Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

BACKGROUND: The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems. RESULTS: We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal opsins were lost, probably in conjunction with the degeneration of the parietal organ. Eleven of the 15 avian opsins evolved in a non-neutral pattern, confirming the adaptive importance of vision in birds. Visual conopsins sw1, sw2 and lw evolved under negative selection, while the dim-light RH1 photopigment diversified. The evolutionary patterns of sw1 and of violet/ultraviolet sensitivity in birds suggest that avian ancestors had violet-sensitive vision. Additionally, we demonstrate an adaptive association between the RH2 opsin and the MC1R plumage color gene, suggesting that plumage coloration has been photic mediated. At the intra-avian level we observed some unique adaptive patterns. For example, barn owl showed early signs of pseudogenization in RH2, perhaps in response to nocturnal behavior, and penguins had amino acid deletions in RH2 sites responsible for the red shift and retinal binding. These patterns in the barn owl and penguins were convergent with adaptive strategies in nocturnal and aquatic mammals, respectively. CONCLUSIONS: We conclude that birds have evolved diverse opsin adaptations through gene loss, adaptive selection and coevolution with plumage coloration, and that differentiated selective patterns at the species level suggest novel photic pressures to influence evolutionary patterns of more-recent lineages.

Olfactory Receptor Subgenomes Linked with Broad Ecological Adaptations in Sauropsida.

Olfactory receptors (ORs) govern a prime sensory function. Extant birds have distinct olfactory abilities, but the molecular mechanisms underlining diversification and specialization remain mostly unknown. We explored OR diversity in 48 phylogenetic and ecologically diverse birds and 2 reptiles (alligator and green sea turtle). OR subgenomes showed species- and lineage-specific variation related with ecological requirements. Overall 1,953 OR genes were identified in reptiles and 16,503 in birds. The two reptiles had larger OR gene repertoires (989 and 964 genes, respectively) than birds (182-688 genes). Overall, birds had more pseudogenes (7,855) than intact genes (1,944). The alligator had significantly more functional genes than sea turtle, likely because of distinct foraging habits. We found rapid species-specific expansion and positive selection in OR14 (detects hydrophobic compounds) in birds and in OR51 and OR52 (detect hydrophilic compounds) in sea turtle, suggestive of terrestrial and aquatic adaptations, respectively. Ecological partitioning among birds of prey, water birds, land birds, and vocal learners showed that diverse ecological factors determined olfactory ability and influenced corresponding olfactory-receptor subgenome. OR5/8/9 was expanded in predatory birds and alligator, suggesting adaptive specialization for carnivory. OR families 2/13, 51, and 52 were correlated with aquatic adaptations (water birds), OR families 6 and 10 were more pronounced in vocal-learning birds, whereas most specialized land birds had an expanded OR family 14. Olfactory bulb ratio (OBR) and OR gene repertoire were correlated. Birds that forage for prey (carnivores/piscivores) had relatively complex OBR and OR gene repertoires compared with modern birds, including passerines, perhaps due to highly developed cognitive capacities facilitating foraging innovations.

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged before the Cretaceous-Paleogene mass extinction event 66 million years ago instead of after. However, their interpretations of the fossil record and timetrees are incorrect.

Practice-Level Variation in Outpatient Cardiac Care and Association With Outcomes.

BACKGROUND: Utilization of cardiac services varies across regions and hospitals, yet little is known regarding variation in the intensity of outpatient cardiac care across cardiology physician practices or the association with clinical endpoints, an area of potential importance to promote efficient care. METHODS AND RESULTS: We included 7 160 732 Medicare beneficiaries who received services from 5635 cardiology practices in 2012. Beneficiaries were assigned to practices providing the plurality of office visits, and practices were ranked and assigned to quartiles using the ratio of observed to predicted annual payments per beneficiary for common cardiac services (outpatient intensity index). The median (interquartile range) outpatient intensity index was 1.00 (0.81-1.24). Mean payments for beneficiaries attributed to practices in the highest (Q4) and lowest (Q1) quartile of outpatient intensity were: all cardiac payments (Q4 $1272 vs Q1 $581; ratio, 2.2); cardiac catheterization (Q4 $215 vs Q1 $64; ratio, 3.4); myocardial perfusion imaging (Q4 $253 vs Q1 $83; ratio, 3.0); and electrophysiology device procedures (Q4 $353 vs Q1 $142; ratio, 2.5). The adjusted odds ratios (95% CI) for 1 incremental quartile of outpatient intensity for each outcome was: cardiac surgical/procedural hospitalization (1.09 [1.09, 1.10]); cardiac medical hospitalization (1.00 [0.99, 1.00]); noncardiac hospitalization (0.99 [0.99, 0.99]); and death at 1 year (1.00 [0.99, 1.00]). CONCLUSION: Substantial variation in the intensity of outpatient care exists at the cardiology practice level, and higher intensity is not associated with reduced mortality or hospitalizations. Outpatient cardiac care is a potentially important target for efforts to improve efficiency in the Medicare population.

CT Scan Dosimetric Parameters Routine Monitoring: First Results of Radiation Dose Optimization Strategies Promptly Provided by a Multidisciplinary Team

CONCLUSION Radiation dose reduction, while saving image quality could be easily implemented with this approach. Furthermore, the availability of a dosimetric data archive provides immediate feedbacks, related to the implemented optimization strategies. Background JCI Standards and European Legislation (EURATOM 59/2013) require the implementation of patient radiation protection programs in diagnostic radiology. Aim of this study is to demonstrate the possibility to reduce patients radiation exposure without decreasing image quality, through a multidisciplinary team (MT), which analyzes dosimetric data of diagnostic examinations. Evaluation Data from CT examinations performed with two different scanners (Siemens DefinitionTM and GE LightSpeed UltraTM) between November and December 2013 are considered. CT scanners are configured to automatically send images to DoseWatch© software, which is able to store output parameters (e.g. kVp, mAs, pitch ) and exposure data (e.g. CTDIvol, DLP, SSDE). Data are analyzed and discussed by a MT composed by Medical Physicists and Radiologists, to identify protocols which show critical dosimetric values, then suggest possible improvement actions to be implemented. Furthermore, the large amount of data available allows to monitor diagnostic protocols currently in use and to identify different statistic populations for each of them. Discussion We identified critical values of average CTDIvol for head and facial bones examinations (respectively 61.8 mGy, 151 scans; 61.6 mGy, 72 scans), performed with the GE LightSpeed CTTM. Statistic analysis allowed us to identify the presence of two different populations for head scan, one of which was only 10% of the total number of scans and corresponded to lower exposure values. The MT adopted this protocol as standard. Moreover, the constant output parameters monitoring allowed us to identify unusual values in facial bones exams, due to changes during maintenance service, which the team promptly suggested to correct. This resulted in a substantial dose saving in CTDIvol average values of approximately 15% and 50% for head and facial bones exams, respectively. Diagnostic image quality was deemed suitable for clinical use by radiologists.

Competing Actions of Type 1 Angiotensin II Receptors Expressed on T Lymphocytes and Kidney Epithelium during Cisplatin-Induced AKI.

Inappropriate activation of the renin-angiotensin system (RAS) contributes to many CKDs. However, the role of the RAS in modulating AKI requires elucidation, particularly because stimulating type 1 angiotensin II (AT1) receptors in the kidney or circulating inflammatory cells can have opposing effects on the generation of inflammatory mediators that underpin the pathogenesis of AKI. For example, TNF-α is a fundamental driver of cisplatin nephrotoxicity, and generation of TNF-α is suppressed or enhanced by AT1 receptor signaling in T lymphocytes or the distal nephron, respectively. In this study, cell tracking experiments with CD4-Cre mT/mG reporter mice revealed robust infiltration of T lymphocytes into the kidney after cisplatin injection. Notably, knockout of AT1 receptors on T lymphocytes exacerbated the severity of cisplatin-induced AKI and enhanced the cisplatin-induced increase in TNF-α levels locally within the kidney and in the systemic circulation. In contrast, knockout of AT1 receptors on kidney epithelial cells ameliorated the severity of AKI and suppressed local and systemic TNF-α production induced by cisplatin. Finally, disrupting TNF-α production specifically within the renal tubular epithelium attenuated the AKI and the increase in circulating TNF-α levels induced by cisplatin. These results illustrate discrepant tissue-specific effects of RAS stimulation on cisplatin nephrotoxicity and raise the concern that inflammatory mediators produced by renal parenchymal cells may influence the function of remote organs by altering systemic cytokine levels. Our findings suggest selective inhibition of AT1 receptors within the nephron as a promising intervention for protecting patients from cisplatin-induced nephrotoxicity.

Predictive immunomonitoring-The COST ENTIRE initiative

SCOPUS: ed.j

Análisis de una alternativa de manejo de la vaca de descarte en tambos

El objetivo de este trabajo fue evaluar una estrategia productiva de manejo de la vaca de descarte orientada a generar un mayor valor residual de esta categoría y aumentar los ingresos obtenidos por el subsistema de producción de carne en el tambo. Se partió del supuesto de que al aplicar una estrategia nutricional en las vacas de descarte se lograría incrementar su peso y su precio de comercialización, de modo que permita mejorar el resultado económico del subsistema de producción de carne. El análisis se realizó sobre datos reales obtenidos en un establecimiento lechero regional (Modelo Tradicional - MT) y datos simulados a partir de un modelo mejorado sobre la situación inicial (Modelo Modificado - MM). Los resultados obtenidos indican que, en el marco de una amplia variación de precios planteados, 30 por ciento por arriba o por debajo del valor actual en la carne y/o en la leche, en todos los casos los presupuestos parciales son superiores en los modelos modificados, aún en los escenarios más desfavorables. El valor de venta de la vaca de descarte es mayor cuando al efecto del incremento en peso vivo se le suma el acceso a una categoría comercial superior generado por la mejora en un proceso de engorde de vacas. En el caso de no lograrse el cambio de categoría comercial buscado, el aumento de peso vivo dentro de la misma categoría igualmente permitiría obtener un beneficio económico debido a la mayor cantidad de kg vendidos

Water sorption/desorption in polyacid-modified composite resins for dentistry

The water sorption and desorption behaviour of three commercial polyacid-modified composite resins used in clinical dentistry have been studied in detail. Cured specimens of each material were subjected to two successive water uptake cycles in an atmosphere of 93% relative humidity, with one intervening desorption cycle in a desiccating atmosphere over concentrated sulfuric acid. Specimens were found to absorb and desorb water according Fick's law until Mt/M(infinity) values of approximately 0.5. Diffusion rates for uptake varied between cycles, ranging from 2.37-4.53 x 10(-9 )cm(2) s(-1) for 1st cycle to 0.85-2.72 x 10(-8 )cm(2 )s(-1) for 2nd cycle. Desorption rates were similar to those for 2nd cycle sorption, and ranged from 0.86 to 5.47 x 10(-8 )cm(2 )s(-1). Equilibration times for 1st cycle water uptake were greater than for 2nd cycle sorption and for desorption and overall the behaviour of polyacid-modified composites in a high humidity atmosphere was similar to that of conventional composites in water. It is concluded that the hydrophilic components of the former do not bring about an enhanced rate of water transport.

Water transport in zinc oxy-chloride cements

The water uptake and water loss behaviour in three different formulations of zinc oxy-chloride cement have been studied in detail. Specimens of each material were subjected to a high humidity atmosphere (93% RH) over saturated aqueous sodium sulfate, and a low humidity desiccating atmosphere over concentrated sulfuric acid. In high humidity, the cement formulated from the nominal 75% ZnCl2 solutions gained mass, eventually becoming too sticky to weigh further. The specimens at 25% and 50% ZnCl2 by contrast lost mass by a diffusion process, though by 1 week the 50% cement had stated to gain mass and was also too sticky to weigh. In low humidity, all three cements lost mass, again by a diffusion process. Both water gain and water loss followed Fick's law for a considerable time. In the case of water loss under desiccating conditions, this corresponded to values of Mt/MĄ well above 0.5. However, plots did not go through the origin, showing that there was an induction period before true diffusion began. Diffusion coefficients varied from 1.56 x 10-5 (75% ZnCl2) to 2.75 x 10-5 cm2/s (50% ZnCl2), and appeared to be influenced not simply by composition. The drying of the 25% and 50% ZnCl2 cements in high humidity conditions occurred at a much lower rate, with a value of D of 2.5 x 10-8 cm2/s for the 25% ZnCl2 cement. This cement was found to equilibrate slowly, but total water loss did not differ significantly from that of the cements stored under desiccating conditions. Equilibration times for water loss in desiccating conditions were of the order of 2-4 hours, depending on ZnCl2 content; equilibrium water losses were respectively 28.8 [25% ZnCl2], 16.2 [50%] and 12.4 [75%] which followed the order of ZnCl2 content. It is concluded that the water transport processes are strongly influenced by the ZnCl2 content of the cement.

Recovery of a biodiversity action plans species in northwest England: possible role of climate change, artificial habitat and water quality amelioration. Occasional Publication of the Marine Biological Association 16

The honeycomb reef worm Sabellaria alveolata is recognised as being an important component of intertidal communities. It is a priority habitat within the UK Biodiversity Action Plan and as a biogenic reef forming species is covered by Annex 1 of the EC habitats directive. S. alveolata has a lusitanean (southern) distribution, being largely restricted to the south and west coasts of England. A broad-scale survey of S. alveolata distribution along the north-west coasts was undertaken in 2003/2004. These records were then compared with previous distribution records, mainly those collected by Cunningham in 1984. More detailed mapping was carried out at Hilbre Island at the mouth of the River Dee, due to recent reports that S. alveolata had become re-established there after a long absence.

Marine biodiversity and climate change: assessing and predicting the influence of climatic change using intertidal rocky shore biota. Occasional Publication of the Marine Biological Association 20

In the last 60 years climate change has altered the distribution and abundance of many seashore species. Below is a summary of the findings of this project. The MarClim project was a four year multi-partner funded project created to investigate the effects of climatic warming on marine biodiversity. In particular the project aimed to use intertidal species, whose abundances had been shown to fluctuate with changes in climatic conditions, as indicator species of likely responses of species not only on rocky shores, but also those found offshore. The project used historic time series data, from in some cases the 1950s onwards, and contemporary data collected as part of the MarClim project (2001-2005), to provide evidence of changes in the abundance, range and population structure of intertidal species and relate these changes to recent rapid climatic warming. In particular quantitative counts of barnacles, limpets and trochids were made as well as semi-quantitative surveys of up to 56 intertidal taxa.Historic and contemporary data informed experiments to understand the mechanisms behind these changes and models to predict future species ranges and abundances.

The evaluation of time series: their scientific value and contribution to policy needs. Occasional Publication of the Marine Biological Association 22

In 2000 a Review of Current Marine Observations in relation to present and future needs was undertaken by the Inter-Agency Committee for Marine Science and Technology (IACMST). The Marine Environmental Change Network (MECN) was initiated in 2002 as a direct response to the recommendations of the report. A key part of the current phase of the MECN is to ensure that information from the network is provided to policy makers and other end-users to enable them to produce more accurate assessments of ecosystem state and gain a clearer understanding of factors influencing change in marine ecosystems. The MECN holds workshops on an annual basis, bringing together partners maintaining time-series and long-term datasets as well as end-users interested in outputs from the network. It was decided that the first workshop of the MECN continuation phase should consist of an evaluation of the time series and data sets maintained by partners in the MECN with regard to their ‘fit for purpose’ for answering key science questions and informing policy development. This report is based on the outcomes of the workshop. Section one of the report contains a brief introduction to monitoring, time series and long-term datasets. The various terms are defined and the need for MECN type data to complement compliance monitoring programmes is discussed. Outlines are also given of initiatives such as the United Kingdom Marine Monitoring and Assessment Strategy (UKMMAS) and Oceans 2025. Section two contains detailed information for each of the MECN time series / long-term datasets including information on scientific outputs and current objectives. This information is mainly based on the presentations given at the workshop and therefore follows a format whereby the following headings are addressed: Origin of time series including original objectives; current objectives; policy relevance; products (advice, publications, science and society). Section three consists of comments made by the review panel concerning all the time series and the network. Needs or issues highlighted by the panel with regard to the future of long-term datasets and time-series in the UK are shown along with advice and potential solutions where offered. The recommendations are divided into 4 categories; ‘The MECN and end-user requirements’; ‘Procedures & protocols’; ‘Securing data series’ and ‘Future developments’. Ever since marine environmental protection issues really came to the fore in the 1960s, it has been recognised that there is a requirement for a suitable evidence base on environmental change in order to support policy and management for UK waters. Section four gives a brief summary of the development of marine policy in the UK along with comments on the availability and necessity of long-term marine observations for the implementation of this policy. Policy relating to three main areas is discussed; Marine Conservation (protecting biodiversity and marine ecosystems); Marine Pollution and Fisheries. The conclusion of this section is that there has always been a specific requirement for information on long-term change in marine ecosystems around the UK in order to address concerns over pollution, fishing and general conservation. It is now imperative that this need is addressed in order for the UK to be able to fulfil its policy commitments and manage marine ecosystems in the light of climate change and other factors.

Larval development of the intertidal barnacles Chthamalus stellatus and Chthamalus montagui

Two recently-distinguished species of Chthamalus (Cirripedia) are found on rocky shores in the north-eastern Atlantic: C. stellatus predominant on islands and headlands and C. montagui more abundant in bays. Larvae of the two species were produced in laboratory cultures to describe and compare the morphology and to allow identification in plankton samples. Nauplius larvae of C. stellatus are up to 30% larger than those of C. montagui. Differences in setation are minor. The two species are easily distinguishable from the size and shape of the cephalic shield. Chthamalus stellatus has a subcircular shield with longer body processes in later stages while C. montagui is more ovoid. The former develop more slowly in culture than the latter. Chthamalus stellatus larvae in a culture at 19 °C reached stage VI in 16 d compared to 11 d for larvae of C. montagui at the same temperature. The morphology and longer development time of C. stellatus larvae suggests adaptation to a more oceanic lifestyle and wider dispersal to reach more fragmented habitats than larvae of C. montagui. --------------------------------------------------------------------------------