With the steady increase in the precision of flavour physics measurements collected during LHC Run 2, the LHCb experiment requires simulated data samples of larger and larger sizes to study the ...detector response in detail. The simulation of the detector response is the main contribution to the time needed to simulate full events. This time scales linearly with the particle multiplicity. Of the dozens of particles present in the simulation only the few participating in the signal decay under study are of interest, while all remaining particles mainly affect the resolutions and efficiencies of the detector. This paper presents a novel development for the LHCb simulation software which re-uses the rest of the event from previously simulated events. This approach achieves an order of magnitude increase in speed and the same quality compared to the nominal simulation.
The LHCb simulation application, Gauss, is based on the Gaudi framework and on experiment basic components such as the Event Model and Detector Description. Gauss also depends on external libraries ...for the generation of the primary events (PYTHIA 6, EvtGen, etc.) and on GEANT4 for particle transport in the experimental setup. The application supports the production of different types of events from minimum bias to B physics signals and particle guns. It is used for purely generator-level studies as well as full simulations. Gauss is used both directly by users and in massive central productions on the grid. The design and implementation of the application and its evolution due to evolving requirements will be described as in the case of the recently adopted Python-based configuration or the possibility of taking into account detectors conditions via a Simulation Conditions database. The challenge of supporting at the same time the flexibililty needed for the different tasks for which it is used, from evaluation of physics reach to background modeling, together with the stability and reliabilty of the code will also be described.
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.
Neonatal intensive care units (NICUs) greatly expand the use of technology. There is a need to accurately diagnose discomfort, pain, and complications, such as sepsis, mainly before they occur. While ...specific treatments are possible, they are often time-consuming, invasive, or painful, with detrimental effects for the development of the infant. In the last 40 years, heart rate variability (HRV) has emerged as a non-invasive measurement to monitor newborns and infants, but it still is underused. Hence, the present paper aims to review the utility of HRV in neonatology and the instruments available to assess it, showing how HRV could be an innovative tool in the years to come. When continuously monitored, HRV could help assess the baby's overall wellbeing and neurological development to detect stress-/pain-related behaviors or pathological conditions, such as respiratory distress syndrome and hyperbilirubinemia, to address when to perform procedures to reduce the baby's stress/pain and interventions, such as therapeutic hypothermia, and to avoid severe complications, such as sepsis and necrotizing enterocolitis, thus reducing mortality. Based on literature and previous experiences, the first step to efficiently introduce HRV in the NICUs could consist in a monitoring system that uses photoplethysmography, which is low-cost and non-invasive, and displays one or a few metrics with good clinical utility. However, to fully harness HRV clinical potential and to greatly improve neonatal care, the monitoring systems will have to rely on modern bioinformatics (machine learning and artificial intelligence algorithms), which could easily integrate infant's HRV metrics, vital signs, and especially past history, thus elaborating models capable to efficiently monitor and predict the infant's clinical conditions. For this reason, hospitals and institutions will have to establish tight collaborations between the obstetric, neonatal, and pediatric departments: this way, healthcare would truly improve in every stage of the perinatal period (from conception to the first years of life), since information about patients' health would flow freely among different professionals, and high-quality research could be performed integrating the data recorded in those departments.
Transient elastography (TE) has received increasing attention as a means to evaluate disease progression in patients with chronic liver disease.
To assess the value of TE for predicting the stage of ...fibrosis.
Liver biopsy and TE were performed in 150 consecutive patients with chronic hepatitis C-related hepatitis (92 men and 58 women, age 50.6 (SD 12.5) years on the same day. Necro-inflammatory activity and the degree of steatosis at biopsy were also evaluated.
The areas under the curve for the prediction of significant fibrosis (> or = F2), advanced fibrosis (> or = F3) or cirrhosis were 0.91, 0.99 and 0.98, respectively. Calculation of multilevel likelihood ratios showed that values of TE < 6 or > or = 12, < 9 or > or = 12, and < 12 or > or = 18, clearly indicated the absence or presence of significant fibrosis, advanced fibrosis, and cirrhosis, respectively. Intermediate values could not be reliably associated with the absence or presence of the target condition. The presence of inflammation significantly affected TE measurements in patients who did not have cirrhosis (p<0.0001), even after adjusting for the stage of fibrosis. Importantly, TE measurements were not influenced by the degree of steatosis.
TE is more suitable for the identification of patients with advanced fibrosis than of those with cirrhosis or significant fibrosis. In patients in whom likelihood ratios are not optimal and do not provide a reliable indication of the disease stage, liver biopsy should be considered when clinically indicated. Necro-inflammatory activity, but not steatosis, strongly and independently influences TE measurement in patients who do not have cirrhosis.
Phosphorus (P) is an important nutrient for plant growth but its availability in soil is limited. Although plants are able to respond to the P shortage, climatic factors might modify the ...soil-plant-microorganisms system and reduce P availability. In this study we evaluated the rhizosphere effect of beech (Fagus sylvatica L.) in forest soils of Apennines mountains (central Italy) at two altitudes (800 and 1000m) and along 1° of latitudinal gradient, using latitude and altitude as proxies for temperature change. Specifically, we tested if 1) soil organic C, total N, and organic and available P decrease with increasing latitude and altitude, and 2) the rhizosphere effect on P availability becomes more pronounced when potential nutrient limitations are more severe, as it happens with increasing latitude and altitude. The results showed that the small latitudinal gradient has no effect on soil properties. Conversely, significant changes occurred between 800 and 1000m above sea level, as the soils at higher altitude showed greater total organic C (TOC) content, organic and available P contents, and alkaline mono-phosphatases activity than the soils at lower altitude. Further, at the higher altitude, a marked rhizosphere effect was detected, as indicated by greater concentration of TOC, water extractable organic C, and available P, and its fulfillment was mainly attributed to the release of labile organics through rhizodeposition. The availability of easy degradable compounds in the rhizosphere should foster the mineralization of the organic matter with a consequent increase of available P. Hence, we speculate that at high altitude the energy supplied by the plants through rhizodeposition to the rhizosphere heterotrophic microbial community is key for fuelling the rhizospheric processes and, in particular, P cycling.
•Rhizosphere effect of Fagus sylvatica L. was evaluated at different altitudes (800 and 1000m).•Mean annual air temperature was about 10°C at 800m, and about 9°C at 1000ma.s.l.•Significant changes in soil properties occurred between 800 and 1000ma.s.l.•A marked rhizosphere effect was found only at 1000ma.s.l.•At the higher altitude, rhizodeposition is key for fuelling the rhizosphere processes and P cycling.
Environmental pollution caused by petrochemical hydrocarbons (HC) and plastic waste is a pressing global challenge. However, there is a promising solution in the form of bacteria that possess the ...ability to degrade HC, making them valuable tools for remediating contaminated environments and effluents. Moreover, some of these bacteria offer far-reaching potential beyond bioremediation, as they can also be utilized to produce polyhydroxyalkanoates (PHAs), a common type of bioplastics. The accumulation of PHAs in bacterial cells is facilitated in environments with high C/N or C/P ratio, which are often found in HC-contaminated environments and effluents. Consequently, some HC-degrading bacteria can be employed to simultaneously produce PHAs and conduct biodegradation processes. Although bacterial bioplastic production has been thoroughly studied, production costs are still too high compared to petroleum-derived plastics. This article aims to provide a comprehensive review of recent scientific advancements concerning the capacity of HC-degrading bacteria to produce PHAs. It will delve into the microbial strains involved and the types of bioplastics generated, as well as the primary pathways for HC biodegradation and PHAs production. In essence, we propose the potential utilization of HC-degrading bacteria as a versatile tool to tackle two major environmental challenges: HC pollution and the accumulation of plastic waste. Through a comprehensive analysis of strengths and weaknesses in this aspect, this review aims to pave the way for future research in this area, with the goal of facilitating and promoting investigation in a field where obtaining PHAs from HC remains a costly and challenging process.
Recent advances in machine learning research, combined with the reduced sequencing costs enabled by modern next-generation sequencing, paved the way to the implementation of precision medicine ...through routine multi-omics molecular profiling of tumours. Thus, there is an emerging need of reliable models exploiting such data to retrieve clinically useful information. Here, we introduce an original consensus clustering approach, overcoming the intrinsic instability of common clustering methods based on molecular data. This approach is applied to the case of non-small cell lung cancer (NSCLC), integrating data of an ongoing clinical study (PROMOLE) with those made available by The Cancer Genome Atlas, to define a molecular-based stratification of the patients beyond, but still preserving, histological subtyping. The resulting subgroups are biologically characterized by well-defined mutational and gene-expression profiles and are significantly related to disease-free survival (DFS). Interestingly, it was observed that (1) cluster B, characterized by a short DFS, is enriched in KEAP1 and SKP2 mutations, that makes it an ideal candidate for further studies with inhibitors, and (2) over- and under-representation of inflammation and immune systems pathways in squamous-cell carcinomas subgroups could be potentially exploited to stratify patients treated with immunotherapy.
Rift‐Rift‐Rift triple junctions are key features of emergent plate boundary networks during fragmentation of a continent. A key example of such a setting is the Afar triple junction where the ...African, Arabian and Somalian plates interact. We performed analog and numerical models simulating continental break‐up in a Rift‐Rift‐Rift setting to investigate the resulting structural pattern and evolution. We modified the ratio between plate velocities, and we performed single‐stage (with all plates moving at the same time) and two‐stage (where one plate first moves alone and then all the plates move simultaneously) models. Additionally, the direction of extension was changed to induce orthogonal extension in one of the three rift branches. Our models suggest that differential extension velocities in the rift branches determine the localization of the structural triple junction, which is located closer to the rift branch experiencing slower extension velocities. Furthermore, imposed velocities affect the deformation resulting in end‐member fault patterns. The effect of applying similar velocities in all rift arms is to induce a symmetric fault pattern (generating a Y‐shaped geometry). In contrast, a faster plate generates structures trending orthogonal to dominant velocity vectors, while faults associated with the movement of the slower plates remain subordinate (generating a T‐shaped pattern). Two‐stage models reveal high‐angle faults interacting at the triple junction, confirming that differential extension velocities strongly affect fault patterns. These latter models show large‐scale similarities with fault patterns observed in the Afar triple junction, providing insights into the factors controlling the structural evolution of this area.
Plain Language Summary
When continents break‐up a rift valley can form and eventually grow to form an ocean. For particular conditions, more than two tectonic plates can be involved in this process. In this case, a “triple junction” is formed that consists of three rift branches. This process shaped the Afar region, where the movement of the Arabian, African, and Somalian plates, which separate at different rates of motion, created the Gulf of Aden, Red Sea, and Ethiopian rifts. The way in which triple junctions work can be difficult to study due to their large extent and several million year‐long activity. Therefore, we performed physical laboratory experiments and numerical experiments on the computer to investigate how triple junction form. We performed models with different rates of motion for the three plates, simulating one or two tectonic stages. The models show that the difference in the rate of motion between the three plates is the main control on the distribution and type of faults forming at triple junctions. Our results suggest that the fault pattern at the Afar triple junction observed nowadays may be explained by two tectonic stages and a lower extension rate occurring between the African and Somalian plates.
Key Points
We perform single and two‐stage analog and numerical models of Rift‐Rift‐Rift triple junctions
Models show that differential velocity of extension between the plates is key for the geometry of fault patterns at triple junctions
Two‐stage models shed light on the geometry and evolution of the Afar triple junction
The Afar region in East Africa represents a key location to study continental breakup. We present an integrated structural analysis of the Western Afar Margin (WAM) aiming to better understand rifted ...margin development and the role of plate rotation during rifting. New structural information from remote sensing, fieldwork, and earthquake data sets reveals that the N‐S striking WAM is still actively deforming and is characterized by NNW‐SSE normal faulting as well as a series of marginal grabens. Seismicity distribution analysis and the first‐ever borehole‐calibrated sections of this developing passive margin show recent slip concentrated along antithetic faults. Tectonic stress parameters derived from earthquake focal mechanisms reveal different extension directions along the WAM (82°N), in Afar (66°N) and in the Main Ethiopian Rift (108°N). Fault slip analysis along the WAM yields the same extension direction. Combined with GPS data, this shows that current tectonics in Afar is dominated by the local rotation of the Danakil Block, considered to have occurred since 11 Ma. Earlier stages of Afar development (since 31–25 Ma) were most likely related to the large‐scale rotation of the Arabian plate. Various authors have proposed scenarios for the evolution of the WAM. Any complete model should consider, among other factors, the multiphase tectonic history and antithetic fault activity of the margin. The findings of this study are not only relevant for a better understanding of the WAM but also provide insights into the role of multiphase rotational extension during rifting and passive margin formation in general.
Plain Language Summary
The Earth's continents are in gradual but perpetual motion, driven by large plate tectonic forces in the Earth's deep interior. A crucial process is the stretching and breaking up of continents, initially forming localized rift or graben depressions, followed by the opening of a new ocean flanked by the margins of the newly divided continents (passive margins). Rifts and passive margins are important because of their vast resource potential (e.g., oil, gas, geothermal energy), but pose also severe risks (volcanism, earthquakes, and landslides) since they are often home to large populations.
We focus on the Western Afar Margin in Ethiopia, where the African continent is currently splitting apart, providing a unique research opportunity. In the framework of an international collaborative effort, we combined satellite imagery, topography data, field observations, GPS, and earthquake measurements in order to map out the present‐day geology and tectonic activity along the margin.
Our results show the complexity of tectonic plate movements: We find evidence for two phases of continental stretching in Ethiopia that both involve the rotation of tectonic plates. We also observe active faulting, which may help to assess seismic risks in the area. Our study helps to better understand passive margins worldwide.
Key Points
Structural, borehole, and seismicity data from the Western Afar Margin serve to study continental breakup processes and rotational rifting
Antithetic faults bounding marginal grabens are currently accommodating significant deformation along the margin
Current extension is due to rotation of the Danakil Block; a previous oblique extension phase was likely related to Arabian plate motion
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