Explore the vast range of titles available.

The LHCb simulation application, Gauss, consists of two independent phases, the generation of the primary event and the tracking of particles produced in the experimental setup. For the LHCb experimental program it is particularly important to model B meson decays: the EvtGen code developed in CLEO and BABAR has been chosen and customized for non-coherent B production as occuring in pp collisions at the LHC. The initial proton-proton collision is provided by a different generator engine, currently PYTHIA 6 for massive production of signal and generic pp collisions events. Beam gas events, background events originating from proton halo, cosmics and calibration events for different detectors can be generated in addition to pp collisions. Different generator packages as available in the physics community or specifically developed in LHCb are used for the different purposes. Running conditions affecting the generated events such as the size of the luminous region, the number of collisions occuring in a bunch crossing and the number of spill-over events from neighbouring bunches are modeled via dedicated algorithms appropriately configured. The design of the generator phase of Gauss will be described: a modular structure with well defined interfaces specific to the various tasks, e.g. pp collisions, particle decays, selections, etc. has been chosen. Different implementations are available for the various tasks allowing selecting and combining them as most appropriate at run time as in the case of PYTHIA 6 for pp collisions or HIJING for beam gas. The advantages of such structure, allowing for example to adopt transparently new generators packages, will be discussed.

Carbon use efficiency (CUE), the ratio of net primary production (NPP) over gross primary production (GPP), is a functional parameter that could possibly link the current increasingly accurate global GPP estimates with those of net ecosystem exchange, for which global predictors are still unavailable. Nevertheless, CUE estimates are actually available for only a few ecosystem types, while information regarding agro-ecosystems is scarce, in spite of the simplified spatial structure of these ecosystems that facilitates studies on allocation patterns and temporal growth dynamics. We combined three largely deployed methods, eddy covariance, soil respiration and biometric measurements, to assess monthly values of CUE, NPP and allocation patterns in different plant organs in an apple orchard during a complete year (2010). We applied a measurement protocol optimized for quantifying monthly values of carbon fluxes in this ecosystem type, which allows for a cross check between estimates obtained from different methods. We also attributed NPP components to standing biomass increments, detritus cycle feeding and lateral exports. We found that in the apple orchard, both net ecosystem production and gross primary production on a yearly basis, 380 ± 30 g C m−2 and 1263 ± 189 g C m−2 respectively, were of a magnitude comparable to those of natural forests growing in similar climate conditions. The largest differences with respect to forests are in the allocation pattern and in the fate of produced biomass. The carbon sequestered from the atmosphere was largely allocated to production of fruit: 49% of annual NPP was taken away from the ecosystem through apple production. Organic material (leaves, fine root litter, pruned wood and early fruit falls) contributing to the detritus cycle was 46% of the NPP. Only 5% was attributable to standing biomass increment, while this NPP component is generally the largest in forests. The CUE, with an annual average of 0.71 ± 0.12, was higher than the previously suggested constant values of 0.47–0.50. Low nitrogen investment in fruit, the limited root apparatus, and the optimal growth temperature and nutritional condition observed at the site are suggested to be explanatory variables for the high CUE observed.

Changes in snow cover depth and duration predicted by climate change scenarios are expected to strongly affect high-altitude ecosystem processes. This study investigates the effect of an exceptionally short snow season on the phenology and carbon dioxide source/sink strength of a subalpine grassland. An earlier snowmelt of more than one month caused a considerable advancement (40 days) of the beginning of the carbon uptake period (CUP) and, together with a delayed establishment of the snow season in autumn, contributed to a two-month longer CUP. The combined effect of the shorter snow season and the extended CUP led to an increase of about 100% in annual carbon net uptake. Nevertheless, the unusual environmental conditions imposed by the early snowmelt led to changes in canopy structure and functioning, with a reduction of the carbon sequestration rate during the snow-free period.

Rice paddy fields are one of the greatest anthropogenic sources of methane (CH4), the third most important greenhouse gas after water vapour and carbon dioxide. In agricultural fields, CH4 is usually measured with the closed chamber technique, resulting in discontinuous series of measurements performed over a limited area, that generally do not provide sufficient information on the short-term variation of the fluxes. On the contrary, aerodynamic techniques have been rarely applied for the measurement of CH4 fluxes in rice paddy fields. The eddy covariance (EC) technique provides integrated continuous measurements over a large area and may increase our understanding of the underlying processes and diurnal and seasonal pattern of CH4 emissions in this ecosystem. For this purpose a Fast Methane Analyzer (Los Gatos Research Ltd.) was installed in a rice paddy field in the Po Valley (Northern Italy). Methane fluxes were measured during the rice growing season with both EC and manually operated closed chambers. Methane fluxes were strongly influenced by the height of the water table, with emissions peaking when it was above 10–12 cm. Soil temperature and the developmental stage of rice plants were also responsible of the seasonal variation on the fluxes. The measured EC fluxes showed a diurnal cycle in the emissions, which was more relevant during the vegetative period, and with CH4 emissions being higher in the late evening, possibly associated with higher water temperature. The comparison between the two measurement techniques shows that greater fluxes are measured with the chambers, especially when higher fluxes are being produced, resulting in 30 % higher seasonal estimations with the chambers than with the EC (41.1 and 31.7 g CH4 m−2 measured with chambers and EC respectively) and even greater differences are found if shorter periods with high chamber sampling frequency are compared. The differences may be a result of the combined effect of overestimation with the chambers and of the possible underestimation by the EC technique.

During the summer of 2018, a widespread drought developed over Northern and Central Europe. The increase in temperature and the reduction of soil moisture have influenced carbon dioxide (CO2) exchange between the atmosphere and terrestrial ecosystems in various ways, such as a reduction of photosynthesis, changes in ecosystem respiration, or allowing more frequent fires. In this study, we characterize the resulting perturbation of the atmospheric CO2 seasonal cycles. 2018 has a good coverage of European regions affected by drought, allowing the investigation of how ecosystem flux anomalies impacted spatial CO2 gradients between stations. This density of stations is unprecedented compared to previous drought events in 2003 and 2015, particularly thanks to the deployment of the Integrated Carbon Observation System (ICOS) network of atmospheric greenhouse gas monitoring stations in recent years. Seasonal CO2 cycles from 48 European stations were available for 2017 and 2018. Earlier data were retrieved for comparison from international databases or national networks. Here, we show that the usual summer minimum in CO2 due to the surface carbon uptake was reduced by 1.4 ppm in 2018 for the 10 stations located in the area most affected by the temperature anomaly, mostly in Northern Europe. Notwithstanding, the CO2 transition phases before and after July were slower in 2018 compared to 2017, suggesting an extension of the growing season, with either continued CO2 uptake by photosynthesis and/or a reduction in respiration driven by the depletion of substrate for respiration inherited from the previous months due to the drought. For stations with sufficiently long time series, the CO2 anomaly observed in 2018 was compared to previous European droughts in 2003 and 2015. Considering the areas most affected by the temperature anomalies, we found a higher CO2 anomaly in 2003 (+3 ppm averaged over 4 sites), and a smaller anomaly in 2015 (+1 ppm averaged over 11 sites) compared to 2018. This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.

Wild aquatic birds are crucial in maintaining the high pathogenicity avian influenza (HPAI) viruses. However, the HPAI dynamic at the wild‐domestic interface is still poorly known, and a comprehensive understanding of species that could potentially act as a bridge between wetlands and poultry farms is still lacking. In this study, an eco‐epidemiological framework was used to build species distribution models for 40 wild bird species camera‐trapped at 10 poultry farms in northeastern Italy. The predicted wild bird favorability distributions were used to estimate HPAI outbreak occurrences in the area of interest, using an ensemble approach that included five methodologies: generalized linear model (GLM), generalized additive model (GAM), boosted regression trees (BRTs), random forest (RF), and maximum entropy (MaxEnt). The group of species that included most of the Ardeidae (i.e., great egret, purple heron, little egret, and cattle egret), one Galliformes (i.e., common pheasant), and one Gruiformes (i.e., common moorhen) showed the highest importance (IMP = 28%) in explaining the HPAI outbreak probability of occurrence in poultry, highlighting their potential bridging role between the reservoir species and the domestic populations. The second most important group of species (IMP = 17%) included one Anseriformes (i.e., mallard), two Charadriiformes (i.e., black‐headed gull and yellow‐legged gull), and one Ardeidae (i.e., gray heron), remarking their role in the disease ecology. These results underline the complex role of the wild‐domestic interface in the epidemiology of HPAI, suggesting that a broader range of species than what is typically considered might be involved in HPAI virus ecology. Including these groups of species in targeted surveillance programs would help in fine‐tuning sampling efforts and identifying early warning signals of possible transmission to poultry holdings.

After the heatwave The European heatwave in the summer of 2003 was probably the hottest in the region since AD 1500. Its immediate effects are well documented: the Earth Policy Institute has estimated that it caused at least 35,000 deaths. Now the longer-term effects are beginning to emerge. Based on measurements of ecosystem CO 2 flux, radiation absorption by plants, crop yields and a model simulating the terrestrial biosphere, a multinational team of researchers has found that during July and August 2003, 500 million tonnes of carbon escaped from the forests and fields across Europe as a result of extreme heat and drought. The model results and historical data suggest that this dramatic fall in primary productivity is unprecedented during the past century. If the incidence of extreme droughts like this were to increase, temperate ecosystems could become carbon sources with the potential to accelerate global warming, as has been anticipated for the tropics. Future climate warming is expected to enhance plant growth in temperate ecosystems and to increase carbon sequestration 1 , 2 . But although severe regional heatwaves may become more frequent in a changing climate 3 , 4 , their impact on terrestrial carbon cycling is unclear. Here we report measurements of ecosystem carbon dioxide fluxes, remotely sensed radiation absorbed by plants, and country-level crop yields taken during the European heatwave in 2003. We use a terrestrial biosphere simulation model 5 to assess continental-scale changes in primary productivity during 2003, and their consequences for the net carbon balance. We estimate a 30 per cent reduction in gross primary productivity over Europe, which resulted in a strong anomalous net source of carbon dioxide (0.5 Pg C yr -1 ) to the atmosphere and reversed the effect of four years of net ecosystem carbon sequestration 6 . Our results suggest that productivity reduction in eastern and western Europe can be explained by rainfall deficit and extreme summer heat, respectively. We also find that ecosystem respiration decreased together with gross primary productivity, rather than accelerating with the temperature rise. Model results, corroborated by historical records of crop yields, suggest that such a reduction in Europe's primary productivity is unprecedented during the last century. An increase in future drought events could turn temperate ecosystems into carbon sources, contributing to positive carbon-climate feedbacks already anticipated in the tropics and at high latitudes 1 , 2 .

PurposeSecretory breast cancer (SBC) is one of the rarest breast cancer (BC), representing the majority of BC in childhood. Nevertheless, it elicits a lot of interest both for the peculiar morphology and the characteristic genetic features. Currently, there is no consensus on optimal treatment strategy. Therefore, it is useful to report every case in order to establish treatment algorithms.MethodsWe describe the case of a 6-year-old boy diagnosed with a SBC, with peculiar genomic and immunohistochemical features. Moreover, we carried out a review of the literature in order to analyze the present state of knowledge about this rare entity.ResultsTo the best of our knowledge, there are only 120 cases published in literature, only 32 in males and only 2 younger than 6 years. Furthermore, this one had peculiar genomic and immunohistochemical features. Indeed, even if SBC expresses basal-cell markers, our patient had a triple-negative tumor expressing both basal and luminal cell markers. Furthermore, the boy’s genomic profile revealed not only positivity for the typical SBC’s translocation t(12;15), but also for a 3q28 duplication, found in his father (healthy) and paternal grandfather (with a previous BC). None were positive for BRCA mutation. This locus includes only one gene encoding for a growth factor recently linked to Early Infantile Epileptic Encephalopathy-47 and Idiopathic ventricular tachycardia. Even if the literature does not provide evidence of a pathogenic role it is not possible to exclude a cancer-predisposing activity.ConclusionsSBC is a rare type of BC, characterized by triple-negative features with an unexpectedly good prognosis. More data are needed to fully understand the behavior of this cancer and genomic profiling could be helpful in improving its diagnosis and management.

During the summer of 2018, a widespread drought developed over Northern and Central Europe. The increase in temperature and the reduction of soil moisture have influenced carbon dioxide (CO 2 ) exchange between the atmosphere and terrestrial ecosystems in various ways, such as a reduction of photosynthesis, changes in ecosystem respiration, or allowing more frequent fires. In this study, we characterize the resulting perturbation of the atmospheric CO 2 seasonal cycles. 2018 has a good coverage of European regions affected by drought, allowing the investigation of how ecosystem flux anomalies impacted spatial CO 2 gradients between stations. This density of stations is unprecedented compared to previous drought events in 2003 and 2015, particularly thanks to the deployment of the Integrated Carbon Observation System (ICOS) network of atmospheric greenhouse gas monitoring stations in recent years. Seasonal CO 2 cycles from 48 European stations were available for 2017 and 2018. Earlier data were retrieved for comparison from international databases or national networks. Here, we show that the usual summer minimum in CO 2 due to the surface carbon uptake was reduced by 1.4 ppm in 2018 for the 10 stations located in the area most affected by the temperature anomaly, mostly in Northern Europe. Notwithstanding, the CO 2 transition phases before and after July were slower in 2018 compared to 2017, suggesting an extension of the growing season, with either continued CO 2 uptake by photosynthesis and/or a reduction in respiration driven by the depletion of substrate for respiration inherited from the previous months due to the drought. For stations with sufficiently long time series, the CO 2 anomaly observed in 2018 was compared to previous European droughts in 2003 and 2015. Considering the areas most affected by the temperature anomalies, we found a higher CO 2 anomaly in 2003 (+3 ppm averaged over 4 sites), and a smaller anomaly in 2015 (+1 ppm averaged over 11 sites) compared to 2018. This article is part of the theme issue ‘Impacts of the 2018 severe drought and heatwave in Europe: from site to continental scale'.

We evaluate the capability of the global atmospheric transport model TM5 to simulate the boundary layer dynamics and associated variability of trace gases close to the surface, using radon (222Rn). Focusing on the European scale, we compare the boundary layer height (BLH) in the TM5 model with observations from the National Oceanic and Atmospheric Admnistration (NOAA) Integrated Global Radiosonde Archive (IGRA) and also with ceilometer and lidar (light detection and ranging) BLH retrievals at two stations. Furthermore, we compare TM5 simulations of 222Rn activity concentrations, using a novel, process-based 222Rn flux map over Europe (Karstens et al., 2015), with harmonised 222Rn measurements at 10 stations. The TM5 model reproduces relatively well the daytime BLH (within 10-20 % for most of the stations), except for coastal sites, for which differences are usually larger due to model representation errors. During night, however, TM5 overestimates the shallow nocturnal BLHs, especially for the very low observed BLHs (< 100 m) during summer. The 222Rn activity concentration simulations based on the new 222Rn flux map show significant improvements especially regarding the average seasonal variability, compared to simulations using constant 222Rn fluxes. Nevertheless, the (relative) differences between simulated and observed daytime minimum 222Rn activity concentrations are larger for several stations (on the order of 50 %) than the (relative) differences between simulated and observed BLH at noon. Although the nocturnal BLH is often higher in the model than observed, simulated 222Rn nighttime maxima are actually larger at several continental stations. This counterintuitive behaviour points to potential deficiencies of TM5 to correctly simulate the vertical gradients within the nocturnal boundary layer, limitations of the 222Rn flux map, or issues related to the definition of the nocturnal BLH. At several stations the simulated decrease of 222Rn activity concentrations in the morning is faster than observed. In addition, simulated vertical 222Rn activity concentration gradients at Cabauw decrease faster than observations during the morning transition period, and are in general lower than observed gradients during daytime. Although these effects may be partially due to the slow response time of the radon detectors, they clearly point to too fast vertical mixing in the TM5 boundary layer during daytime. Furthermore, the capability of the TM5 model to simulate the diurnal BLH cycle is limited by the current coarse temporal resolution (3 h/6 h) of the TM5 input meteorology.