The Influence of Taxon Sampling and Tree Shape on Molecular Dating: An Empirical Example from Mammalian Mitochondrial Genomes

Over the last decade, molecular dating methods have been among the most studied subjects in statistical phylogenetics. Although the evolutionary modelling of substitution rates and the handling of calibration information are the primary focus of species divergence time research, parameters that influence topological estimation, such as taxon sampling and tree shape, also have the potential to influence evolutionary age estimates. However, the impact of topological parameters on chronological estimates is rarely considered. In this study, we use mitochondrial genomes to evaluate the influence of tree shape and taxon sampling on the divergence times of selected nodes of the mammalian tree. Our results show that taxon sampling affects divergence time estimates; the credibility intervals for age estimates decrease as taxonomic sampling increases (i.e., estimates become more precise). The influence of taxonomic sampling was not observed on nodes that lay deep in the mammalian phylogeny, although the means of the posterior distributions tend to converge with increased taxon sampling, an effect that is independent of the location of the node. In the majority of cases, the effect of tree shape was negligible

Influence of fluid-mechanical coupling in gas generation in undersaturated petroleum reservoirs

Among the several mechanisms of producing an oil reservoir, the gas expansion mechanism is an important primary recovery process. During the depletion of the reservoir, the pore pressure may reach values below the bubble pressure of the oil, allowing the gas release. From the geomechanical point of view, the change in pore volume, due to production, changes the dynamics of gas generation, since it is dependent upon the change in pore pressure. Studies considering the fluid-mechanical coupling show the relationship between variations of fluid pressure and porous structure of the reservoir. This work aims to study the influence of the fluid-mechanical partial coupling (one and two-way) in the process of gas release during recovery of hydrocarbon. It was used the partial coupling methodology developed by ATHENA/GTEP – PUC-Rio. The model called “A” has only one producing well, while the model called “B” has four injection wells, besides the producer. Initially, the oil present in the reservoir is in undersaturated condition. In model “A” was observed that the pressure drop of fluid is more accentuated, until it reaches the bubble pressure, when considering the two-way coupling. Consequently, the gas release initiation occurs earlier than one-way coupling scheme. After starting gas generation, the rates of pressure change in both partial coupling scenarios tend to equalize. In terms of compaction and subsidence, it was observed most significant displacements values in two-way coupling, highlighting the rigorous consideration of the geomechanical effects in the applied methodology. In model “B”, it was observed that the consideration of the two-way coupling resulted in a recovery scenario without generation of gas, unlike the results shown by the one-way coupling in which gas was generated during 40% of total simulation time. In geomechanical terms it was observed, as presented previously, that the values of vertical displacement were greater in the two-way coupling. The methodology used in this paper proved to be capable of simulating coupled process in a blackoil reservoir, as could be observed by the results. Furthermore, the use of one-way partial coupling scheme, which is widely used in the oil industry, showed results quite different in terms of gas liberation, when are compared with the two-way partial coupling scheme, which was developed in a more rigorous way

Evidencia experimental de la abundancia de bacterias del suelo como el principal iniciador del efecto de preparación de la rizosfera

Se piensa que las comunidades microbianas del suelo son responsables del efecto de preparación de la rizósfera (RPE). Sin embargo, desde que las comunidades microbiales están compuestas de diversos componentes, se conoce muy poco acerca de cuál es el componente que tiene el rol principal en dicho efecto. En este estudio, se hicieron crecer soja y algodón en dos lugares a diferentes latitudes con diferentes condiciones de luz y temperatura in situ. Se cuantificó RPE usando un método natural de δC13 y se midió la abundancia, riqueza y composición de las comunidades de hongos y bacterias con métodos moleculares basados en el ADN. Entre todas las variables potenciales, incluyendo los tres índices de comunidades de hongos y bacterias anteriormente mencionados, e índices vegetales y físico-químicos del suelo, se mostró que la abundancia de bacterias explicó una gran proporción de la variación en RPE. Nuestro estudio identificó el mecanismo biológico que subyace este importante proceso ecológico.Soil microbial communities are thougth to be responsible for the rhizosphere priming effect (RPE). However, because soil microbial communities are comprised of diverse components, very little is known about which component plays the critical role. Here, soybean and cottonwood were grown at two latitudinal locations with different temperature and light conditions in-situ. We quantified RPE using a natural 13C method, and measured the abundance, richness and composition of bacteria and fungi communities with DNA-based molecular methods. Among all potential variables, including the three aforementioned indexes of bacteria and fungi communities and soil physiochemical and plant indexes, bacterial abundance was found to explain a large proportion of variation in RPE. Our study identified the biological mechanism underlying this important ecological process.Fil: Ma, Y.P.. Chinese Academy of Sciences. Institute of Applied Ecology; China. Chinese Academy of Agricultural Sciences. Institute of Environment and Sustainable Development in Agriculture. Key Laboratory of Dryland Agriculture;; China. University of Chinese Academy of Science; ChinaFil: Zhang, Z.J.. Chinese Academy of Sciences. Institute of Applied Ecology; China. Chinese Academy of Agricultural Sciences. Institute of Environment and Sustainable Development in Agriculture. Key Laboratory of Dryland Agriculture;; ChinaFil: Su, T.Q.. Chinese Academy of Sciences. Institute of Applied Ecology; ChinaFil: Busso, Carlos Alberto. Universidad Nacional del Sur. Departamento de Agronomía; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Johnston, E.R.. Georgia Institute of Technology. School of Civil and Environmental Engineering; Estados UnidosFil: Han, X.G.. Chinese Academy of Sciences. Institute of Applied Ecology; China. Chinese Academy of Sciences. Institute of Botany. State Key Laboratory of Vegetation and Environmental Change; ChinaFil: Zhang, X.M.. Chinese Academy of Agricultural Sciences. Institute of Environment and Sustainable Development in Agriculture. Key Laboratory of Dryland Agriculture;; Chin

Evidence for eosinophil recruitment, leukotriene B4 production and mast cell hyperplasia following Toxocara canis infection in rats

It is well known that eosinophilia is a key pathogenetic component of toxocariasis. The objective of the present study was to determine if there is an association between peritoneal and blood eosinophil influx, mast cell hyperplasia and leukotriene B4 (LTB4) production after Toxocara canis infection. Oral inoculation of 56-day-old Wistar rats (N = 5-7 per group) with 1000 embryonated eggs containing third-stage (L3) T. canis larvae led to a robust accumulation of total leukocytes in blood beginning on day 3 and peaking on day 18, mainly characterized by eosinophils and accompanied by higher serum LTB4 levels. At that time, we also noted increased eosinophil numbers in the peritoneal cavity. In addition, we observed increased peritoneal mast cell number in the peritoneal cavity, which correlated with the time course of eosinophilia during toxocariasis. We also demonstrated that mast cell hyperplasia in the intestines and lungs began soon after the T. canis larvae migrated to these compartments, reaching maximal levels on day 24, which correlated with the complete elimination of the parasite. Therefore, mast cells appear to be involved in peritoneal and blood eosinophil infiltration through an LTB4-dependent mechanism following T. canis infection in rats. Our data also demonstrate a tight association between larval migratory stages and intestinal and pulmonary mast cell hyperplasia in the toxocariasis model

Lagochilascariasis leading to severe involvement of ocular globes, ears and meninges

A case report of a 31 year-old woman from Paraíba State (North-Eastern Brazil) that presented severe involvement of ocular globes, ears and meninges. Diagnosis was established after enucleation of her left eye, when adult worms were seen in the midst of a granulomatous inflammatory process. Her response to the initial treatment with levamisole and cambendazole was good, but there was a relapse after the fifth month of treatment even with maintenance doses of both medications. She later received ivermectin and albendazol and responded well.Paciente do sexo feminino, com 31 anos, procedente da Paraíba, apresentava envolvimento severo de ambos os globos oculares, com perda da visão à esquerda, comprometimento da audição e das meninges. Após enucleação do olho esquerdo fragmento de helminto identificado como Lagochilascaris minor foi observado em processo inflamatório granulomatoso. Inicialmente a paciente foi tratada com levamisol e cambendazol, com bom resultado. Verificou-se, todavia, piora do quadro após cinco meses, com eliminação de larvas do ascarídeo em lesão presente na órbita esquerda, embora a medicação fosse mantida com administração periódica. Houve boa resposta terapêutica, com regressão do quadro, após substituição dos anti-helmínticos anteriores pela associação ivermectina e albendazol

Palliative care coverage across European National Health Systems: proposal of a synthetic indicator

Background: The coverage of palliative care (PC) may be understood as a country’s capacity to offer prevention and relief from serious health-related suffering in relation to an existing need. The aim of this study is to estimate European countries´ coverage capacities. Method: Secondary analysis of three indicators, including the number of specialized services (SSPC), integration capacity scores (ICS) and the PC needs. By means of a K-medians clustering supervised algorithm, three coverage profiles were obtained: (1) Advanced: countries with high ICS and SSPC, and low PC needs; (2) Limited: countries with low ICS and SSPC, and low PC needs; and (3) Low: countries with low ICS and SSPC and high PC needs. Results: On average, the ratio of specialized services per population was 0.79 per 100,000 inhabitants, the average ICS was 19.62 and the average number of deceased patients with SHS per 100,000 inhabitants was 5.69. Twenty countries (41%) reached an advanced coverage profile. Nine countries (18%) demonstrated a limited coverage profile; and 20 countries (41%) fell under a low-coverage capacity. Conclusion: The level of palliative care coverage across Europe shows that 59% of European countries have either limited or very low availability of PC resources as regards their palliative care needs

Semi-automatic rubble counting system for superheated droplet detectors

Neutron dose rate measurements are normally performed by means of PADC, CR-39 and TLD detectors. Although, none of these devices can give instant reading of the neutron dose, recently new kind of detectors are being developed, based on the formation of tiny drops in a superheated liquid suspended in a polymer or gel solution, called superheated droplet detector (SDD) or also as bubble detectors (BD), with no response for gamma radiation. This work describes the experimental setup and the developed procedures for acquiring and processing digital images obtained with bubble detector spectrometer (BDS), developed by Bubble Technology Industries, for personal neutron dosimeter and/or neutron energy fluence measurements in nuclear facilities. The results of the neutron measurements obtained during the F-18 production, at the RDS-111 cyclotron, are presented. These neutron measurements were the first ones with this type of BDS detectors in a particle accelerator facility in Brazil and it was very important to estimate neutron dose rate received by occupationally exposed individuals

Palliative care in the Eastern Mediterranean: comparative analysis using specific indicators

Background Monitoring the development of palliative care (PC) illustrates the capacity of health systems to respond to the needs of people experiencing serious health-related suffering. Aim To analyse comparatively the situation of PC in the countries of the Easter Mediterranean region using context-specific indicators. Method An online questionnaire with 15 context-specific PC indicators investigating service provision, use of medicines, policy, education, and vitality was designed. Authors Institution 1 nominated in-country experts to complete the survey. Data were analysed using a comparative description of indicators per domain and a multivariate analysis. Results In-country experts were identified in 17/22 countries. 12/17 contributed to the survey. In total, 117 specialized PC services were identified. Specialized services per population ranges from 0.09 per 100,000 inhabitants in Lebanon and Saudi Arabia, Qatar and Kuwait; to zero services in the Occupied Palestinian Territories. On average, opioid consumption was 2.40 mg/capita/year. National PC strategies were reported in nine countries. In six countries, PC is officially accredited either as a specialty or sub-specialty, and PC mandatory courses are implemented in 36% of medical schools and 46% of nursing schools. National PC associations were documented in six countries. A higher pattern of development was identified in Jordan, Kuwait, Saudi Arabia, Oman, Lebanon, Qatar. Conclusions Despite a higher development in the Arabian Peninsula, the region is characterised by a very low provision of specialized PC services and opioid consumption. Policy improvements represent an opportunity to improve access to PC

Counting Domain Walls in N=1 Super Yang-Mills Theory

We study the multiplicity of BPS domain walls in N=1 super Yang-Mills theory, by passing to a weakly coupled Higgs phase through the addition of fundamental matter. The number of domain walls connecting two specified vacuum states is then determined via the Witten index of the induced worldvolume theory, which is invariant under the deformation to the Higgs phase. The worldvolume theory is a sigma model with a Grassmanian target space which arises as the coset associated with the global symmetries broken by the wall solution. Imposing a suitable infrared regulator, the result is found to agree with recent work of Acharya and Vafa in which the walls were realized as wrapped D4-branes in IIA string theory.Comment: 28 pages, RevTeX, 3 figures; v2: discussion of the index slightly expanded, using an alternative regulator, and references added; v3: typos corrected, to appear in Phys. Rev.