classifiers) is available at https://doi.org/10.5281/zenodo.6586559Animals and fungi have radically distinct morphologies, yet both evolved within the same eukaryotic supergroup: Opisthokonta1,2. Here we reconstructed the trajectory of genetic changes that accompanied the origin of Metazoa and Fungi since the divergence of Opisthokonta with a dataset that includes four novel genomes from crucial positions in the Opisthokonta phylogeny. We show that animals arose only after the accumulation of genes functionally important for their multicellularity, a tendency that began in the pre-metazoan ancestors and later accelerated in the metazoan root. By contrast, the pre-fungal ancestors experienced net losses of most functional categories, including those gained in the path to Metazoa. On a broad-scale functional level, fungal genomes contain a higher proportion of metabolic genes and diverged less from the last common ancestor of Opisthokonta than did the gene repertoires of Metazoa. Metazoa and Fungi also show differences regarding gene gain mechanisms. Gene fusions are more prevalent in Metazoa, whereas a larger fraction of gene gains were detected as horizontal gene transfers in Fungi and protists, in agreement with the long-standing idea that transfers would be less relevant in Metazoa due to germline isolation3,4,5. Together, our results indicate that animals and fungi evolved under two contrasting trajectories of genetic change that predated the origin of both groups. The gradual establishment of two clearly differentiated genomic contexts thus set the stage for the emergence of Metazoa and FungiE.O.-P. was supported by a predoctoral FPI grant from MINECO (BES-2015-072241) and by ESF Investing in your future. E.O.-P., D.L-E., A.S.A. and I.R.-T. received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7-2007-2013) (Grant agreement No. 616960) and also from grants (BFU2014-57779-P and PID2020-120609GB-I00) by MCIN/AEI/10.13039/501100011033 and ‘ERDF A way of making Europe’. E.O.-P. and G.J.Sz. received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 714774). T.A.W. was supported by a Royal Society University Research Fellowship (URF\R\201024) and NERC standard grant NE/P00251X/1. This work was supported by the Gordon and Betty Moore Foundation through grant GBMF9741 to T.A.W. and G.J.Sz. J.S.P. and E.B. received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7-2007-2013) (Grant agreement No. 615274). D.V.T. and cell culturing were supported by the Russian Science Foundation grant no. 18-14-00239, https://rscf.ru/project/18-14-00239/. Culture of P. vietnamica was obtained as the result of field work in Vietnam as part of the project ‘Ecolan 3.2’ of the Russian–Vietnam Tropical Center. P.J.K. is supported by an Investigator Award from the Gordon and Betty Moore Foundation (https://doi.org/10.37807/GBMF9201)With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

Extensive Plasmid Library to Prepare Tau Protein Variants and Study Their Functional Biochemistry

Tau neurofibrillary tangles are key pathological features of Alzheimer’s disease and other tauopathies. Recombinant protein technology is vital for studying the structure and function of tau in physiology and aggregation in pathophysiology. However, open-source and well-characterized plasmids for efficiently expressing and purifying different tau variants are lacking. We generated 44 sequence-verified plasmids including those encoding full length (FL) tau-441, its four-repeat microtubule-binding (K18) fragment, and their respective selected familial pathological variants (N279K, V337M, P301L, C291R, and S356T). Moreover, plasmids for expressing single (C291A), double (C291A/C322A), and triple (C291A/C322A/I260C) cysteine-modified variants were generated to study alterations in cysteine content and locations. Furthermore, protocols for producing representative tau forms were developed. We produced and characterized the aggregation behavior of the triple cysteine-modified tau-K18, often used in real-time cell internalization and aggregation studies because it can be fluorescently labeled on a cysteine outside the microtubule-binding core. Similar to the wild type (WT), triple cysteine-modified tau-K18 aggregated by progressive β-sheet enrichment, albeit at a slower rate. On prolonged incubation, cysteine-modified K18 formed paired helical filaments similar to those in Alzheimer’s disease, sharing morphological phenotypes with WT tau-K18 filaments. Nonetheless, cysteine-modified tau-K18 filaments were significantly shorter (p = 0.002) and mostly wider than WT filaments, explainable by their different principal filament elongation pathways: vertical (end-to-end) and lateral growth for WT and cysteine-modified, respectively. Cysteine rearrangement may therefore induce filament polymorphism. Together, the plasmid library, the protein production methods, and the new insights into cysteine-dependent aggregation should facilitate further studies and the design of antiaggregation agents

Indeterminate and discrepant rapid HIV test results in couples' HIV testing and counselling centres in Africa

<p>Abstract</p> <p>Background</p> <p>Many HIV voluntary testing and counselling centres in Africa use rapid antibody tests, in parallel or in sequence, to establish same-day HIV status. The interpretation of indeterminate or discrepant results between different rapid tests on one sample poses a challenge. We investigated the use of an algorithm using three serial rapid HIV tests in cohabiting couples to resolve unclear serostatuses.</p> <p>Methods</p> <p>Heterosexual couples visited the Rwanda Zambia HIV Research Group testing centres in Kigali, Rwanda, and Lusaka, Zambia, to assess HIV infection status. Individuals with unclear HIV rapid antibody test results (indeterminate) or discrepant results were asked to return for repeat testing to resolve HIV status. If either partner of a couple tested positive or indeterminate with the screening test, both partners were tested with a confirmatory test. Individuals with indeterminate or discrepant results were further tested with a tie-breaker and monthly retesting. HIV-RNA viral load was determined when HIV status was not resolved by follow-up rapid testing. Individuals were classified based on two of three initial tests as "Positive", "Negative" or "Other". Follow-up testing and/or HIV-RNA viral load testing determined them as "Infected", "Uninfected" or "Unresolved".</p> <p>Results</p> <p>Of 45,820 individuals tested as couples, 2.3% (4.1% of couples) had at least one discrepant or indeterminate rapid result. A total of 65% of those individuals had follow-up testing and of those individuals initially classified as "Negative" by three initial rapid tests, less than 1% were resolved as "Infected". In contrast, of those individuals with at least one discrepant or indeterminate result who were initially classified as "Positive", only 46% were resolved as "Infected", while the remainder was resolved as "Uninfected" (46%) or "Unresolved" (8%). A positive HIV serostatus of one of the partners was a strong predictor of infection in the other partner as 48% of individuals who resolved as "Infected" had an HIV-infected spouse.</p> <p>Conclusions</p> <p>In more than 45,000 individuals counselled and tested as couples, only 5% of individuals with indeterminate or discrepant rapid HIV test results were HIV infected. This represented only 0.1% of all individuals tested. Thus, algorithms using screening, confirmatory and tie-breaker rapid tests are reliable with two of three tests negative, but not when two of three tests are positive. False positive antibody tests may persist. HIV-positive partner serostatus should prompt repeat testing.</p

Drivers for Rift Valley fever emergence in Mayotte: A Bayesian modelling approach

Rift Valley fever (RVF) is a major zoonotic and arboviral hemorrhagic fever. The conditions leading to RVF epidemics are still unclear, and the relative role of climatic and anthropogenic factors may vary between ecosystems. Here, we estimate the most likely scenario that led to RVF emergence on the island of Mayotte, following the 2006–2007 African epidemic. We developed the first mathematical model for RVF that accounts for climate, animal imports and livestock susceptibility, which is fitted to a 12-years dataset. RVF emergence was found to be triggered by the import of infectious animals, whilst transmissibility was approximated as a linear or exponential function of vegetation density. Model forecasts indicated a very low probability of virus endemicity in 2017, and therefore of re-emergence in a closed system (i.e. without import of infected animals). However, the very high proportion of naive animals reached in 2016 implies that the island remains vulnerable to the import of infectious animals. We recommend reinforcing surveillance in livestock, should RVF be reported is neighbouring territories. Our model should be tested elsewhere, with ecosystem-specific data

An interdisciplinary co-authorship networking perspective on AR and human behavior: taking stock and moving ahead

The field of augmented reality (AR) and human behavior emerged when Azuma et al. (2001) refined the term augmented reality in 2001. Research on the topic has grown steadily in the past decade, yet there is a notable lack of consensus on humans' motivations and outcomes in interacting with AR. The present research takes a bibliographic approach to shed light on current research on AR and human-computer interaction and, using topic modeling, to identify and classify the topics that have drawn researchers’ interest. The results reveal three major topics of interest to researchers, namely “Education, Learning & Training Research”, “Marketing, Consumer Behavior & Business Research”, and “Digital Tourism & Cultural Heritage Research”. Drawing upon co-authorship theory, we identify prominent AR expert co-authorship networks that work on similar topics, yet also highlight that AR research is concentrated in a few research groups that publish articles with similar groups of authors and little outside their own networks. Together with AR experts from the four largest co-authorship networks, we highlight the common challenges that emerge in AR research, suggest solutions, and jointly propose a research agenda for AR and human behavior research

Modelling Costs of Interventional Pulmonary Embolism Treatment: Implications of US Trends for a European Healthcare System

BACKGROUND Catheter-directed treatment (CDT) of acute pulmonary embolism (PE) is entering a growth phase in Europe following a steady increase in the United States (US) in the past decade, but the potential economic impact on European healthcare systems remains unknown. METHODS AND RESULTS We built two statistical models for the monthly trend of proportion of CDT among patients with severe (intermediate- or high-risk) PE in the US. The conservative model was based on admission data from the National Inpatient Sample (NIS) 2016-2020, and the model reflecting increasing access to advanced treatment from the PERTTM national quality assurance database registry 2018-2021. By applying these models to the forecast of annual PE-related hospitalizations in Germany, we calculated the annual number of severe PE cases and the expected increase in CDT use for the period 2025-2030. The NIS-based model yielded a slow increase, reaching 3.1% (95% CI 3.0-3.2%) among all hospitalizations with PE in 2030; in the PERT-based model, increase would be steeper, reaching 8.7% (8.3-9.2%). Based on current reimbursement rates, we estimated an increase of annual costs for PE-related hospitalizations in Germany ranging from 15.3 to 49.8 million euros by 2030. This calculation does not account for potential cost savings, including those from reduced length of hospital stay. CONCLUSION Our approach and results, which may be adapted to other European healthcare systems, provide a benchmark for healthcare costs expected to result from CDT. Data from ongoing trials on clinical benefits and cost savings are needed to determine cost-effectiveness and inform reimbursement decisions