Zoonotic causes of febrile illness in malaria endemic countries:a systematic review

Fever is one of the most common reasons for seeking health care globally and most human pathogens are zoonotic. We conducted a systematic review to describe the occurrence and distribution of zoonotic causes of human febrile illness reported in malaria endemic countries. We included data from 53 (48·2%) of 110 malaria endemic countries and 244 articles that described diagnosis of 30 zoonoses in febrile people. The majority (17) of zoonoses were bacterial, with nine viruses, three protozoa, and one helminth also identified. Leptospira species and non-typhoidal salmonella serovars were the most frequently reported pathogens. Despite evidence of profound data gaps, this Review reveals widespread distribution of multiple zoonoses that cause febrile illness. Greater understanding of the epidemiology of zoonoses in different settings is needed to improve awareness about these pathogens and the management of febrile illness

Relative importance of black carbon, brown carbon, and absorption enhancement from clear coatings in biomass burning emissions

A wide range of globally significant biomass fuels were burned during the fourth Fire Lab at Missoula Experiment (FLAME-4). A multi-channel photoacoustic absorption spectrometer (PAS) measured dry absorption at 405, 532, and 660 nm and thermally denuded (250 °C) absorption at 405 and 660 nm. Absorption coefficients were broken into contributions from black carbon (BC), brown carbon (BrC), and lensing following three different methodologies, with one extreme being a method that assumes the thermal denuder effectively removes organics and the other extreme being a method based on the assumption that black carbon (BC) has an Ångström exponent of unity. The methodologies employed provide ranges of potential importance of BrC to absorption but, on average, there was a difference of a factor of 2 in the ratio of the fraction of absorption attributable to BrC estimated by the two methods. BrC absorption at shorter visible wavelengths is of equal or greater importance to that of BC, with maximum contributions of up to 92 % of total aerosol absorption at 405 nm and up to 58 % of total absorption at 532 nm. Lensing is estimated to contribute a maximum of 30 % of total absorption, but typically contributes much less than this. Absorption enhancements and the estimated fraction of absorption from BrC show good correlation with the elemental-carbon-to-organic-carbon ratio (EC/OC) of emitted aerosols and weaker correlation with the modified combustion efficiency (MCE). Previous studies have shown that BrC grows darker (larger imaginary refractive index) as the ratio of black to organic aerosol (OA) mass increases. This study is consistent with those findings but also demonstrates that the fraction of total absorption attributable to BrC shows the opposite trend: increasing as the organic fraction of aerosol emissions increases and the EC/OC ratio decreases

Whitepaper: Understanding land-atmosphere interactions through tower-based flux and continuous atmospheric boundary layer measurements

Executive summary ● Target audience: AmeriFlux community, AmeriFlux Science Steering Committee & Department of Energy (DOE) program managers [ARM/ASR (atmosphere), TES (surface), and SBR (subsurface)] ● Problem statement: The atmospheric boundary layer mediates the exchange of energy and matter between the land surface and the free troposphere integrating a range of physical, chemical, and biological processes. However, continuous atmospheric boundary layer observations at AmeriFlux sites are still scarce. How can adding measurements of the atmospheric boundary layer enhance the scientific value of the AmeriFlux network? ● Research opportunities: We highlight four key opportunities to integrate tower-based flux measurements with continuous, long-term atmospheric boundary layer measurements: (1) to interpret surface flux and atmospheric boundary layer exchange dynamics at flux tower sites, (2) to support regionalscale modeling and upscaling of surface fluxes to continental scales, (3) to validate land-atmosphere coupling in Earth system models, and (4) to support flux footprint modelling, the interpretation of surface fluxes in heterogeneous terrain, and quality control of eddy covariance flux measurements. ● Recommended actions: Adding a suite of atmospheric boundary layer measurements to eddy covariance flux tower sites would allow the Earth science community to address new emerging research questions, to better interpret ongoing flux tower measurements, and would present novel opportunities for collaboration between AmeriFlux scientists and atmospheric and remote sensing scientists. We therefore recommend that (1) a set of instrumentation for continuous atmospheric boundary layer observations be added to a subset of AmeriFlux sites spanning a range of ecosystem types and climate zones, that (2) funding agencies (e.g., Department of Energy, NASA) solicit research on land-atmosphere processes where the benefits of fully integrated atmospheric boundary layer observations can add value to key scientific questions, and that (3) the AmeriFlux Management Project acquires loaner instrumentation for atmospheric boundary layer observations for use in experiments and short-term duration campaigns

Sociocultural and Health System Factors Associated With Mortality Among Febrile Inpatients in Tanzania: A Prospective Social Biopsy Cohort Study

Introduction Communicable diseases are the leading causes of death in Tanzania despite the existence of effective treatment tools. We aimed to assess the sociocultural and health system factors associated with mortality from febrile illness in northern Tanzania. Methods We interviewed febrile inpatients to determine prevalence of barriers in seeking or receiving care and grouped these barriers using the Three Delays model (delays at home, in transport and at healthcare facilities). We assessed 6-week mortality and, after matching on age, gender and severity of illness, measured the association between delays and mortality using conditional logistic regression. Results We enrolled 475 children, of whom 18 (3.8%) died, and 260 adults, of whom 34 (13.0%) died. For children, home delays were not associated with mortality. Among adults, a delay in care-seeking due to not recognising severe symptoms was associated with mortality (OR: 3.01; 95% CI 1.24 to 7.32). For transport delays, taking \u3e1 hour to reach a facility increased odds of death in children (OR: 3.27; 95% CI 1.11 to 9.66) and adults (OR: 3.03; 95% CI 1.32 to 6.99). For health system delays, each additional facility visited was associated with mortality for children (OR: 1.59; 95% CI 1.06 to 2.38) and adults (OR: 2.00; 95% CI 1.17 to 3.41), as was spending \u3e4 days between the first facility visit and reaching tertiary care (OR: 4.39; 95% CI 1.49 to 12.93). Conclusion Our findings suggest that delays at home, in transport and in accessing tertiary care are risk factors for mortality from febrile illness in northern Tanzania. Interventions that may reduce mortality include community education regarding severe symptoms, expanding transportation infrastructure and streamlining referrals to tertiary care for the sickest patients

Global transpiration data from sap flow measurements: The SAPFLUXNET database

Plant transpiration links physiological responses of vegetation to water supply and demand with hydrological, energy, and carbon budgets at the land-atmosphere interface. However, despite being the main land evaporative flux at the global scale, transpiration and its response to environmental drivers are currently not well constrained by observations. Here we introduce the first global compilation of whole-plant transpiration data from sap flow measurements (SAPFLUXNET, https://sapfluxnet.creaf.cat/, last access: 8 June 2021). We harmonized and quality-controlled individual datasets supplied by contributors worldwide in a semi-automatic data workflow implemented in the R programming language. Datasets include sub-daily time series of sap flow and hydrometeorological drivers for one or more growing seasons, as well as metadata on the stand characteristics, plant attributes, and technical details of the measurements. SAPFLUXNET contains 202 globally distributed datasets with sap flow time series for 2714 plants, mostly trees, of 174 species. SAPFLUXNET has a broad bioclimatic coverage, with woodland/shrubland and temperate forest biomes especially well represented (80% of the datasets). The measurements cover a wide variety of stand structural characteristics and plant sizes. The datasets encompass the period between 1995 and 2018, with 50% of the datasets being at least 3 years long. Accompanying radiation and vapour pressure deficit data are available for most of the datasets, while on-site soil water content is available for 56% of the datasets. Many datasets contain data for species that make up 90% or more of the total stand basal area, allowing the estimation of stand transpiration in diverse ecological settings. SAPFLUXNET adds to existing plant trait datasets, ecosystem flux networks, and remote sensing products to help increase our understanding of plant water use, plant responses to drought, and ecohydrological processes. SAPFLUXNET version 0.1.5 is freely available from the Zenodo repository (10.5281/zenodo.3971689; Poyatos et al., 2020a). The "sapfluxnetr"R package-designed to access, visualize, and process SAPFLUXNET data-is available from CRAN. © 2021 Rafael Poyatos et al.This research was supported by the Minis-terio de Economía y Competitividad (grant no. CGL2014-55883-JIN), the Ministerio de Ciencia e Innovación (grant no. RTI2018-095297-J-I00), the Ministerio de Ciencia e Innovación (grant no. CAS16/00207), the Agència de Gestió d’Ajuts Universitaris i de Recerca (grant no. SGR1001), the Alexander von Humboldt-Stiftung (Humboldt Research Fellowship for Experienced Researchers (RP)), and the Institució Catalana de Recerca i Estudis Avançats (Academia Award (JMV)). Víctor Flo was supported by the doctoral fellowship FPU15/03939 (MECD, Spain)

Author Correction: The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The following authors were omitted from the original version of this Data Descriptor: Markus Reichstein and Nicolas Vuichard. Both contributed to the code development and N. Vuichard contributed to the processing of the ERA-Interim data downscaling. Furthermore, the contribution of the co-author Frank Tiedemann was re-evaluated relative to the colleague Corinna Rebmann, both working at the same sites, and based on this re-evaluation a substitution in the co-author list is implemented (with Rebmann replacing Tiedemann). Finally, two affiliations were listed incorrectly and are corrected here (entries 190 and 193). The author list and affiliations have been amended to address these omissions in both the HTML and PDF versions

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data.

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible

Global transpiration data from sap flow measurements : the SAPFLUXNET database

Plant transpiration links physiological responses of vegetation to water supply and demand with hydrological, energy, and carbon budgets at the land-atmosphere interface. However, despite being the main land evaporative flux at the global scale, transpiration and its response to environmental drivers are currently not well constrained by observations. Here we introduce the first global compilation of whole-plant transpiration data from sap flow measurements (SAPFLUXNET, https://sapfluxnet.creaf.cat/, last access: 8 June 2021). We harmonized and quality-controlled individual datasets supplied by contributors worldwide in a semi-automatic data workflow implemented in the R programming language. Datasets include sub-daily time series of sap flow and hydrometeorological drivers for one or more growing seasons, as well as metadata on the stand characteristics, plant attributes, and technical details of the measurements. SAPFLUXNET contains 202 globally distributed datasets with sap flow time series for 2714 plants, mostly trees, of 174 species. SAPFLUXNET has a broad bioclimatic coverage, with woodland/shrubland and temperate forest biomes especially well represented (80 % of the datasets). The measurements cover a wide variety of stand structural characteristics and plant sizes. The datasets encompass the period between 1995 and 2018, with 50 % of the datasets being at least 3 years long. Accompanying radiation and vapour pressure deficit data are available for most of the datasets, while on-site soil water content is available for 56 % of the datasets. Many datasets contain data for species that make up 90 % or more of the total stand basal area, allowing the estimation of stand transpiration in diverse ecological settings. SAPFLUXNET adds to existing plant trait datasets, ecosystem flux networks, and remote sensing products to help increase our understanding of plant water use, plant responses to drought, and ecohydrological processes. SAPFLUXNET version 0.1.5 is freely available from the Zenodo repository (https://doi.org/10.5281/zenodo.3971689; Poyatos et al., 2020a). The "sapfluxnetr" R package - designed to access, visualize, and process SAPFLUXNET data - is available from CRAN.Peer reviewe

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.Peer reviewe