Comparative genomic data of the Avian Phylogenomics Project.

BACKGROUND: The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders, and used the genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomics analyses (Jarvis et al. in press; Zhang et al. in press). Here we release assemblies and datasets associated with the comparative genome analyses, which include 38 newly sequenced avian genomes plus previously released or simultaneously released genomes of Chicken, Zebra finch, Turkey, Pigeon, Peregrine falcon, Duck, Budgerigar, Adelie penguin, Emperor penguin and the Medium Ground Finch. We hope that this resource will serve future efforts in phylogenomics and comparative genomics. FINDINGS: The 38 bird genomes were sequenced using the Illumina HiSeq 2000 platform and assembled using a whole genome shotgun strategy. The 48 genomes were categorized into two groups according to the N50 scaffold size of the assemblies: a high depth group comprising 23 species sequenced at high coverage (>50X) with multiple insert size libraries resulting in N50 scaffold sizes greater than 1 Mb (except the White-throated Tinamou and Bald Eagle); and a low depth group comprising 25 species sequenced at a low coverage (~30X) with two insert size libraries resulting in an average N50 scaffold size of about 50 kb. Repetitive elements comprised 4%-22% of the bird genomes. The assembled scaffolds allowed the homology-based annotation of 13,000 ~ 17000 protein coding genes in each avian genome relative to chicken, zebra finch and human, as well as comparative and sequence conservation analyses. CONCLUSIONS: Here we release full genome assemblies of 38 newly sequenced avian species, link genome assembly downloads for the 7 of the remaining 10 species, and provide a guideline of genomic data that has been generated and used in our Avian Phylogenomics Project. To the best of our knowledge, the Avian Phylogenomics Project is the biggest vertebrate comparative genomics project to date. The genomic data presented here is expected to accelerate further analyses in many fields, including phylogenetics, comparative genomics, evolution, neurobiology, development biology, and other related areas.

Air pollution, Fuel Usage and Health Outcomes in Madre de Dios, Peru: a Comparative Cross Sectional Study

Air pollution is a common problem. Particulate matter generated from air pollution has been tied to adverse health outcomes associated with cardiovascular disease. Biomass fuels are a specific contributor to increased particulate matter and arise as a result of indoor heating, cook stoves and indoor food preparation. This is a two part cross sectional study looking at communities in the Madre de Dios region. Survey data was collected from 9 communities along the Madre de Dios River. Individual level household PM2.5 was also collected as a means to generate average PM data stratified by fuel use. Data collection was affected by a number of outside factors, which resulted in a loss of data. Results from the cross-sectional study indicate that hypertension is not a significant source of morbidity. Obesity is prevalent and significantly associated with kitchen venting method indicating a potential relationship.

Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays.

Determination of copy number variants (CNVs) inferred in genome wide single nucleotide polymorphism arrays has shown increasing utility in genetic variant disease associations. Several CNV detection methods are available, but differences in CNV call thresholds and characteristics exist. We evaluated the relative performance of seven methods: circular binary segmentation, CNVFinder, cnvPartition, gain and loss of DNA, Nexus algorithms, PennCNV and QuantiSNP. Tested data included real and simulated Illumina HumHap 550 data from the Singapore cohort study of the risk factors for Myopia (SCORM) and simulated data from Affymetrix 6.0 and platform-independent distributions. The normalized singleton ratio (NSR) is proposed as a metric for parameter optimization before enacting full analysis. We used 10 SCORM samples for optimizing parameter settings for each method and then evaluated method performance at optimal parameters using 100 SCORM samples. The statistical power, false positive rates, and receiver operating characteristic (ROC) curve residuals were evaluated by simulation studies. Optimal parameters, as determined by NSR and ROC curve residuals, were consistent across datasets. QuantiSNP outperformed other methods based on ROC curve residuals over most datasets. Nexus Rank and SNPRank have low specificity and high power. Nexus Rank calls oversized CNVs. PennCNV detects one of the fewest numbers of CNVs.

Comparative analyses of clinical and environmental populations of Cryptococcus neoformans in Botswana.

Cryptococcus neoformans var. grubii (Cng) is the most common cause of fungal meningitis, and its prevalence is highest in sub-Saharan Africa. Patients become infected by inhaling airborne spores or desiccated yeast cells from the environment, where the fungus thrives in avian droppings, trees and soil. To investigate the prevalence and population structure of Cng in southern Africa, we analysed isolates from 77 environmental samples and 64 patients. We detected significant genetic diversity among isolates and strong evidence of geographic structure at the local level. High proportions of isolates with the rare MATa allele were observed in both clinical and environmental isolates; however, the mating-type alleles were unevenly distributed among different subpopulations. Nearly equal proportions of the MATa and MATα mating types were observed among all clinical isolates and in one environmental subpopulation from the eastern part of Botswana. As previously reported, there was evidence of both clonality and recombination in different geographic areas. These results provide a foundation for subsequent genomewide association studies to identify genes and genotypes linked to pathogenicity in humans.

The IGNITE network: a model for genomic medicine implementation and research.

BACKGROUND: Patients, clinicians, researchers and payers are seeking to understand the value of using genomic information (as reflected by genotyping, sequencing, family history or other data) to inform clinical decision-making. However, challenges exist to widespread clinical implementation of genomic medicine, a prerequisite for developing evidence of its real-world utility. METHODS: To address these challenges, the National Institutes of Health-funded IGNITE (Implementing GeNomics In pracTicE; www.ignite-genomics.org ) Network, comprised of six projects and a coordinating center, was established in 2013 to support the development, investigation and dissemination of genomic medicine practice models that seamlessly integrate genomic data into the electronic health record and that deploy tools for point of care decision making. IGNITE site projects are aligned in their purpose of testing these models, but individual projects vary in scope and design, including exploring genetic markers for disease risk prediction and prevention, developing tools for using family history data, incorporating pharmacogenomic data into clinical care, refining disease diagnosis using sequence-based mutation discovery, and creating novel educational approaches. RESULTS: This paper describes the IGNITE Network and member projects, including network structure, collaborative initiatives, clinical decision support strategies, methods for return of genomic test results, and educational initiatives for patients and providers. Clinical and outcomes data from individual sites and network-wide projects are anticipated to begin being published over the next few years. CONCLUSIONS: The IGNITE Network is an innovative series of projects and pilot demonstrations aiming to enhance translation of validated actionable genomic information into clinical settings and develop and use measures of outcome in response to genome-based clinical interventions using a pragmatic framework to provide early data and proofs of concept on the utility of these interventions. Through these efforts and collaboration with other stakeholders, IGNITE is poised to have a significant impact on the acceleration of genomic information into medical practice.

A Comparative Study of the Chinese Trickster Hero Sun Wukong

Sun Wukong is a fictional hero from the Chinese classic The Journey to the West. As a well-known trickster, Wukong has a lot of similarities with several other tricksters around the world. In order to analyze him, I try to explain both his similarities with, and differences from, other tricksters, especially in the Ancient Greek folklore and myth traditions. The first half of the paper focuses on the general characteristics of tricksters. As a very distinctive group in global mythology, tricksters have particular features. The definition and symbolization of tricksters are illustrated by comparing Wukong and major Greek tricksters, such as Hermes, Odysseus, and Prometheus. The second part of the paper is concentrated on the heroic features of tricksters and the cultural values reflected in the Wukong narrative. How tricksters become cultural heroes is the main theme of Chapter Three. I explain their evolution by elaborating on the change in their nature mentioned in the second chapter. The fourth chapter illustrates the reason why Wukong is an East Asian cultural hero.I explore the personalities of Wukong and see how they fit the dominant philosophy and cultural values of the region. The last chapter briefly shows how popular Wukong is in Chinese and the entire East Asian culture.

Analyse phytogéographique comparative des savanes et des forêts de Ngotto (République Centrafricaine)

After several investigations on the savanna and forest of Ngotto (Central African Republic), we propose a phytogeographical interpretation of our data on the systematic (level family), the biological forms, the dispersion of diaspores and phytogeographical elements spectra. These spectra are given regarding both formation type (savanna, forest) to appreciate their originality. Then, a comparaison is driven in order to set up the differences between these two formations.

Methylation-dependent T cell immunity to Mycobacterium tuberculosis heparin-binding hemagglutinin.

Although post-translational modifications of protein antigens may be important componenets of some B cell epitopes, the determinants of T cell immunity are generally nonmodified peptides. Here we show that methylation of the Mycobacterium tuberculosis heparin-binding hemagglutinin (HBHA) by the bacterium is essential for effective T cell immunity to this antigen in infected healthy humans and in mice. Methylated HBHA provides high levels of protection against M. tuberculosis challenge in mice, whereas nonmethylated HBHA does not. Protective immunity induced by methylated HBHA is comparable to that afforded by vaccination with bacille Calmette et Guérin, the only available anti-tuberculosis vaccine. Thus, post-translational modifications of proteins may be crucial for their ability to induce protective T cell-mediated immunity against infectious diseases such as tuberculosis.

Comparative wetting behavior of Sn-0.7Cu and Sn-0.7Cu-0.3Ni solders on Cu and Ni substrates

Electronic packaging industries are now in great challenge to find a suitable lead-free solder as an interconnection material to replace the conventional SnPb solders. Many solders such as SnCu, SnAg, SnAgCu, SnZn, SnBi have already been proposed as the replacement but none of them has reached the physical and metallurgical properties similar to the SnPb solder. However, wetting is one of the basic problems that make the lead-free solder inferior as compared to the SnPb solder. Therefore, alloying with the help of third, fourth or fifth element is the researchers' interest to improve the wetting behavior of lead-free solders. This paper describes the comparative wetting behavior of Sn-0.7Cu and Sn-0.7Cu-0.3Ni solders on Cu and Ni substrates. Wetting balance tests were performed to assess the wetting behaviors. Three different commercial fluxes namely no-clean (NC), non-activated (R) and water soluble organic acid (WS)fluxes were used to assess the wettability for three solder bath temperatures. It was found that Sn0.7Cu-03Ni solder exhibits better wettability on Cu substrate for NC and WS fluxes whereas reverse results were found for R-type flux. In the case of Ni substrate, Sn-0.7Cu-0.3Ni solder showed better wetting behavior compared to the well-known Sn-0.7Cu solder. Among the three fluxes, R-type flux showed the worst performance. Very large contact angles were documented for both solders with this flux. Higher solder bath temperature lowered the contact angles, increased the wetting forces and enhanced the wettability. Computer modeling of wetting balance test revealed that both the wetting force and meniscus height are inversely proportional to the contact angles. Modeling results also reveal that increase in solder bath depths and radiuses do not affect significantly on the wetting behavior.

Comparative antioxidant, prooxidant and cytotoxic activity of sigmoidin A and eriodictyol

Sigmoidin A (SGN) is a prenylated flavanone derivative of eriodictyol (ERD) with reported moderate antioxidant, antimicrobial and anti-inflammatory activity. Since ERD and other structurally similar antioxidant phenolic compounds have been shown to induce prooxidative macromolecular damage and cytotoxicity in cancer cells, the comparative in vitro effects of these structural analogues on cancer cell viability and Cu(II)-dependent DNA damage were studied. In the presence of Cu(II) ions, both SGN and ERD (7.4-236 µM) caused comparable concentration-dependent pBR322 plasmid DNA strand scission. The DNA damage induced by SGN and ERD could be abolished by ROS scavengers, glutathione (GSH) and catalase as well as EDTA and a specific Cu(I) chelator neocuproine. Both ERD and SGN readily reduce Cu(II) to Cu(I) suggesting a prooxidative mechanism of DNA damage. In a cell free system, ERD and SGN did also show comparable radical scavenging activity. SGN was, however, by an order of magnitude more cytotoxic to cancer cells than ERD and this effect was significantly attenuated by GSH suggesting a prooxidative mechanism of cell death. A depletion of intracellular GSH level by SGN in cancer cells is also demonstrated.

We could make a meal out of nothing: contested explanations of inequalities in health

This paper reports on the qualitative findings from a comparative study of public health and lifestyles in South East England and Northern France, regions with similar geographic and economic characteristics. Data from health surveys showed that both countries had an increasing BMI with age, particularly in Northern France. This was despite the finding that the percentage eating fresh fruit and vegetable at least five days a week in Northern France increased with age (from well over 50% to over 90%) compared to around 50% to around 75% in South East England. Qualitative data on health inequalities and how they could be addressed were gathered by focus groups sampling from five tiers using the Townsend Index for comparability (14 in England with 106 participants overall; 13 in France with 143 participants). Both had about two thirds women participants, with a preponderance of middle aged and older people. There was a striking difference in the salience of diet between the two countries; in the French data it was raised only 14 times, whereas in England there were 165 occurrences, and these were often distinguished by their use of narrative. Older respondents contrasted the pressures on families today and the expense of fresh fruit and vegetables with their own childhood or childrearing, when cheap meals could be created using skills which have now been lost. These data therefore provide further evidence that providing food is a moral activity.

The comparative advantage of the public sector in the development of urban water supply

This paper addresses the potential of public water operations in achieving developmental goals such as the Millennium Development Goals, and argues that the public sector has a comparative advantage in developing water services. The global importance of the public sector in urban water supply is examined through a review of current practice in the world's largest cities, including operational presence and distribution and ongoing trends. Empirical evidence shows that, in transition and developing countries, public operators are capable of undergoing successful reform. One explanatory factor is proposed to be the creation through the public sphere of highly interconnected networks among stakeholders. Such accountability networks act as vehicles for the generation and distribution of public knowledge among stakeholders, which in turn inform rational decision making on the reform and management of operations.