On unrooted and root-uncertain variants of several well-known phylogenetic network problems

The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic tree is notoriously difficult and poor root placement can artificially inflate the hybridization number. To this end we study a number of relaxed variants of this problem. We start by showing that the fundamental problem of determining whether an \emph{unrooted} phylogenetic network displays (i.e. embeds) an \emph{unrooted} phylogenetic tree, is NP-hard. On the positive side we show that this problem is FPT in reticulation number. In the rooted case the corresponding FPT result is trivial, but here we require more subtle argumentation. Next we show that the hybridization number problem for unrooted networks (when given two unrooted trees) is equivalent to the problem of computing the Tree Bisection and Reconnect (TBR) distance of the two unrooted trees. In the third part of the paper we consider the "root uncertain" variant of hybridization number. Here we are free to choose the root location in each of a set of unrooted input trees such that the hybridization number of the resulting rooted trees is minimized. On the negative side we show that this problem is APX-hard. On the positive side, we show that the problem is FPT in the hybridization number, via kernelization, for any number of input trees.Comment: 28 pages, 8 Figure

Using GIS and Remote Sensing to build Master Sampling Frames for Agricultural Statistics

This report is a JRC contribution to the FAO Global Strategy to improve Agricultural and Rural Statistics (GSARS). Its aim is providing guidelines on the suitable ways to use satellite images and geographic information tools to build master sampling frames that can be used both for agricultural and environmental statistics. The main readers to which the report is addressed are agricultural and environmental statisticians in developing countries. We consider separately the use of technological tools for area sampling frames and for list sampling frames. The use of Global Navigation Satellite Systems (GNSS), better known as GPS, is also discussed, although its use is more connected to carrying out field surveys rather than to the design of sampling frames.JRC.H.4-Monitoring Agricultural Resource

CGMS Version 9.2 - User Manual and Technical Documentation

Detailed information on the installation and use of the new CGMS version 9.2JRC.G.3-Monitoring agricultural resource

Remote Sensing Based Yield Estimation in a Stochastic Framework – Case Study of Durum Wheat in Tunisia

Multitemporal optical remote sensing constitutes a useful, cost efficient method for crop status monitoring over large areas. Modelers interested in yield monitoring can rely on past and recent observations of crop reflectance to estimate aboveground biomass and infer the likely yield. Therefore, in a framework constrained by the information availability, remote sensing data to yield conversion parameters are to be estimated. Statistical models are suitable for this purpose given their ability to deal with statistical errors. This paper explores the performance in yield estimation of various remote sensing indicators based on varying degrees of bio-physical insight, in interaction with statistical methods (linear regressions) that rely on different hypotheses. Jackknifed results (leave one year out) are presented for the case of wheat yield regional estimation in Tunisia using the SPOT-VEGETATION instrument.JRC.H.4-Monitoring Agricultural Resource

The 2015-2016 El Niño event: expected impact on food security and main response scenarios in East and Southern Africa

El Niño is a periodic climate phenomenon defined by anomalously warm sea surface temperatures in the eastern and central tropical Pacific Ocean which affect local weather worldwide and generally leads to increased drought risk at global level. In 2015, since July a strong El Niño is being observed with increasing intensity in September and October. It is expected to last for the first 3 months of 2016 and could reach a very high level of intensity in this period. To date, it has already affected climate in many parts of Asia and in the Northern parts of East Africa, causing serious rainfall deficits. Although the impact on agriculture is not directly proportional to the intensity of the climatic anomalies, the event is expected to impact East and Southern Africa in different ways. In East Africa, for the bimodal areas, El Niño events in the second half of the year usually lead to wetter than average conditions and are generally beneficial for agriculture. In other areas with a long crop season in the second half of the year, such as parts of Ethiopia, Sudan and Eritrea, it can cause drier than average conditions followed by rainfall at harvesting time causing drying problems. For both bimodal and single season zones it can lead to flooding in riverine areas and increase the risk of livestock diseases. On the contrary, in Southern Africa, strong El Niño events frequently cause drought and reduce crop production and this effect could be particularly dangerous considering the low crop production of this region in the 2014-2015 season. These risks need to be taken into consideration for response planning in East and Southern Africa and this report lists some main recommeJRC.H.4-Monitoring Agricultural Resource

Refractory chronic GVHD emerging after splenectomy in a marrow transplant recipient with accelerated phase CML

We report a 39-year-old female patient who underwent HLA-identical sibling allogeneic BMT for CML in accelerated phase. Severe pancytopenia refractory to G-CSF associated with progressive splenomegaly and RBC/ platelet transfusion dependency were present from day + 60 after BMT. MRD assessed by FISH and RT-PCR multiplex for BCR-ABL rearrangement was negative, and complete chimerism was documented by VNTR on days + 100, + 180, + 360 and 2 years after BMT. Splenectomy was performed on day + 225 and pancytopenia resolved but chronic extensive graft-versus-host disease developed, with hepatic cholestasis, diffuse scleroderma and sicca-like syndrome. She was sequentially and progressively treated with different immunosuppressive therapy combinations with no clear benefit. On day + 940, she presented with infection over the previously present ulcers on both limbs, which culminated in septic shock and death on day + 1041. We conclude that, although splenectomy may reverse poor graft function after allogeneic BMT, hyposplenism may trigger or worsen chronic extensive GVHD leading to increased morbidity and mortality.Hosp São Paulo, São Paulo, BrazilHosp São Paulo, São Paulo, BrazilWeb of Scienc

Testing VGT data continuity between SPOT and PROBA-V missions for operational yield forecasting in North African countries

The SPOT-VEGETATION mission operationally provided 15 years of remote sensing indicators of vegetation status. The mission reached its end-of-life in May 2014 and was timely replaced by the PROBA-V mission, aiming to ensure, among other objectives, the seamless continuity of provision of VGT-like products, including Normalized Difference Vegetation Index (NDVI). Exploiting the period of overlap when both instruments were functioning (November 2013 –May 2014), this study compared NDVI data provided by the SPOT-VGT and the PROBA-V instruments from the point of view of the user interested in operational crop monitoring and yield forecasting. The comparison is performed for the three North Africa country of Morocco, Algeria and Tunisia. All such countries, through different agencies and institutional arrangements, had in place an operational crop monitoring system that was based on 10-day composites of SPOT-VGT NDVI. In view of the operational crop monitoring season of 2015, when they will have to decide whether to continue their business-as-usual activities with the PROBA-V data (instead of SPOT-VGT), this study analysed the impact of the use of this new data source on the information being operationally derived and analysed for crop monitoring and yield forecasting: anomaly maps, temporal profiles and cereal yield figures (for barley, durum and soft wheat) estimated using semi-empirical regression models.JRC.H.4 - Monitoring Agricultural Resource

A simulation interface designed for improved user interaction and learning in water quality modelling software

Traditional simulation software that supports management decisions is configured and run by experienced scientists. However, it is often criticised for its lack of interactivity, not only in the application of decisions but also in the display of results. This paper presents the simulation interface of software with management strategy evaluation capabilities and its capacity to enable resource managers to learn about water quality management as evaluated in a workshop setting. The software ‘MSE Tool’ is not intended to produce definitive real-world advice but provides a test-bed for managers to interactively design strategies and explore the complexities inherent to water quality management using a simple, yet effective, user interface. MSE Tool has been used in a pilot application that simulated the effects of management strategies applied in catchments and their effects on riverine, estuarine and marine water quality in South East Queensland, Australia. The approach and the software are suitable for reuse in other management strategy evaluation projects

MARS Bulletin Vol. 21 No. 5

MARS Bulletin Vol. 21 No. 5JRC.H.4-Monitoring Agricultural Resource

MARS Bulletin Vol.21 No. 8

MARS Bulletin Vol.21 No. 8JRC.H.4-Monitoring Agricultural Resource