Interactive effects of altitude, microclimate and shading system on coffee leaf rust

Shade effects on coffee diseases are ambiguous because they vary depending on the season and environment. Using Coffee Leaf Rust (CLR) as an example, we demonstrate relationships between the environment and shading systems and their effects on disease intensity. We characterized seasonal variations in microclimate and CLR incidence across different altitudes and shading systems, and integrated effects between the environment, shading systems, microclimate and CLR into a piecewise structural equation model. The diurnal temperature range was higher in unshaded systems, but differences decreased with altitude. Humidity related indicators in shaded systems decreased with altitude. At mid and high altitudes, high CLR incidence occurred in the shading system showing a low diurnal temperature range and a high dew point temperature. Our study demonstrates how microclimatic indicators vary as a function of the season, altitude and the coffee shading system, and how this in turn is related to CLR

Characterisation of microclimatic indicators in coffee production systems under varying biophysical contexts and its relation to fungal coffee diseases

The comparison of performance of coffee under shaded and sun-exposed conditions has been explored in numerous studies. The beneficial effects of shading on coffee sustainability through the mitigation of microclimatic extremes have been quantified and are generally wellestablished. It has also been acknowledged that the extent to which shaded systems are advantageous depends on the biophysical context. Particularly in studies on pest and disease dynamics, this variability of shade effects across sites has resulted in contradictory assumptions. In this study, we (i) quantified microclimatic differences between three coffee production systems (coffee shaded by trees, (CT), intercropped with banana (CB), or sun exposed (CO) as a function of different environmental sites. We then (ii) related microclimatic indicators to the intensity of two fungal diseases (Coffee Leaf Rust (CLR), and Coffee Berry Disease, (CBD) of Arabica coffee. Along an altitudinal gradient from 1000 to 2200 m.a.s.l.) and in diverse production systems on the slopes of Mount Elgon, Uganda, we collected hourly data on temperature and relative humidity during the 2015/2016 season in 27 plots. Microclimatic indicators to compare included diurnal temperature range (DTR), the accumulated hours of relative humidity above 95 % (RH>95) during night, and the accumulated hours of temperatures below the dew point (Temp95 and Temp95. Our findings confirm the mitigation property of shading to microclimatic extremes. However, the widely accepted assumption of shade conserving moisture is not applicable considering the spatio-temporal context. (ii) The fact that unshaded systems at high altitudes expose better conditions for dew formation than compared to shaded systems could be a key mechanism explaining the high CBD intensity under unshaded systems and the contradictory CLR responses along the gradient of altitude and shading intensities

Guidelines for the good practice of surface wave analysis: a product of the InterPACIFIC project

Surface wave methods gained in the past decades a primary role in many seismic projects. Specifically, they are often used to retrieve a 1D shear wave velocity model or to estimate the VS,30 at a site. The complexity of the interpretation process and the variety of possible approaches to surface wave analysis make it very hard to set a fixed standard to assure quality and reliability of the results. The present guidelines provide practical information on the acquisition and analysis of surface wave data by giving some basic principles and specific suggestions related to the most common situations. They are primarily targeted to non-expert users approaching surface wave testing, but can be useful to specialists in the field as a general reference. The guidelines are based on the experience gained within the InterPACIFIC project and on the expertise of the participants in acquisition and analysis of surface wave data.Published2367-24205T. Sismologia, geofisica e geologia per l'ingegneria sismicaJCR Journa

Comparing Pandemic to Seasonal Influenza Mortality: Moderate Impact Overall but High Mortality in Young Children

Background: We assessed the severity of the 2009 influenza pandemic by comparing pandemic mortality to seasonal influenza mortality. However, reported pandemic deaths were laboratory-confirmed - and thus an underestimation - whereas seasonal influenza mortality is often more inclusively estimated. For a valid comparison, our study used the same statistical methodology and data types to estimate pandemic and seasonal influenza mortality. Methods and Findings: We used data on all-cause mortality (1999-2010, 100% coverage, 16.5 million Dutch population) and influenza-like-illness (ILI) incidence (0.8% coverage). Data was aggregated by week and age category. Using generalized estimating equation regression models, we attributed mortality to influenza by associating mortality with ILI-incidence, while adjusting for annual shifts in association. We also adjusted for respiratory syncytial virus, hot/cold weather, other seasonal factors and autocorrelation. For the 2009 pandemic season, we estimated 612 (range 266-958) influenza-attributed deaths; for seasonal influen

Towards a collaborative research: A case study on linking science to farmers' perceptions and knowledge on Arabica coffee pests and diseases and its management

The scientific community has recognized the importance of integrating farmer's perceptions and knowledge (FPK) for the development of sustainable pest and disease management strategies. However, the knowledge gap between indigenous and scientific knowledge still contributes to misidentification of plant health constraints and poor adoption of management solutions. This is particularly the case in the context of smallholder farming in developing countries. In this paper, we present a case study on coffee production in Uganda, a sector depending mostly on smallholder farming facing a simultaneous and increasing number of socio-ecological pressures. The objectives of this study were (i) to examine and relate FPK on Arabica Coffee Pests and Diseases (CPaD) to altitude and the vegetation structure of the production systems; (ii) to contrast results with perceptions from experts and (iii) to compare results with field observations, in order to identify constraints for improving the information flow between scientists and farmers. Data were acquired by means of interviews and workshops. One hundred and fifty farmer households managing coffee either at sun exposure, under shade trees or inter-cropped with bananas and spread across an altitudinal gradient were selected. Field sampling of the two most important CPaD was conducted on a subset of 34 plots. The study revealed the following findings: (i) Perceptions on CPaD with respect to their distribution across altitudes and perceived impact are partially concordant among farmers, experts and field observations (ii) There are discrepancies among farmers and experts regarding management practices and the development of CPaD issues of the previous years. (iii) Field observations comparing CPaD in different altitudes and production systems indicate ambiguity of the role of shade trees. According to the locality-specific variability in CPaD pressure as well as in FPK, the importance of developing spatially variable and relevant CPaD control practices is proposed. (Résumé d'auteur

Temporal changes in HCV genotype distribution in three different high risk populations in San Francisco, California

Abstract Background Hepatitis C virus (HCV) genotype (GT) has become an important measure in the diagnosis and monitoring of HCV infection treatment. In the United States (U.S.) HCV GT 1 is reported as the most common infecting GT among chronically infected patients. In Europe, however, recent studies have suggested that the epidemiology of HCV GTs is changing. Methods We assessed HCV GT distribution in 460 patients from three HCV-infected high risk populations in San Francisco, and examined patterns by birth cohort to assess temporal trends. Multiple logistic regression was used to assess factors independently associated with GT 1 infection compared to other GTs (2, 3, and 4). Results Overall, GT 1 was predominant (72.4%), however younger injection drug users (IDU) had a lower proportion of GT 1 infections (54.7%) compared to older IDU and HIV-infected patients (80.5% and 76.6%, respectively). Analysis by birth cohort showed increasing proportions of non-GT 1 infections associated with year of birth: birth before 1970 was independently associated with higher adjusted odds of GT 1: AOR 2.03 (95% CI: 1.23, 3.34). African-Americans as compared to whites also had higher adjusted odds of GT 1 infection (AOR: 3.37; 95% CI: 1.89, 5.99). Conclusions Although, HCV GT 1 remains the most prevalent GT, especially among older groups, changes in GT distribution could have significant implications for how HCV might be controlled on a population level and treated on an individual level