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

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

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

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

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

In-Situ catalytic surface modification of micro-structured La0.6Sr0.4Co0.2Fe0.8O3-δ (LSCF) Oxygen Permeable Membrane Using Vacuum-Assisted technique

This paper aims at investigating the means to carry out in-situ surface modification of La0.6Sr0.4Co0.2Fe0.8O3-δ (LSCF) oxygen permeable membrane by using vacuum assisted technique. The unique structure of the LSCF hollow fibre membrane used in this study, which consists of an outer dense oxygen separation layer and conical-shaped microchannels open at the inner surface has allowed the membrane to be used as oxygen separation membrane and as a structured substrate for where catalyst can be deposited. A catalyst solution of similar material, LSCF was prepared using sol-gel technique. Effects of calcination temperature and heating rate were investigated using XRD and TGA to ensure pure perovskites structure of LSCF was obtained. It was found that a lower calcination temperature can be used to obtain pure perovskite phase if slower heating rate is used. The SEM photograph shows that the distribution of catalyst onto the membrane microchannels using in-situ deposition technique was strongly related to the viscosity of LSCF catalytic sol. Interestingly, it was found that the amount of catalyst deposited using viscous solution was slightly higher than the less viscous sol. This might be due to the difficulty of catalyst sol to infiltrate the membrane and as a result, thicker catalyst layer was observed at the lumen rather than onto the conical-shaped microchannels. Therefore, the viscosity of catalyst solution and calcination process should be precisely controlled to ensure homogeneous catalyst layer deposition. Analysis of the elemental composition will be studied in the future using energy dispersive X-ray Spectroscopy (EDX) to determine the elements deposited onto the membranes. Once the elemental analysis is confirmed, oxygen permeation analysis will be carried out

Geographic origin of migratory birds based on stable isotope analysis: the case of the greylag goose (Anser anser) wintering in Camargue, southern France

International audienceProper delineation of flyways is a prerequisite for adequate management of migratory birds. The implementation of coordinated international management for greylag goose (Anser anser) is currently underway in Europe for the north-west/south-west (NW/ SW) population. Some uncertainty remained as to whether greylags wintering in Camargue, Southern France, belonged to this population and bred in Norway, Sweden and Finland,or rather originated from the Central European population, especially since most neck collar observations were of birds ringed in the Czech Republic. Stable hydrogen isotope (δ 2 H) analyses of feathers from 147 individuals hunted or trapped during winter in Camargue provide some insight into this question and suggest north-central Europe as a more likely area of origin. This indicates that greylags wintering along the Mediterranean coast maybe largely separate from the birds of the NW/SW European population breeding in Fennoscandia, although some individuals may also come from the Polish or German regions of the NW/SW flyway, since the combined ringing and stable isotope analyses suggest these birds are mostly breeding and moulting in an isotopic area consistent with the Czech Republic, Poland and northern Germany. Earlier studies show birds wintering in other French regions rather originate from Sweden and Norway. These results should be considered for the management plan currently being developed for greylag goose in Europe. More generally, they question whether birds from two distinct populations /flyways should be applied similar or potentially different management plans within a given country

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

Widely Tunable Quantum-Dot Source Around 3 μm

We propose a widely tunable parametric source in the 3 μm range, based on intracavity spontaneous parametric down conversion (SPDC) of a quantum-dot (QD) laser emitting at 1.55 μm into signal and idler modes around 3.11 μm. To compensate for material dispersion, we engineer the laser structure to emit in a higher-order transverse mode of the waveguide. The width of the latter is used as a degree of freedom to reach phase matching in narrow, deeply etched ridges, where the in-plane confinement of the QDs avoids non-radiative sidewall electron-hole recombination. Since this design depends critically on the knowledge of the refractive index of In1−xGaxAsyP1−y lattice matched to InP at wavelengths where no data are available in the literature, we have accurately determined them as a function of wavelength (λ = 1.55, 2.12 and 3 μm) and arsenic molar fraction (y = 0.55, 0.7 and 0.72) with a precision of ±4 × 10−3. A pair of dichroic dielectric mirrors on the waveguide facets is shown to result in a continuous-wave optical parametric oscillator (OPO), with a threshold around 60 mW. Emission is tunable over hundreds of nanometers and expected to achieve mW levels