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1.	Abbafati, C, et al. (author) Five insights from the Global Burden of Disease Study 2019 2020 In: Lancet (London, England). - 1474-547X .- 0140-6736. ; 396:10258, s. 1135-1159 Journal article (peer-reviewed)
2.	Lozano, R, et al. (author) Measuring universal health coverage based on an index of effective coverage of health services in 204 countries and territories, 1990-2019: a systematic analysis for the Global Burden of Disease Study 2019 2020 In: Lancet (London, England). - : Elsevier BV. - 1474-547X .- 0140-6736. ; 396:10258, s. 1250-1284 Journal article (peer-reviewed)
3.	Abbafati, Cristiana, et al. (author) 2020 Journal article (peer-reviewed)
4.	Forouzanfar, Mohammad H, et al. (author) Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks in 188 countries, 1990-2013 : a systematic analysis for the Global Burden of Disease Study 2013. 2015 In: The Lancet. - 0140-6736 .- 1474-547X. ; 386:10010, s. 2287-2323 Journal article (peer-reviewed)abstract BACKGROUND: The Global Burden of Disease, Injuries, and Risk Factor study 2013 (GBD 2013) is the first of a series of annual updates of the GBD. Risk factor quantification, particularly of modifiable risk factors, can help to identify emerging threats to population health and opportunities for prevention. The GBD 2013 provides a timely opportunity to update the comparative risk assessment with new data for exposure, relative risks, and evidence on the appropriate counterfactual risk distribution.METHODS: Attributable deaths, years of life lost, years lived with disability, and disability-adjusted life-years (DALYs) have been estimated for 79 risks or clusters of risks using the GBD 2010 methods. Risk-outcome pairs meeting explicit evidence criteria were assessed for 188 countries for the period 1990-2013 by age and sex using three inputs: risk exposure, relative risks, and the theoretical minimum risk exposure level (TMREL). Risks are organised into a hierarchy with blocks of behavioural, environmental and occupational, and metabolic risks at the first level of the hierarchy. The next level in the hierarchy includes nine clusters of related risks and two individual risks, with more detail provided at levels 3 and 4 of the hierarchy. Compared with GBD 2010, six new risk factors have been added: handwashing practices, occupational exposure to trichloroethylene, childhood wasting, childhood stunting, unsafe sex, and low glomerular filtration rate. For most risks, data for exposure were synthesised with a Bayesian meta-regression method, DisMod-MR 2.0, or spatial-temporal Gaussian process regression. Relative risks were based on meta-regressions of published cohort and intervention studies. Attributable burden for clusters of risks and all risks combined took into account evidence on the mediation of some risks such as high body-mass index (BMI) through other risks such as high systolic blood pressure and high cholesterol.FINDINGS: All risks combined account for 57·2% (95% uncertainty interval [UI] 55·8-58·5) of deaths and 41·6% (40·1-43·0) of DALYs. Risks quantified account for 87·9% (86·5-89·3) of cardiovascular disease DALYs, ranging to a low of 0% for neonatal disorders and neglected tropical diseases and malaria. In terms of global DALYs in 2013, six risks or clusters of risks each caused more than 5% of DALYs: dietary risks accounting for 11·3 million deaths and 241·4 million DALYs, high systolic blood pressure for 10·4 million deaths and 208·1 million DALYs, child and maternal malnutrition for 1·7 million deaths and 176·9 million DALYs, tobacco smoke for 6·1 million deaths and 143·5 million DALYs, air pollution for 5·5 million deaths and 141·5 million DALYs, and high BMI for 4·4 million deaths and 134·0 million DALYs. Risk factor patterns vary across regions and countries and with time. In sub-Saharan Africa, the leading risk factors are child and maternal malnutrition, unsafe sex, and unsafe water, sanitation, and handwashing. In women, in nearly all countries in the Americas, north Africa, and the Middle East, and in many other high-income countries, high BMI is the leading risk factor, with high systolic blood pressure as the leading risk in most of Central and Eastern Europe and south and east Asia. For men, high systolic blood pressure or tobacco use are the leading risks in nearly all high-income countries, in north Africa and the Middle East, Europe, and Asia. For men and women, unsafe sex is the leading risk in a corridor from Kenya to South Africa.INTERPRETATION: Behavioural, environmental and occupational, and metabolic risks can explain half of global mortality and more than one-third of global DALYs providing many opportunities for prevention. Of the larger risks, the attributable burden of high BMI has increased in the past 23 years. In view of the prominence of behavioural risk factors, behavioural and social science research on interventions for these risks should be strengthened. Many prevention and primary care policy options are available now to act on key risks.FUNDING: Bill & Melinda Gates Foundation.
5.	Galles, NC, et al. (author) Measuring routine childhood vaccination coverage in 204 countries and territories, 1980-2019: a systematic analysis for the Global Burden of Disease Study 2020, Release 1 2021 In: Lancet (London, England). - 1474-547X. ; 398:10299, s. 503-521 Journal article (peer-reviewed)
6.	Vos, Theo, et al. (author) Global, regional, and national incidence, prevalence, and years lived with disability for 301 acute and chronic diseases and injuries in 188 countries, 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013 2015 In: The Lancet. - 1474-547X .- 0140-6736. ; 386:9995, s. 743-800 Journal article (peer-reviewed)abstract Background Up-to-date evidence about levels and trends in disease and injury incidence, prevalence, and years lived with disability (YLDs) is an essential input into global, regional, and national health policies. In the Global Burden of Disease Study 2013 (GBD 2013), we estimated these quantities for acute and chronic diseases and injuries for 188 countries between 1990 and 2013. Methods Estimates were calculated for disease and injury incidence, prevalence, and YLDs using GBD 2010 methods with some important refinements. Results for incidence of acute disorders and prevalence of chronic disorders are new additions to the analysis. Key improvements include expansion to the cause and sequelae list, updated systematic reviews, use of detailed injury codes, improvements to the Bayesian meta-regression method (DisMod-MR), and use of severity splits for various causes. An index of data representativeness, showing data availability, was calculated for each cause and impairment during three periods globally and at the country level for 2013. In total, 35 620 distinct sources of data were used and documented to calculated estimates for 301 diseases and injuries and 2337 sequelae. The comorbidity simulation provides estimates for the number of sequelae, concurrently, by individuals by country, year, age, and sex. Disability weights were updated with the addition of new population-based survey data from four countries. Findings Disease and injury were highly prevalent; only a small fraction of individuals had no sequelae. Comorbidity rose substantially with age and in absolute terms from 1990 to 2013. Incidence of acute sequelae were predominantly infectious diseases and short-term injuries, with over 2 billion cases of upper respiratory infections and diarrhoeal disease episodes in 2013, with the notable exception of tooth pain due to permanent caries with more than 200 million incident cases in 2013. Conversely, leading chronic sequelae were largely attributable to non-communicable diseases, with prevalence estimates for asymptomatic permanent caries and tension-type headache of 2.4 billion and 1.6 billion, respectively. The distribution of the number of sequelae in populations varied widely across regions, with an expected relation between age and disease prevalence. YLDs for both sexes increased from 537.6 million in 1990 to 764.8 million in 2013 due to population growth and ageing, whereas the age-standardised rate decreased little from 114.87 per 1000 people to 110.31 per 1000 people between 1990 and 2013. Leading causes of YLDs included low back pain and major depressive disorder among the top ten causes of YLDs in every country. YLD rates per person, by major cause groups, indicated the main drivers of increases were due to musculoskeletal, mental, and substance use disorders, neurological disorders, and chronic respiratory diseases; however HIV/AIDS was a notable driver of increasing YLDs in sub-Saharan Africa. Also, the proportion of disability-adjusted life years due to YLDs increased globally from 21.1% in 1990 to 31.2% in 2013. Interpretation Ageing of the world's population is leading to a substantial increase in the numbers of individuals with sequelae of diseases and injuries. Rates of YLDs are declining much more slowly than mortality rates. The non-fatal dimensions of disease and injury will require more and more attention from health systems. The transition to non-fatal outcomes as the dominant source of burden of disease is occurring rapidly outside of sub-Saharan Africa. Our results can guide future health initiatives through examination of epidemiological trends and a better understanding of variation across countries.
7.	Lozano, Rafael, et al. (author) Measuring progress from 1990 to 2017 and projecting attainment to 2030 of the health-related Sustainable Development Goals for 195 countries and territories: a systematic analysis for the Global Burden of Disease Study 2017 2018 In: The Lancet. - : Elsevier. - 1474-547X .- 0140-6736. ; 392:10159, s. 2091-2138 Journal article (peer-reviewed)abstract Background: Efforts to establish the 2015 baseline and monitor early implementation of the UN Sustainable Development Goals (SDGs) highlight both great potential for and threats to improving health by 2030. To fully deliver on the SDG aim of “leaving no one behind”, it is increasingly important to examine the health-related SDGs beyond national-level estimates. As part of the Global Burden of Diseases, Injuries, and Risk Factors Study 2017 (GBD 2017), we measured progress on 41 of 52 health-related SDG indicators and estimated the health-related SDG index for 195 countries and territories for the period 1990–2017, projected indicators to 2030, and analysed global attainment. Methods: We measured progress on 41 health-related SDG indicators from 1990 to 2017, an increase of four indicators since GBD 2016 (new indicators were health worker density, sexual violence by non-intimate partners, population census status, and prevalence of physical and sexual violence [reported separately]). We also improved the measurement of several previously reported indicators. We constructed national-level estimates and, for a subset of health-related SDGs, examined indicator-level differences by sex and Socio-demographic Index (SDI) quintile. We also did subnational assessments of performance for selected countries. To construct the health-related SDG index, we transformed the value for each indicator on a scale of 0–100, with 0 as the 2·5th percentile and 100 as the 97·5th percentile of 1000 draws calculated from 1990 to 2030, and took the geometric mean of the scaled indicators by target. To generate projections through 2030, we used a forecasting framework that drew estimates from the broader GBD study and used weighted averages of indicator-specific and country-specific annualised rates of change from 1990 to 2017 to inform future estimates. We assessed attainment of indicators with defined targets in two ways: first, using mean values projected for 2030, and then using the probability of attainment in 2030 calculated from 1000 draws. We also did a global attainment analysis of the feasibility of attaining SDG targets on the basis of past trends. Using 2015 global averages of indicators with defined SDG targets, we calculated the global annualised rates of change required from 2015 to 2030 to meet these targets, and then identified in what percentiles the required global annualised rates of change fell in the distribution of country-level rates of change from 1990 to 2015. We took the mean of these global percentile values across indicators and applied the past rate of change at this mean global percentile to all health-related SDG indicators, irrespective of target definition, to estimate the equivalent 2030 global average value and percentage change from 2015 to 2030 for each indicator. Findings: The global median health-related SDG index in 2017 was 59·4 (IQR 35·4–67·3), ranging from a low of 11·6 (95% uncertainty interval 9·6–14·0) to a high of 84·9 (83·1–86·7). SDG index values in countries assessed at the subnational level varied substantially, particularly in China and India, although scores in Japan and the UK were more homogeneous. Indicators also varied by SDI quintile and sex, with males having worse outcomes than females for non-communicable disease (NCD) mortality, alcohol use, and smoking, among others. Most countries were projected to have a higher health-related SDG index in 2030 than in 2017, while country-level probabilities of attainment by 2030 varied widely by indicator. Under-5 mortality, neonatal mortality, maternal mortality ratio, and malaria indicators had the most countries with at least 95% probability of target attainment. Other indicators, including NCD mortality and suicide mortality, had no countries projected to meet corresponding SDG targets on the basis of projected mean values for 2030 but showed some probability of attainment by 2030. For some indicators, including child malnutrition, several infectious diseases, and most violence measures, the annualised rates of change required to meet SDG targets far exceeded the pace of progress achieved by any country in the recent past. We found that applying the mean global annualised rate of change to indicators without defined targets would equate to about 19% and 22% reductions in global smoking and alcohol consumption, respectively; a 47% decline in adolescent birth rates; and a more than 85% increase in health worker density per 1000 population by 2030. Interpretation: The GBD study offers a unique, robust platform for monitoring the health-related SDGs across demographic and geographic dimensions. Our findings underscore the importance of increased collection and analysis of disaggregated data and highlight where more deliberate design or targeting of interventions could accelerate progress in attaining the SDGs. Current projections show that many health-related SDG indicators, NCDs, NCD-related risks, and violence-related indicators will require a concerted shift away from what might have driven past gains—curative interventions in the case of NCDs—towards multisectoral, prevention-oriented policy action and investments to achieve SDG aims. Notably, several targets, if they are to be met by 2030, demand a pace of progress that no country has achieved in the recent past. The future is fundamentally uncertain, and no model can fully predict what breakthroughs or events might alter the course of the SDGs. What is clear is that our actions—or inaction—today will ultimately dictate how close the world, collectively, can get to leaving no one behind by 2030.
8.	Naghavi, Mohsen, et al. (author) Global, regional, and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990-2013: a systematic analysis for the Global Burden of Disease Study 2013 2015 In: The Lancet. - 1474-547X .- 0140-6736. ; 385:9963, s. 117-171 Journal article (peer-reviewed)abstract Background Up-to-date evidence on levels and trends for age-sex-specifi c all-cause and cause-specifi c mortality is essential for the formation of global, regional, and national health policies. In the Global Burden of Disease Study 2013 (GBD 2013) we estimated yearly deaths for 188 countries between 1990, and 2013. We used the results to assess whether there is epidemiological convergence across countries. Methods We estimated age-sex-specifi c all-cause mortality using the GBD 2010 methods with some refinements to improve accuracy applied to an updated database of vital registration, survey, and census data. We generally estimated cause of death as in the GBD 2010. Key improvements included the addition of more recent vital registration data for 72 countries, an updated verbal autopsy literature review, two new and detailed data systems for China, and more detail for Mexico, UK, Turkey, and Russia. We improved statistical models for garbage code redistribution. We used six different modelling strategies across the 240 causes; cause of death ensemble modelling (CODEm) was the dominant strategy for causes with sufficient information. Trends for Alzheimer's disease and other dementias were informed by meta-regression of prevalence studies. For pathogen-specifi c causes of diarrhoea and lower respiratory infections we used a counterfactual approach. We computed two measures of convergence (inequality) across countries: the average relative difference across all pairs of countries (Gini coefficient) and the average absolute difference across countries. To summarise broad findings, we used multiple decrement life-tables to decompose probabilities of death from birth to exact age 15 years, from exact age 15 years to exact age 50 years, and from exact age 50 years to exact age 75 years, and life expectancy at birth into major causes. For all quantities reported, we computed 95% uncertainty intervals (UIs). We constrained cause-specific fractions within each age-sex-country-year group to sum to all-cause mortality based on draws from the uncertainty distributions. Findings Global life expectancy for both sexes increased from 65.3 years (UI 65.0-65.6) in 1990, to 71.5 years (UI 71.0-71.9) in 2013, while the number of deaths increased from 47.5 million (UI 46.8-48.2) to 54.9 million (UI 53.6-56.3) over the same interval. Global progress masked variation by age and sex: for children, average absolute diff erences between countries decreased but relative diff erences increased. For women aged 25-39 years and older than 75 years and for men aged 20-49 years and 65 years and older, both absolute and relative diff erences increased. Decomposition of global and regional life expectancy showed the prominent role of reductions in age-standardised death rates for cardiovascular diseases and cancers in high-income regions, and reductions in child deaths from diarrhoea, lower respiratory infections, and neonatal causes in low-income regions. HIV/AIDS reduced life expectancy in southern sub-Saharan Africa. For most communicable causes of death both numbers of deaths and age-standardised death rates fell whereas for most non-communicable causes, demographic shifts have increased numbers of deaths but decreased age-standardised death rates. Global deaths from injury increased by 10.7%, from 4.3 million deaths in 1990 to 4.8 million in 2013; but age-standardised rates declined over the same period by 21%. For some causes of more than 100 000 deaths per year in 2013, age-standardised death rates increased between 1990 and 2013, including HIV/AIDS, pancreatic cancer, atrial fibrillation and flutter, drug use disorders, diabetes, chronic kidney disease, and sickle-cell anaemias. Diarrhoeal diseases, lower respiratory infections, neonatal causes, and malaria are still in the top five causes of death in children younger than 5 years. The most important pathogens are rotavirus for diarrhoea and pneumococcus for lower respiratory infections. Country-specific probabilities of death over three phases of life were substantially varied between and within regions. Interpretation For most countries, the general pattern of reductions in age-sex specifi c mortality has been associated with a progressive shift towards a larger share of the remaining deaths caused by non-communicable disease and injuries. Assessing epidemiological convergence across countries depends on whether an absolute or relative measure of inequality is used. Nevertheless, age-standardised death rates for seven substantial causes are increasing, suggesting the potential for reversals in some countries. Important gaps exist in the empirical data for cause of death estimates for some countries; for example, no national data for India are available for the past decade.
9.	Sartorius, B, et al. (author) Subnational mapping of HIV incidence and mortality among individuals aged 15-49 years in sub-Saharan Africa, 2000-18: a modelling study 2021 In: The lancet. HIV. - 2352-3018. ; 8:6, s. E363-E375 Journal article (peer-reviewed)
10.	Stanaway, Jeffrey D., et al. (author) Global, regional, and national comparative risk assessment of 84 behavioural, environmental and occupational, and metabolic risks or clusters of risks for 195 countries and territories, 1990-2017: A systematic analysis for the Global Burden of Disease Study 2017 2018 In: The Lancet. - 1474-547X .- 0140-6736. ; 392:10159, s. 1923-1994 Journal article (peer-reviewed)abstract Background The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 comparative risk assessment (CRA) is a comprehensive approach to risk factor quantification that offers a useful tool for synthesising evidence on risks and risk-outcome associations. With each annual GBD study, we update the GBD CRA to incorporate improved methods, new risks and risk-outcome pairs, and new data on risk exposure levels and risk- outcome associations. Methods We used the CRA framework developed for previous iterations of GBD to estimate levels and trends in exposure, attributable deaths, and attributable disability-adjusted life-years (DALYs), by age group, sex, year, and location for 84 behavioural, environmental and occupational, and metabolic risks or groups of risks from 1990 to 2017. This study included 476 risk-outcome pairs that met the GBD study criteria for convincing or probable evidence of causation. We extracted relative risk and exposure estimates from 46 749 randomised controlled trials, cohort studies, household surveys, census data, satellite data, and other sources. We used statistical models to pool data, adjust for bias, and incorporate covariates. Using the counterfactual scenario of theoretical minimum risk exposure level (TMREL), we estimated the portion of deaths and DALYs that could be attributed to a given risk. We explored the relationship between development and risk exposure by modelling the relationship between the Socio-demographic Index (SDI) and risk-weighted exposure prevalence and estimated expected levels of exposure and risk-attributable burden by SDI. Finally, we explored temporal changes in risk-attributable DALYs by decomposing those changes into six main component drivers of change as follows: (1) population growth; (2) changes in population age structures; (3) changes in exposure to environmental and occupational risks; (4) changes in exposure to behavioural risks; (5) changes in exposure to metabolic risks; and (6) changes due to all other factors, approximated as the risk-deleted death and DALY rates, where the risk-deleted rate is the rate that would be observed had we reduced the exposure levels to the TMREL for all risk factors included in GBD 2017.
11.	Wang, Haidong, et al. (author) Global, regional, and national life expectancy, all-cause mortality, and cause-specific mortality for 249 causes of death, 1980-2015 : a systematic analysis for the Global Burden of Disease Study 2015 2016 In: The Lancet. - 0140-6736 .- 1474-547X. ; 388:10053, s. 1459-1544 Journal article (peer-reviewed)abstract BACKGROUND: Improving survival and extending the longevity of life for all populations requires timely, robust evidence on local mortality levels and trends. The Global Burden of Disease 2015 Study (GBD 2015) provides a comprehensive assessment of all-cause and cause-specific mortality for 249 causes in 195 countries and territories from 1980 to 2015. These results informed an in-depth investigation of observed and expected mortality patterns based on sociodemographic measures.METHODS: We estimated all-cause mortality by age, sex, geography, and year using an improved analytical approach originally developed for GBD 2013 and GBD 2010. Improvements included refinements to the estimation of child and adult mortality and corresponding uncertainty, parameter selection for under-5 mortality synthesis by spatiotemporal Gaussian process regression, and sibling history data processing. We also expanded the database of vital registration, survey, and census data to 14 294 geography-year datapoints. For GBD 2015, eight causes, including Ebola virus disease, were added to the previous GBD cause list for mortality. We used six modelling approaches to assess cause-specific mortality, with the Cause of Death Ensemble Model (CODEm) generating estimates for most causes. We used a series of novel analyses to systematically quantify the drivers of trends in mortality across geographies. First, we assessed observed and expected levels and trends of cause-specific mortality as they relate to the Socio-demographic Index (SDI), a summary indicator derived from measures of income per capita, educational attainment, and fertility. Second, we examined factors affecting total mortality patterns through a series of counterfactual scenarios, testing the magnitude by which population growth, population age structures, and epidemiological changes contributed to shifts in mortality. Finally, we attributed changes in life expectancy to changes in cause of death. We documented each step of the GBD 2015 estimation processes, as well as data sources, in accordance with Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER).FINDINGS: Globally, life expectancy from birth increased from 61·7 years (95% uncertainty interval 61·4-61·9) in 1980 to 71·8 years (71·5-72·2) in 2015. Several countries in sub-Saharan Africa had very large gains in life expectancy from 2005 to 2015, rebounding from an era of exceedingly high loss of life due to HIV/AIDS. At the same time, many geographies saw life expectancy stagnate or decline, particularly for men and in countries with rising mortality from war or interpersonal violence. From 2005 to 2015, male life expectancy in Syria dropped by 11·3 years (3·7-17·4), to 62·6 years (56·5-70·2). Total deaths increased by 4·1% (2·6-5·6) from 2005 to 2015, rising to 55·8 million (54·9 million to 56·6 million) in 2015, but age-standardised death rates fell by 17·0% (15·8-18·1) during this time, underscoring changes in population growth and shifts in global age structures. The result was similar for non-communicable diseases (NCDs), with total deaths from these causes increasing by 14·1% (12·6-16·0) to 39·8 million (39·2 million to 40·5 million) in 2015, whereas age-standardised rates decreased by 13·1% (11·9-14·3). Globally, this mortality pattern emerged for several NCDs, including several types of cancer, ischaemic heart disease, cirrhosis, and Alzheimer's disease and other dementias. By contrast, both total deaths and age-standardised death rates due to communicable, maternal, neonatal, and nutritional conditions significantly declined from 2005 to 2015, gains largely attributable to decreases in mortality rates due to HIV/AIDS (42·1%, 39·1-44·6), malaria (43·1%, 34·7-51·8), neonatal preterm birth complications (29·8%, 24·8-34·9), and maternal disorders (29·1%, 19·3-37·1). Progress was slower for several causes, such as lower respiratory infections and nutritional deficiencies, whereas deaths increased for others, including dengue and drug use disorders. Age-standardised death rates due to injuries significantly declined from 2005 to 2015, yet interpersonal violence and war claimed increasingly more lives in some regions, particularly in the Middle East. In 2015, rotaviral enteritis (rotavirus) was the leading cause of under-5 deaths due to diarrhoea (146 000 deaths, 118 000-183 000) and pneumococcal pneumonia was the leading cause of under-5 deaths due to lower respiratory infections (393 000 deaths, 228 000-532 000), although pathogen-specific mortality varied by region. Globally, the effects of population growth, ageing, and changes in age-standardised death rates substantially differed by cause. Our analyses on the expected associations between cause-specific mortality and SDI show the regular shifts in cause of death composition and population age structure with rising SDI. Country patterns of premature mortality (measured as years of life lost [YLLs]) and how they differ from the level expected on the basis of SDI alone revealed distinct but highly heterogeneous patterns by region and country or territory. Ischaemic heart disease, stroke, and diabetes were among the leading causes of YLLs in most regions, but in many cases, intraregional results sharply diverged for ratios of observed and expected YLLs based on SDI. Communicable, maternal, neonatal, and nutritional diseases caused the most YLLs throughout sub-Saharan Africa, with observed YLLs far exceeding expected YLLs for countries in which malaria or HIV/AIDS remained the leading causes of early death.INTERPRETATION: At the global scale, age-specific mortality has steadily improved over the past 35 years; this pattern of general progress continued in the past decade. Progress has been faster in most countries than expected on the basis of development measured by the SDI. Against this background of progress, some countries have seen falls in life expectancy, and age-standardised death rates for some causes are increasing. Despite progress in reducing age-standardised death rates, population growth and ageing mean that the number of deaths from most non-communicable causes are increasing in most countries, putting increased demands on health systems.
12.	Kassebaum, Nicholas J., et al. (author) Global, regional, and national disability-adjusted life-years (DALYs) for 315 diseases and injuries and healthy life expectancy (HALE), 1990-2015 : a systematic analysis for the Global Burden of Disease Study 2015 2016 In: The Lancet. - 0140-6736 .- 1474-547X. ; 388:10053, s. 1603-1658 Journal article (peer-reviewed)abstract Background Healthy life expectancy (HALE) and disability-adjusted life-years (DALYs) provide summary measures of health across geographies and time that can inform assessments of epidemiological patterns and health system performance, help to prioritise investments in research and development, and monitor progress toward the Sustainable Development Goals (SDGs). We aimed to provide updated HALE and DALYs for geographies worldwide and evaluate how disease burden changes with development. Methods We used results from the Global Burden of Diseases, Injuries, and Risk Factors Study 2015 (GBD 2015) for all-cause mortality, cause-specific mortality, and non-fatal disease burden to derive HALE and DALYs by sex for 195 countries and territories from 1990 to 2015. We calculated DALYs by summing years of life lost (YLLs) and years of life lived with disability (YLDs) for each geography, age group, sex, and year. We estimated HALE using the Sullivan method, which draws from age-specific death rates and YLDs per capita. We then assessed how observed levels of DALYs and HALE differed from expected trends calculated with the Socio-demographic Index (SDI), a composite indicator constructed from measures of income per capita, average years of schooling, and total fertility rate. Findings Total global DALYs remained largely unchanged from 1990 to 2015, with decreases in communicable, neonatal, maternal, and nutritional (Group 1) disease DALYs off set by increased DALYs due to non-communicable diseases (NCDs). Much of this epidemiological transition was caused by changes in population growth and ageing, but it was accelerated by widespread improvements in SDI that also correlated strongly with the increasing importance of NCDs. Both total DALYs and age-standardised DALY rates due to most Group 1 causes significantly decreased by 2015, and although total burden climbed for the majority of NCDs, age-standardised DALY rates due to NCDs declined. Nonetheless, age-standardised DALY rates due to several high-burden NCDs (including osteoarthritis, drug use disorders, depression, diabetes, congenital birth defects, and skin, oral, and sense organ diseases) either increased or remained unchanged, leading to increases in their relative ranking in many geographies. From 2005 to 2015, HALE at birth increased by an average of 2.9 years (95% uncertainty interval 2.9-3.0) for men and 3.5 years (3.4-3.7) for women, while HALE at age 65 years improved by 0.85 years (0.78-0.92) and 1.2 years (1.1-1.3), respectively. Rising SDI was associated with consistently higher HALE and a somewhat smaller proportion of life spent with functional health loss; however, rising SDI was related to increases in total disability. Many countries and territories in central America and eastern sub-Saharan Africa had increasingly lower rates of disease burden than expected given their SDI. At the same time, a subset of geographies recorded a growing gap between observed and expected levels of DALYs, a trend driven mainly by rising burden due to war, interpersonal violence, and various NCDs. Interpretation Health is improving globally, but this means more populations are spending more time with functional health loss, an absolute expansion of morbidity. The proportion of life spent in ill health decreases somewhat with increasing SDI, a relative compression of morbidity, which supports continued efforts to elevate personal income, improve education, and limit fertility. Our analysis of DALYs and HALE and their relationship to SDI represents a robust framework on which to benchmark geography-specific health performance and SDG progress. Country-specific drivers of disease burden, particularly for causes with higher-than-expected DALYs, should inform financial and research investments, prevention efforts, health policies, and health system improvement initiatives for all countries along the development continuum.
13.	Bikbov, B, et al. (author) Global, regional, and national burden of chronic kidney disease, 1990-2017: a systematic analysis for the Global Burden of Disease Study 2017 2020 In: Lancet (London, England). - : Elsevier BV. - 1474-547X .- 0140-6736. ; 395:10225, s. 709-733 Journal article (peer-reviewed)
14.	Wang, Haidong, et al. (author) Estimates of global, regional, and national incidence, prevalence, and mortality of HIV, 1980-2015 : the Global Burden of Disease Study 2015. 2016 In: The lancet. HIV. - : Elsevier. - 2352-3018. ; 3:8, s. e361-e387 Journal article (peer-reviewed)abstract BACKGROUND: Timely assessment of the burden of HIV/AIDS is essential for policy setting and programme evaluation. In this report from the Global Burden of Disease Study 2015 (GBD 2015), we provide national estimates of levels and trends of HIV/AIDS incidence, prevalence, coverage of antiretroviral therapy (ART), and mortality for 195 countries and territories from 1980 to 2015.METHODS: For countries without high-quality vital registration data, we estimated prevalence and incidence with data from antenatal care clinics and population-based seroprevalence surveys, and with assumptions by age and sex on initial CD4 distribution at infection, CD4 progression rates (probability of progression from higher to lower CD4 cell-count category), on and off antiretroviral therapy (ART) mortality, and mortality from all other causes. Our estimation strategy links the GBD 2015 assessment of all-cause mortality and estimation of incidence and prevalence so that for each draw from the uncertainty distribution all assumptions used in each step are internally consistent. We estimated incidence, prevalence, and death with GBD versions of the Estimation and Projection Package (EPP) and Spectrum software originally developed by the Joint United Nations Programme on HIV/AIDS (UNAIDS). We used an open-source version of EPP and recoded Spectrum for speed, and used updated assumptions from systematic reviews of the literature and GBD demographic data. For countries with high-quality vital registration data, we developed the cohort incidence bias adjustment model to estimate HIV incidence and prevalence largely from the number of deaths caused by HIV recorded in cause-of-death statistics. We corrected these statistics for garbage coding and HIV misclassification.FINDINGS: Global HIV incidence reached its peak in 1997, at 3·3 million new infections (95% uncertainty interval [UI] 3·1-3·4 million). Annual incidence has stayed relatively constant at about 2·6 million per year (range 2·5-2·8 million) since 2005, after a period of fast decline between 1997 and 2005. The number of people living with HIV/AIDS has been steadily increasing and reached 38·8 million (95% UI 37·6-40·4 million) in 2015. At the same time, HIV/AIDS mortality has been declining at a steady pace, from a peak of 1·8 million deaths (95% UI 1·7-1·9 million) in 2005, to 1·2 million deaths (1·1-1·3 million) in 2015. We recorded substantial heterogeneity in the levels and trends of HIV/AIDS across countries. Although many countries have experienced decreases in HIV/AIDS mortality and in annual new infections, other countries have had slowdowns or increases in rates of change in annual new infections.INTERPRETATION: Scale-up of ART and prevention of mother-to-child transmission has been one of the great successes of global health in the past two decades. However, in the past decade, progress in reducing new infections has been slow, development assistance for health devoted to HIV has stagnated, and resources for health in low-income countries have grown slowly. Achievement of the new ambitious goals for HIV enshrined in Sustainable Development Goal 3 and the 90-90-90 UNAIDS targets will be challenging, and will need continued efforts from governments and international agencies in the next 15 years to end AIDS by 2030.
15.	Sepanlou, Sadaf G., et al. (author) The global, regional, and national burden of cirrhosis by cause in 195 countries and territories, 1990-2017 : a systematic analysis for the Global Burden of Disease Study 2017 2020 In: The Lancet Gastroenterology & Hepatology. - 2468-1253. ; 5:3, s. 245-266 Journal article (peer-reviewed)abstract Background Cirrhosis and other chronic liver diseases (collectively referred to as cirrhosis in this paper) are a major cause of morbidity and mortality globally, although the burden and underlying causes differ across locations and demographic groups. We report on results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 on the burden of cirrhosis and its trends since 1990, by cause, sex, and age, for 195 countries and territories. Methods We used data from vital registrations, vital registration samples, and verbal autopsies to estimate mortality. We modelled prevalence of total, compensated, and decompensated cirrhosis on the basis of hospital and claims data. Disability-adjusted life-years (DALYs) were calculated as the sum of years of life lost due to premature death and years lived with disability. Estimates are presented as numbers and age-standardised or age-specific rates per 100 000 population, with 95% uncertainty intervals (UIs). All estimates are presented for five causes of cirrhosis: hepatitis B, hepatitis C, alcohol-related liver disease, non-alcoholic steatohepatitis (NASH), and other causes. We compared mortality, prevalence, and DALY estimates with those expected according to the Socio-demographic Index (SDI) as a proxy for the development status of regions and countries. Findings In 2017, cirrhosis caused more than 1.32 million (95% UI 1.27-1.45) deaths (440000 [416 000-518 000; 33.3%] in females and 883 000 [838 000-967 000; 66.7%] in males) globally, compared with less than 899 000 (829 000-948 000) deaths in 1990. Deaths due to cirrhosis constituted 2.4% (2.3-2.6) of total deaths globally in 2017 compared with 1.9% (1.8-2.0) in 1990. Despite an increase in the number of deaths, the age-standardised death rate decreased from 21.0 (19.2-22.3) per 100 000 population in 1990 to 16.5 (15.8-18-1) per 100 000 population in 2017. Sub-Saharan Africa had the highest age-standardised death rate among GBD super-regions for all years of the study period (32.2 [25.8-38.6] deaths per 100 000 population in 2017), and the high-income super-region had the lowest (10.1 [9.8-10-5] deaths per 100 000 population in 2017). The age-standardised death rate decreased or remained constant from 1990 to 2017 in all GBD regions except eastern Europe and central Asia, where the age-standardised death rate increased, primarily due to increases in alcohol-related liver disease prevalence. At the national level, the age-standardised death rate of cirrhosis was lowest in Singapore in 2017 (3.7 [3.3-4.0] per 100 000 in 2017) and highest in Egypt in all years since 1990 (103.3 [64.4-133.4] per 100 000 in 2017). There were 10.6 million (10.3-10.9) prevalent cases of decompensated cirrhosis and 112 million (107-119) prevalent cases of compensated cirrhosis globally in 2017. There was a significant increase in age-standardised prevalence rate of decompensated cirrhosis between 1990 and 2017. Cirrhosis caused by NASH had a steady age-standardised death rate throughout the study period, whereas the other four causes showed declines in age-standardised death rate. The age-standardised prevalence of compensated and decompensated cirrhosis due to NASH increased more than for any other cause of cirrhosis (by 33.2% for compensated cirrhosis and 54.8% for decompensated cirrhosis) over the study period. From 1990 to 2017, the number of prevalent cases snore than doubled for compensated cirrhosis due to NASH and more than tripled for decompensated cirrhosis due to NASH. In 2017, age-standardised death and DALY rates were lower among countries and territories with higher SDI. Interpretation Cirrhosis imposes a substantial health burden on many countries and this burden has increased at the global level since 1990, partly due to population growth and ageing. Although the age-standardised death and DALY rates of cirrhosis decreased from 1990 to 2017, numbers of deaths and DALYs and the proportion of all global deaths due to cirrhosis increased. Despite the availability of effective interventions for the prevention and treatment of hepatitis B and C, they were still the main causes of cirrhosis burden worldwide, particularly in low-income countries. The impact of hepatitis B and C is expected to be attenuated and overtaken by that of NASH in the near future. Cost-effective interventions are required to continue the prevention and treatment of viral hepatitis, and to achieve early diagnosis and prevention of cirrhosis due to alcohol-related liver disease and NASH.
16.	Wang, Haidong, et al. (author) Global, regional, and national levels of neonatal, infant, and under-5 mortality during 1990-2013 : a systematic analysis for the Global Burden of Disease Study 2013 2014 In: The Lancet. - 0140-6736 .- 1474-547X. ; 384:9947, s. 957-979 Journal article (peer-reviewed)abstract BACKGROUND: Remarkable financial and political efforts have been focused on the reduction of child mortality during the past few decades. Timely measurements of levels and trends in under-5 mortality are important to assess progress towards the Millennium Development Goal 4 (MDG 4) target of reduction of child mortality by two thirds from 1990 to 2015, and to identify models of success.METHODS: We generated updated estimates of child mortality in early neonatal (age 0-6 days), late neonatal (7-28 days), postneonatal (29-364 days), childhood (1-4 years), and under-5 (0-4 years) age groups for 188 countries from 1970 to 2013, with more than 29 000 survey, census, vital registration, and sample registration datapoints. We used Gaussian process regression with adjustments for bias and non-sampling error to synthesise the data for under-5 mortality for each country, and a separate model to estimate mortality for more detailed age groups. We used explanatory mixed effects regression models to assess the association between under-5 mortality and income per person, maternal education, HIV child death rates, secular shifts, and other factors. To quantify the contribution of these different factors and birth numbers to the change in numbers of deaths in under-5 age groups from 1990 to 2013, we used Shapley decomposition. We used estimated rates of change between 2000 and 2013 to construct under-5 mortality rate scenarios out to 2030.FINDINGS: We estimated that 6·3 million (95% UI 6·0-6·6) children under-5 died in 2013, a 64% reduction from 17·6 million (17·1-18·1) in 1970. In 2013, child mortality rates ranged from 152·5 per 1000 livebirths (130·6-177·4) in Guinea-Bissau to 2·3 (1·8-2·9) per 1000 in Singapore. The annualised rates of change from 1990 to 2013 ranged from -6·8% to 0·1%. 99 of 188 countries, including 43 of 48 countries in sub-Saharan Africa, had faster decreases in child mortality during 2000-13 than during 1990-2000. In 2013, neonatal deaths accounted for 41·6% of under-5 deaths compared with 37·4% in 1990. Compared with 1990, in 2013, rising numbers of births, especially in sub-Saharan Africa, led to 1·4 million more child deaths, and rising income per person and maternal education led to 0·9 million and 2·2 million fewer deaths, respectively. Changes in secular trends led to 4·2 million fewer deaths. Unexplained factors accounted for only -1% of the change in child deaths. In 30 developing countries, decreases since 2000 have been faster than predicted attributable to income, education, and secular shift alone.INTERPRETATION: Only 27 developing countries are expected to achieve MDG 4. Decreases since 2000 in under-5 mortality rates are accelerating in many developing countries, especially in sub-Saharan Africa. The Millennium Declaration and increased development assistance for health might have been a factor in faster decreases in some developing countries. Without further accelerated progress, many countries in west and central Africa will still have high levels of under-5 mortality in 2030.
17.	Ashenafi, S, et al. (author) Progression of clinical tuberculosis is associated with a Th2 immune response signature in combination with elevated levels of SOCS3 2014 In: Clinical immunology (Orlando, Fla.). - : Elsevier BV. - 1521-7035 .- 1521-6616. ; 151:2, s. 84-99 Journal article (peer-reviewed)
18.	Ashenafi, S, et al. (author) BCG-specific IgG-secreting peripheral plasmablasts as a potential biomarker of active tuberculosis in HIV negative and HIV positive patients 2013 In: Thorax. - : BMJ. - 1468-3296 .- 0040-6376. ; 68:3, s. 269-276 Journal article (peer-reviewed)
19.	Ashenafi, S, et al. (author) Immunosuppressive Features of the Microenvironment in Lymph Nodes Granulomas from Tuberculosis and HIV-Co-Infected Patients 2022 In: The American journal of pathology. - : Elsevier BV. - 1525-2191 .- 0002-9440. ; 192:4, s. 653-670 Journal article (peer-reviewed)
20.	Burger, H. F., et al. (author) Bottom-up and top-down drivers of herbivory on Arabica coffee along an environmental and management gradient 2022 In: Basic and Applied Ecology. - : Elsevier BV. - 1439-1791 .- 1618-0089. ; 59, s. 21-32 Journal article (peer-reviewed)abstract While sustainable agriculture relies on natural pest control, we lack insights into the relative importance of bottom-up and top-down factors on pest levels, especially along broad environmental and management gradients. To this aim, we focused on bottom-up and top-down control of herbivore damage in sixty sites in the centre of origin of Arabica coffee in southwestern Ethiopia, where coffee grows along a management gradient ranging from little or no management in the natural forest to commercial plantations. More specifically, we examined how canopy cover, percentage of surrounding forest and management intensity affected caffeine and chlorogenic acid concentration (bottom-up process) and attack of dummy caterpillars by ants and birds (top-down process), and how these in turn affected pest levels. Caffeine and chlorogenic acid concentrations were negatively related to canopy cover, while ant attack rate was positively related to canopy cover. Both ant and bird attack rate increased with the percentage of surrounding forest. Yet, secondary chemistry and caterpillar attack rates were unrelated to herbivory, and herbivory was only directly and positively affected by management intensity. Our study highlights that canopy cover can have contrasting effects on plant defence and predation, and that changes in bottom-up and top-down factors do – unlike often assumed – not necessarily translate into reduced pest levels. Instead, direct effects of management on pest levels may be more important than bottom-up or top-down mediated effects.
21.	Getachew, Merkebu, et al. (author) Within and among farm variability of coffee quality of smallholders in southwest Ethiopia 2023 In: Agroforestry Systems. - : Springer Science and Business Media LLC. - 0167-4366 .- 1572-9680. ; 97:5, s. 883-905 Journal article (peer-reviewed)abstract The biophysical drivers that affect coffee quality vary within and among farms. Quantifying their relative importance is crucial for making informed decisions concerning farm management, marketability and profit for coffee farmers. The present study was designed to quantify the relative importance of biophysical variables affecting coffee bean quality within and among coffee farms and to evaluate a near infrared spectroscopy-based model to predict coffee quality. Twelve coffee plants growing under low, intermediate and dense shade were studied in twelve coffee farms across an elevational gradient (1470–2325 m asl) in Ethiopia. We found large within farm variability, demonstrating that conditions varying at the coffee plant-level are of large importance for physical attributes and cupping scores of green coffee beans. Overall, elevation appeared to be the key biophysical variable influencing all the measured coffee bean quality attributes at the farm level while canopy cover appeared to be the most important biophysical variable driving the above-mentioned coffee bean quality attributes at the coffee plant level. The biophysical variables driving coffee quality (total preliminary and specialty quality) were the same as those driving variations in the near-infrared spectroscopy data, which supports future use of this technology to assess green bean coffee quality. Most importantly, our findings show that random forest is computationally fast and robust to noise, besides having comparable prediction accuracy. Hence, it is a useful machine learning tool for regression studies and has potential for modeling linear and nonlinear multivariate calibrations. The study also confirmed that near-infrared spectroscopic-based predictions can be applied as a supplementary approach for coffee cup quality evaluations.
22.	Hailu, Beyene Zewdie, 1983- (author) Fungal disease dynamics, genetic variation and biodiversity-yield relationships : — a study along a gradient of coffee management in southwestern Ethiopia 2020 Doctoral thesis (other academic/artistic)abstract Intensification of agricultural systems is a major threat to the associated biodiversity and could also affect the dynamics of pests and pathogens. One such system that is currently under an intensification trajectory is the production of Arabica coffee. In this thesis, I studied the relationships between fungal diseases and their natural enemies, the genetic variation in coffee, coffee yield and associated biodiversity along a coffee management gradient in southwestern Ethiopia.The specific goals of this thesis were to investigate variation in fungal diseases on coffee and their natural enemies along a gradient of management (I, II), how genetic variation in coffee among sites relate to variation in incidence of the fungal diseases (III), and to investigate the trade-offs in biodiversity-yield relationships along the gradient of coffee management (IV). To answer these questions, I selected 60 sites along a gradient of management that ranged from coffee naturally growing in only little disturbed forests to intensively managed plantations. I used both observational studies and molecular approaches.In paper I, I examined if the severity of the four major fungal diseases on coffee varied along the gradient and assessed the main drivers of variation in disease severity. I found that two of the fungal diseases were more severe in the intensively managed coffee sites, while the other two were more severe in the less intensively managed sites. Altitude was the main driver for the diseases, but related in a different way to the different diseases. In paper II, I examined the temporal dynamics in coffee leaf rust-hyperparasite interaction, the biocontrol potential of the hyperparasite and environmental drivers for the two species for three consecutive years during the dry and wet seasons. I found that the rust was more common during the dry season and in managed sites while the hyperparasite was common during the wet season and in sites that were less managed. My results also revealed that higher hyperparasite incidence during the wet season resulted in a lower growth rate of the rust during the subsequent dry season. In paper III, I investigated if genetic composition and diversity of coffee sites relate to the incidence of the fungal diseases assessed. I found that genetic composition of the coffee stands was linked to the incidence of the four fungal diseases, but genetic diversity among the coffee sites did not relate to the incidence of the diseases. In paper IV, I examined biodiversity-yield trade-offs and shape of the relationships between biodiversity and yield along the gradient of management. I found a steep, concave shape initial decline in biodiversity values as coffee yield increased to a certain level, after which a further increase in yield did not have much effect on biodiversity values.In conclusion, I found different drivers for the different diseases and for the parasite-hyperparasite interaction. It is difficult to achieve a single management approach that can suit the different pathogen species investigated. High genetic diversity among coffee sites did not reduce disease pressure. While the more complex, less managed sites provide high biodiversity values, and could potentially serve as habitats for natural pest control and in situ conservation for coffee genetic diversity, the yield gap compared to more intensively managed sites was very high. To optimize coffee management and conservation of biodiversity in these landscapes, there is a need to develop strategies whereby the smallholder farmers who depend on coffee and the forest as the main source of livelihood can benefit through for example coffee certification schemes that can pay premium prices for biodiversity-friendly coffee management.
23.	Hailu, Beyene Zewdie, et al. (author) Genetic composition of Arabica coffee explains fungal disease incidence in its area of origin Other publication (other academic/artistic)
24.	Hailu, Beyene Zewdie, et al. (author) Patterns and drivers of fungal disease communities on Arabica coffee along a management gradient 2020 In: Basic and Applied Ecology. - : Elsevier BV. - 1439-1791 .- 1618-0089. ; 47, s. 95-106 Journal article (peer-reviewed)abstract Plants, including those managed by humans, are often attacked by multiple diseases. Yet, most studies focus on single diseases, even if the disease dynamics of multiple species is more interesting from a farmers’ perspective. Moreover, most studies are from single management systems, although it is valuable to understand how diseases are distributed across broad management gradients, especially in cases where less intensive management also provides biodiversity values in the landscape. To understand the spatial dynamics and drivers of diseases across such a broad management gradient, we assessed the four major fungal diseases on Arabica coffee (Coffea arabica) at 60 sites in southwestern Ethiopia along a gradient from only little managed wild coffee in the forest understory to intensively managed coffee plantations. We found that environmental and management factors related to disease incidence and severity differed strongly among the four fungal diseases. Coffee leaf rust (Hemileia vastatrix) and Armillaria root rot (Armillaria mellea) were more severe in intensively managed sites, whereas coffee berry disease (Colletotrichum kahawae) and wilt disease (Gibberella xylarioides) were more severe in less managed sites. Among sites, incidence and severity of the four fungal diseases poorly correlated with each other. Within sites, however, shrubs that were severely attacked by coffee leaf rust also had high levels of berry disease symptoms. A better understanding of disease dynamics is important for providing management recommendations that benefit smallholder farmers, but also to evaluate possibilities for maintaining biodiversity values in the landscape related to shade cover complexity and wild coffee genetic variation.
25.	Koelemeijer, Irena A., et al. (author) Management intensity and landscape configuration affect the potential for woody plant regeneration in coffee agroforestry 2021 In: Agriculture, Ecosystems & Environment. - : Elsevier BV. - 0167-8809 .- 1873-2305. ; 313 Journal article (peer-reviewed)abstract With the current deforestation rates in tropical ecosystems, optimizing biodiversity in managed systems has become fundamental for conservation. Agroforestry has been suggested to conserve biodiversity and buffer deforestation rates, while also sustaining local livelihoods. While many studies have focused on the relation between local management intensity and biodiversity, processes at the landscape scale are often overlooked and remain a knowledge gap. In this study we identified drivers behind woody plant regeneration in coffee agroforestry on both local and landscape scale. We used univariate-, multivariate- and structural equation models to relate seedling species richness, diversity, density, community composition and height to local management intensity and location in the landscape of 60 coffee agroforestry sites in southwestern Ethiopia. Local management intensity, which simplifies and reduces canopy cover, negatively impacted species richness, diversity and density, presumably due to altered microclimatic conditions and a reduction in local seed sources. Seedling height was also reduced by management intensity, including slashing frequency and canopy cover. On the landscape scale, species richness and diversity of seedlings was higher at sites adjacent to continuous forests where seed sources are abundant, and declined with distance to the forest. In particular, late successional species were negatively affected, whereas common shade tree species and pioneers occurred as seedlings throughout the landscape and in more managed systems. This suggests that dispersal limitation is detrimental for the regeneration of late successional species, especially in agroforestry systems where the standing woody plant diversity is largely reduced. Our results indicate that natural regeneration of woody plants still occurs in coffee agroforestry systems, primarily when the canopy structure is dense and diverse and/or when sites are located nearby continuous forests. Management intensification and deforestation will limit the potential for many woody plant species to regenerate in coffee agroforestry sites, by altering the local microclimate, reducing local seed sources and disrupting seed dispersal from the surrounding landscape. This will likely result in a positive feedback loop, as a reduction in woody plant regeneration reduces future seed sources. We therefore stress that both a local and a landscape perspective should be incorporated in conservation and restoration approaches.
26.	Nurihun, Biruk Ayalew, et al. (author) Impact of climate and management on coffee berry disease and yield in Arabica coffee’s native range Other publication (other academic/artistic)abstract Climate change might increase plant diseases, reduce crop yields and threaten the livelihoods of millions of smallholder farmers globally. It is thus important to understand the relationships between climate, disease levels and yield to improve management strategies for sustainable agroforestry in a changing climate. One of the major threats to coffee production in Africa is coffee berry disease, caused by the fungal pathogen Colletotrichum kahawae. To investigate the effects of climatic and management variables on coffee berry disease and yield, we recorded daily minimum and maximum temperature and relative humidity, as well as incidence of coffee berry disease and yield in 58 sites along a broad environmental and management gradient in southwestern Ethiopia in both 2018 and 2019. Coffee berry disease was affected by several climatic and management variables, with relatively high consistency between years. For example, coffee berry disease incidence was higher in sites with high minimum temperatures during the fruit expansion stage from March to April, and was lower in sites with high minimum temperatures during the endosperm filling stage from May to June. Coffee berry disease incidence was negatively affected by the proportion of resistant cultivars, whereas management intensity had no effect on disease incidence. Coffee yield decreased with increasing minimum and maximum temperatures during the flowering period in 2018 and the fruit developmental period in 2019, respectively. Coffee yield was negatively affected by canopy cover, and positively affected by management intensity, in both years. Our findings highlight that coffee berry disease and yield were affected by different climatic and management variables. Yet, managing for low disease-high yield is practically difficult, as the effect of several climatic variables was season-dependent, and at the same time climatic variables were highly correlated between seasons. One way to break the correlation of climatic variables between seasons might be to take advantage of differences among shade trees in the presence or timing of leaf drop. To reduce levels of coffee berry disease, an effective strategy is to use resistant cultivars, but this might threaten the wild coffee genetic reservoir.
27.	Nurihun, Biruk Ayalew, 1983-, et al. (author) Impact of climate and management on coffee berry disease and yield in coffee's native range 2024 In: Basic and Applied Ecology. - 1439-1791 .- 1618-0089. ; 76, s. 25-34 Journal article (peer-reviewed)abstract Climate change might increase plant diseases, reduce crop yields and threaten the livelihoods of millions of smallholder farmers globally. It is thus important to understand the relationships between climate, disease levels and yield to improve management strategies for sustainable agroforestry in a changing climate. One of the major threats to coffee production in Africa is the coffee berry disease (Colletotrichum kahawae). To investigate the effects of climatic and management variables on coffee berry disease (CBD) incidence and yield, we recorded minimum and maximum temperature and relative humidity, as well as CBD and yield, along a broad environmental and management gradient in southwestern Ethiopia during two consecutive years. CBD was affected by several climatic and management variables. For example, CBD incidence increased with minimum temperature during the fruit expansion stage, and decreased with minimum temperature during the endosperm filling stage. CBD incidence was negatively affected by the proportion of resistant cultivars, whereas the coffee structure index (pruning) had no effect on disease incidence. Coffee yield decreased with increasing minimum temperature during the flowering period in 2018 and maximum temperature during the fruit developmental period in 2019. Coffee yield was negatively affected by canopy cover and positively affected by the coffee structure index in both years. Our findings highlight that CBD and yield were affected by different climatic and management variables. Yet, managing for low disease levels and high yield is practically difficult due to season -dependent effects of several climatic variables. One way to break the correlation of climatic variables between seasons might be to take advantage of differences among shade trees in the presence or timing of leaf drop. To reduce CBD incidence, using resistant cultivars is an effective strategy, but this might threaten the wild coffee genetic reservoir.
28.	Nurihun, Biruk Ayalew, et al. (author) Impact of climate on a host-hyperparasite interaction on Arabica coffee in its native range Other publication (other academic/artistic)abstract Natural enemies of plant pathogens might play an important role in suppressing plant disease levels in natural and agricultural systems. Yet, plant pathogen-natural enemy interactions might be sensitive to changes in the climate. Understanding the relationship between climate, plant pathogens, and their natural enemies is thus important for developing climate-resilient, sustainable agriculture.To this aim, we recorded shade cover, daily minimum and maximum temperature, relative humidity, coffee leaf rust, and its hyperparasite at 58 sites in southwestern Ethiopia during the dry and wet season for two yearsCoffee leaf rust severity was positively related to maximum temperature and hyperparasite severity was higher when the minimum temperature was low (i.e. in places with cold night temperatures) during three of the four surveying periods. While canopy cover did not have a direct effect on rust severity, it reduced rust severity indirectly by lowering the maximum temperature. Canopy cover had a direct positive effect on hyperparasite severity.Synthesis and applications. Our findings highlight that coffee leaf rust and its hyperparasite are both affected by shade cover and temperature, but in different ways. On the one hand, these niche differences between coffee leaf rust and its hyperparasite provide opportunities to develop strategies to manage the environment (such as shade cover and microclimate) in such a way that the rust is disfavored and the hyperparasite is favored. On the other hand, these niche differences lead to the worrying prediction that levels of coffee leaf rust will increase, and its hyperparasite will decrease, with climate change.
29.	Nurihun, Biruk Ayalew, 1983-, et al. (author) Impact of climate on a host-hyperparasite interaction on Arabica coffee in its native range 2024 In: Journal of Applied Ecology. - 0021-8901 .- 1365-2664. ; 61:3, s. 538-550 Journal article (peer-reviewed)abstract Natural enemies of plant pathogens might play an important role in controlling plant disease levels in natural and agricultural systems. Yet, plant pathogen–natural enemy interactions might be sensitive to climatic changes. Understanding the relationship between climate, plant pathogens and their natural enemies is thus important for developing climate-resilient, sustainable agriculture.To this aim, we recorded shade cover, daily minimum and maximum temperature, relative humidity, coffee leaf rust and its hyperparasite at 58 sites in southwestern Ethiopia during the dry and wet season for 2 years.Coffee leaf rust severity was positively related to the maximum temperature. Hyperparasite severity was higher when the minimum temperature was low (i.e. in places with cold night temperatures). While canopy cover did not have a direct effect on rust severity, it reduced rust severity indirectly by lowering the maximum temperature. Canopy cover had a direct positive effect on the hyperparasite severity during one surveying period.Synthesis and applications. Our findings highlight that coffee leaf rust and its hyperparasite are both affected by shade cover and temperature, but in different ways. On the one hand, these niche differences lead to the worrying prediction that levels of coffee leaf rust will increase, and its hyperparasite will decrease, with climate change. On the other hand, these niche differences between coffee leaf rust and its hyperparasite provide opportunities to develop strategies to manage the environment (such as shade cover and microclimate) in such a way that the rust is disfavoured and the hyperparasite is favoured.
30.	Nurihun, Biruk Ayalew, et al. (author) The impact of shade tree species identity on coffee pests and diseases 2022 In: Agriculture, Ecosystems & Environment. - : Elsevier BV. - 0167-8809 .- 1873-2305. ; 340 Journal article (peer-reviewed)abstract The multifunctional role of shade trees for conservation of biodiversity and ecosystem services in natural forests and agroforests is well documented, yet we lack insights into the impact of shade tree species identity on pest and disease dynamics on agroforestry crops such as coffee and cacao, and its implications for management. We conducted two surveys on the impact of shade tree species identity and canopy cover on pests, diseases and a fungal hyperparasite on Arabica coffee in southwestern Ethiopia, which is one of the areas of origin of Arabica coffee. One survey was in a commercial plantation, and the other along a management gradient from only little managed coffee growing in the natural forest to intensively managed commercial plantations. To link these findings to current shade tree selection criteria, we complemented these surveys by interviews with farmers and managers. Shade tree species identity left a weak imprint on insect pest levels, and insect pests levels differed strongly in the strength and direction of their response to canopy cover. In contrast to the insect pests, the incidence of coffee leaf rust and its hyperparasite, as well as coffee berry disease, differed among shade tree species, with particularly high levels of coffee leaf rust and the hyperparasite underneath the canopy of the shade trees Acacia abyssinica and Croton macrostachyus, and coffee berry disease underneath the canopy of Acacia abyssinica and Polyscias fulva. Smallholder farmers used many criteria for selecting shade trees, such as leaf traits and competition for soil moisture, but low priority is given to the effect of shade tree species identity on pests and diseases. Our findings help to understand spatial variation in pest and disease dynamics in natural forests and agroforests, and may inform the selection of shade tree species by coffee producers and thereby contribute to ecologically-informed pest and disease management. Importantly, our finding highlight the potential for using tree identity for the sustainable management of pests and diseases, with relevance for global agroforestry systems.
31.	Shimales, Tamiru, et al. (author) Management intensity affects insect pests and natural pest control on Arabica coffee in its native range 2023 In: Journal of Applied Ecology. - 0021-8901 .- 1365-2664. ; 60:5, s. 911-922 Journal article (peer-reviewed)abstract 1. Agroforestry systems provide opportunities to reduce the trade -off between agricultural production and biodiversity, for example by enhancing a diverse community of species potentially acting as natural pest control agents. While management of agroforestry systems is intensifying across the globe, we lack insights into the impact of management intensity on pest levels and natural pest control, especially along broad management gradients and as compared with nat- ural forests.2. We assessed the impact of management intensity on major insect pests (the coffee blotch miner, the serpentine leaf miner, the coffee leaf skeletonizer and damage by other free-feeding herbivores) and natural pest control by parasitoid wasps across sixty sites in the centre of origin of Arabica coffee in southwestern Ethiopia. Within this region, coffee is growing along a broad management gradi- ent ranging from little or no management in the natural forest to intensively man- aged commercial plantations.3. In the wet season, pest levels were largely similar in the natural forest, semi-forest and semi-plantation systems, whereas pests reached outbreak densities in the most intensively managed plantation system. In contrast, management intensity did not significantly affect pest levels in the dry season. The insect pests differed in their seasonal dynamics, consistently declined with elevation and were largely unaffected by shade levels. Parasitism rate of the coffee blotch miner was lower, and the parasitoid community was distinct, in the most intensively managed plan- tation system.4. Synthesis and applications : Our findings support the hypothesis that the weaker top -down control by parasitoids in the intensively managed plantation sites leads to higher pest levels, and that - at least for some pest species - there is a threshold in the effect of management intensity on pest levels and natural pest control. It is important to consider such non-linear relationships to maintain or enhance the sustainability of agroforestry systems during management intensification. Overall, our findings highlight that ecological knowledge of natural pest control can be used to intensify production to improve the livelihood of smallholder farmers without jeopardizing natural pest control but only up to a certain point where it starts to deteriorate.
32.	Stüber, Moritz, et al. (author) Multi-scale mosaics in top-down pest control by ants from natural coffee forests to plantations 2021 In: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 102:7 Journal article (peer-reviewed)abstract While top-down control plays an important role in shaping both natural and agricultural food webs, we lack insights into how top-down control effects vary across spatial scales. We used a multi-scale survey of top-down control of coffee pests and diseases by arboreal ants to examine if colony location creates a small-scale mosaic in top-down control around trees and if the strength of that control varies between sites at the landscape scale. We investigated pest and disease levels on coffee shrubs at different distances from shade trees with and without a Crematogaster spp. ant colony in 59 sites along a coffee management intensity gradient in southwestern Ethiopia. Within sites, ants significantly suppressed herbivory and coffee leaf rust at distances less than 10 m from nesting trees. Top-down control varied between sites, with stronger top-down control of free-feeding herbivory near ant colonies at sites with lower management intensity and stronger top-down control of a skeletonizer at sites with higher canopy cover. We conclude that the strength of top-down control by ants is highly heterogeneous across spatial scales, as a consequence of the biology of the predator at the small scale and herbivore density or changes in herbivore–ant interactions at the landscape scale.
33.	Zewdie, Beyene, et al. (author) A steep decline in biodiversity value with increasing coffee yield across a gradient of management in Arabica coffee’s native range Other publication (other academic/artistic)
34.	Zewdie, Beyene, 1983-, et al. (author) Genetic composition and diversity of Arabica coffee in the crop’s centre of origin and its impact on four major fungal diseases 2023 In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 32:10, s. 2484-2503 Journal article (peer-reviewed)abstract Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the 60 sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels.
35.	Zewdie, Beyene, 1983-, et al. (author) Plant biodiversity declines with increasing coffee yield in Ethiopia's coffee agroforests 2022 In: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. ; 59:5, s. 1198-1208 Journal article (peer-reviewed)abstract Tropical agroforestry systems provide farmers with resources for their livelihoods, but are also well-recognized as refuges for biodiversity. However, the relationship between yield and biodiversity might be negative in these systems, reflecting a potential trade-off between managing for increased yield or biodiversity. The potential for synergies will depend partly on the shape of the biodiversity–yield relationship, where a concave relationship suggests a faster decline in biodiversity with increasing yields than a linear or convex shape.We studied the relationship between biodiversity (plant species richness and composition) and coffee yield along a gradient of management in south-western Ethiopia, coffee's native range. We inventoried species richness and community compoasition of woody plants, herbaceous plants and bryophytes at 60 sites. We also measured coffee management-related variables and assessed coffee yield for 3 consecutive years at each site.Species richness of woody plants had a concave relationship with coffee yield, that is, tree richness declined fast initially before levelling out at higher yields, whereas there was no relationship between coffee yield and species richness of herbaceous plants or bryophytes. Species composition of woody plants, herbaceous plants and bryophytes all had a concave relationship with coffee yield.From a methodological perspective, we found that multi-year data on yield were necessary to reliably assess the relationship between biodiversity and yield, and that the number of coffee shrubs or coffee dominance were poor proxies for yield when trying to capture the biodiversity–yield relationship.Synthesis and applications. The concave relationship between biodiversity components (species richness and composition) and yield suggests that there is a strong conflict between the goals of increasing production and conserving biodiversity. However, it is important to recognize that this pattern is largely driven by the very low-yielding sites in natural forests. Here, even minor intensification of coffee management seems to rapidly erode biodiversity. Along the rest of the productivity gradient, there was generally no negative relationship between yield and biodiversity, implying opportunities for developing strategies for increasing yields without biodiversity loss.
36.	Zewdie, Beyene, et al. (author) Temporal dynamics and biocontrol potential of a hyperparasite on coffee leaf rust across a landscape in Arabica coffee's native range 2021 In: Agriculture, Ecosystems & Environment. - : Elsevier BV. - 0167-8809 .- 1873-2305. ; 311 Journal article (peer-reviewed)abstract Agroforestry systems can provide habitats for a rich biodiversity including multitrophic interactions, which presents opportunities to develop natural pest control. Shade coffee systems in several coffee growing areas of the world host such unique habitats where pests and their natural enemies interact. One of the major global challenges for coffee production, coffee leaf rust caused by the fungal pathogen Hemileia vastatrix is attacked by the fungal hyperparasite, Lecanicillium lecanii. However, we lack insights in the dynamics and biocontrol potential of the hyperparasite on coffee leaf rust from landscapes in Arabica coffee's native range. To understand the temporal dynamics across landscapes and environmental drivers of the rust and hyperparasite, and the potential for biocontrol of the rust by the hyperparasite, we studied the rust and hyperparasite during the dry and wet seasons for three consecutive years at 60 sites across a gradient of coffee management in southwestern Ethiopia. We found that coffee leaf rust was more severe during the dry season, whereas the hyperparasite was more severe during the wet season in two out of three years. The rust growth rate from the wet to the dry season transition was negatively related to the hyperparasite index during the wet season, implying a potential top-down control. Coffee leaf rust was generally more severe at lower altitudes in the dry season, whereas the hyperparasite was more severe at high altitude. The rust incidence increased with management intensity, while the hyperparasite was more common under less intensive management. This study could be interesting in that it represents a landscape where Arabica coffee originated and the rust and hyperparasite might have a long co-evolutionary history. Our findings highlight the potential of the hyperparasite to suppress the rust's growth rate from the wet to dry season transition when the rust severity could otherwise be at its peak. We show that less intensively managed landscapes with dense shade levels are likely to increase hyperparasite abundance and result in an improved top-down control of the rust. However, more detailed knowledge is needed on the interaction of these species to assess its importance for reducing rust induced yield losses or the risk of rust outbreaks.
37.	Zignol, Francesco, et al. (author) The understory microclimate in agroforestry now and in the future-a case study of Arabica coffee in its native range 2023 In: Agricultural and Forest Meteorology. - 0168-1923 .- 1873-2240. ; 340 Journal article (peer-reviewed)abstract Climate change is having a major impact on crop production and food security worldwide, and particularly so for smallholder farmers. As agroforestry is common with smallholder farmers, it is important to not only model the macroclimate, but also the microclimate that crops experience below the canopies. However, there are few highresolution spatiotemporal climate projections for forest understories, because of constraints related to the lack of i) development of models for downscaling global climate projections, ii) high-resolution gridded datasets of environmental factors influencing microclimate, and iii) spatially replicated in-situ microclimate measurements. We focused on a landscape in southwestern Ethiopia where Arabica coffee originated, and, in the present day, is commonly grown as a shade crop. We first examined the relative contribution of in-situ field measurements vs. GIS-derived estimates of vegetation and topographic features in explaining in-situ microclimate. Second, we used a statistical downscaling approach to obtain past and future microclimate maps at 30-meter spatial resolution for the part of the landscape that is covered by trees. Predictive models using in-situ variables performed equal to models with GIS variables, indicating that remote sensing data might substitute for in-situ field measurements. Vegetation and topographic features were both important in explaining microclimatic variation. Our spatiotemporal projections of the microclimate indicate that coffee farming might have to relocate to higher altitudes due to increasing temperatures, that vegetation might buffer the macroclimate at middle altitudes to some extent, and that decreasing trends in relative humidity at the beginning of the wet season might become problematic for coffee production. Taken together, our findings demonstrate that we can rely on remote sensing data to create microclimate maps in landscapes where in-situ field measurements are challenging, and we suggest how these microclimate projections can be used as a tool to promote climate-resilient agriculture at the local and landscape levels.

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