Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies

As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both saliva- and blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the “GCScore,” an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.

Marine aerosol hygroscopicity and volatility, measured on the Chatham Rise (New Zealand)

The Surface Ocean Aerosol Production (SOAP) study was undertaken in February/March 2012 in the biologically active waters of the Chatham Rise, NZ. Aerosol hygroscopicity and volatility were examined with a volatility hygroscopicity tandem differential mobility analyser. These observations confirm results from other hygroscopicity-based studies that the dominant fraction of the observed remote marine particles were non-sea salt sulfates. Further observations are required to clarify the influences of seawater composition, meteorology and analysis techniques seasonally across different ocean basins.

A "Candidate-Interactome" Aggregate Analysis of Genome-Wide Association Data in Multiple Sclerosis

Though difficult, the study of gene-environment interactions in multifactorial diseases is crucial for interpreting the relevance of non-heritable factors and prevents from overlooking genetic associations with small but measurable effects. We propose a "candidate interactome" (i.e. a group of genes whose products are known to physically interact with environmental factors that may be relevant for disease pathogenesis) analysis of genome-wide association data in multiple sclerosis. We looked for statistical enrichment of associations among interactomes that, at the current state of knowledge, may be representative of gene-environment interactions of potential, uncertain or unlikely relevance for multiple sclerosis pathogenesis: Epstein-Barr virus, human immunodeficiency virus, hepatitis B virus, hepatitis C virus, cytomegalovirus, HHV8-Kaposi sarcoma, H1N1-influenza, JC virus, human innate immunity interactome for type I interferon, autoimmune regulator, vitamin D receptor, aryl hydrocarbon receptor and a panel of proteins targeted by 70 innate immune-modulating viral open reading frames from 30 viral species. Interactomes were either obtained from the literature or were manually curated. The P values of all single nucleotide polymorphism mapping to a given interactome were obtained from the last genome-wide association study of the International Multiple Sclerosis Genetics Consortium & the Wellcome Trust Case Control Consortium, 2. The interaction between genotype and Epstein Barr virus emerges as relevant for multiple sclerosis etiology. However, in line with recent data on the coexistence of common and unique strategies used by viruses to perturb the human molecular system, also other viruses have a similar potential, though probably less relevant in epidemiological terms. © 2013 Mechelli et al.

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis

Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis. © 2011 Macmillan Publishers Limited. All rights reserved.

Global, regional, and national comparative risk assessment of 79 behavioural, environmental and occupational, and metabolic risks or clusters of risks in 188 countries, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013

Background The Global Burden of Disease, Injuries, and Risk Factor study 2013 (GBD 2013) is the first of a series of annual updates of the GBD. Risk factor quantification, particularly of modifiable risk factors, can help to identify emerging threats to population health and opportunities for prevention. The GBD 2013 provides a timely opportunity to update the comparative risk assessment with new data for exposure, relative risks, and evidence on the appropriate counterfactual risk distribution. Methods Attributable deaths, years of life lost, years lived with disability, and disability-adjusted life-years (DALYs) have been estimated for 79 risks or clusters of risks using the GBD 2010 methods. Risk–outcome pairs meeting explicit evidence criteria were assessed for 188 countries for the period 1990–2013 by age and sex using three inputs: risk exposure, relative risks, and the theoretical minimum risk exposure level (TMREL). Risks are organised into a hierarchy with blocks of behavioural, environmental and occupational, and metabolic risks at the first level of the hierarchy. The next level in the hierarchy includes nine clusters of related risks and two individual risks, with more detail provided at levels 3 and 4 of the hierarchy. Compared with GBD 2010, six new risk factors have been added: handwashing practices, occupational exposure to trichloroethylene, childhood wasting, childhood stunting, unsafe sex, and low glomerular filtration rate. For most risks, data for exposure were synthesised with a Bayesian meta-regression method, DisMod-MR 2.0, or spatial-temporal Gaussian process regression. Relative risks were based on meta-regressions of published cohort and intervention studies. Attributable burden for clusters of risks and all risks combined took into account evidence on the mediation of some risks such as high body-mass index (BMI) through other risks such as high systolic blood pressure and high cholesterol. Findings All risks combined account for 57·2% (95% uncertainty interval [UI] 55·8–58·5) of deaths and 41·6% (40·1–43·0) of DALYs. Risks quantified account for 87·9% (86·5–89·3) of cardiovascular disease DALYs, ranging to a low of 0% for neonatal disorders and neglected tropical diseases and malaria. In terms of global DALYs in 2013, six risks or clusters of risks each caused more than 5% of DALYs: dietary risks accounting for 11·3 million deaths and 241·4 million DALYs, high systolic blood pressure for 10·4 million deaths and 208·1 million DALYs, child and maternal malnutrition for 1·7 million deaths and 176·9 million DALYs, tobacco smoke for 6·1 million deaths and 143·5 million DALYs, air pollution for 5·5 million deaths and 141·5 million DALYs, and high BMI for 4·4 million deaths and 134·0 million DALYs. Risk factor patterns vary across regions and countries and with time. In sub-Saharan Africa, the leading risk factors are child and maternal malnutrition, unsafe sex, and unsafe water, sanitation, and handwashing. In women, in nearly all countries in the Americas, north Africa, and the Middle East, and in many other high-income countries, high BMI is the leading risk factor, with high systolic blood pressure as the leading risk in most of Central and Eastern Europe and south and east Asia. For men, high systolic blood pressure or tobacco use are the leading risks in nearly all high-income countries, in north Africa and the Middle East, Europe, and Asia. For men and women, unsafe sex is the leading risk in a corridor from Kenya to South Africa. Interpretation Behavioural, environmental and occupational, and metabolic risks can explain half of global mortality and more than one-third of global DALYs providing many opportunities for prevention. Of the larger risks, the attributable burden of high BMI has increased in the past 23 years. In view of the prominence of behavioural risk factors, behavioural and social science research on interventions for these risks should be strengthened. Many prevention and primary care policy options are available now to act on key risks.

Reducing Browning of Fresh-cut ‘Maha’ Carambola with Chemical Additives and Low-oxygen Atmospheres

The greatest attraction to using carambola (Averrhoa carambola L.) in the fresh-cut market is the star shape that the fruit presents after a transverse cut. Carambola is well-suited for minimal processing, but cut surface browning is a main cause of deterioration. This problem is exacerbated as a result of mechanical injuries occurring during processing and is mainly induced by the leakage of phenolic compounds from the vacuole and subsequent oxidation by polyphenol oxidase (PPO) (Augustin et al., 1985). The use of browning inhibitors in processed fruits is restricted to compounds that are non-toxic, ‘wholesome’, and that do not adversely affect taste and flavour (Gil et al., 1998). In the past, browning was mainly controlled by the action of sulphites, but the use of this compound has declined due to allergic reactions in asthmatics (Weller et al., 1995). The shelf life of fresh-cut products may be extended by a combination of oxygen exclusion and the use of enzymatic browning inhibitors. The objectives of this work were to determine the effects of: (1) post-cutting chemical treatments of ascorbic, citric, oxalic acids, and EDTA-Ca; (2) atmospheric modification; and (3) combinations of the above, on the shelf life of carambola slices based on appearance, colour and polyphenol oxidase activity

The conservation status of the world’s reptiles

Effective and targeted conservation action requires detailed information about species, their distribution, systematics and ecology as well as the distribution of threat processes which affect them. Knowledge of reptilian diversity remains surprisingly disparate, and innovative means of gaining rapid insight into the status of reptiles are needed in order to highlight urgent conservation cases and inform environmental policy with appropriate biodiversity information in a timely manner. We present the first ever global analysis of extinction risk in reptiles, based on a random representative sample of 1500 species (16% of all currently known species). To our knowledge, our results provide the first analysis of the global conservation status and distribution patterns of reptiles and the threats affecting them, highlighting conservation priorities and knowledge gaps which need to be addressed urgently to ensure the continued survival of the world’s reptiles. Nearly one in five reptilian species are threatened with extinction, with another one in five species classed as Data Deficient. The proportion of threatened reptile species is highest in freshwater environments, tropical regions and on oceanic islands, while data deficiency was highest in tropical areas, such as Central Africa and Southeast Asia, and among fossorial reptiles. Our results emphasise the need for research attention to be focussed on tropical areas which are experiencing the most dramatic rates of habitat loss, on fossorial reptiles for which there is a chronic lack of data, and on certain taxa such as snakes for which extinction risk may currently be underestimated due to lack of population information. Conservation actions specifically need to mitigate the effects of human-induced habitat loss and harvesting, which are the predominant threats to reptiles.

The Mediated Immediacy : João Batista Libanio and the Question of Latin American Liberation Theology

This study is a systematic analysis of mediated immediacy in the production of the Brazilian professor of theology João Batista Libanio. He stresses both ethical mediation and the immediate character of the faith. Libanio has sought an answer to the problem of science and faith. He makes use of the neo-scholastic distinction between matter and form. According to St. Thomas Aquinas, God cannot be known as a scientific object, but it is possible to predicate a formal theological content of other subject matter with the help of revelation. This viewpoint was emphasized in neo-Thomism and supported by the liberation theologians. For them, the material starting point was social science. It becomes a theologizable or revealable (revelabile) reality. This social science has its roots in Latin American Marxism which was influenced by the school of Louis Althusser and considered Marxism a science of history . The synthesis of Thomism and Marxism is a challenge Libanio faced, especially in his Teologia da libertação from 1987. He emphasized the need for a genuinely spiritual and ethical discernment, and was particularly critical of the ethical implications of class struggle. Libanio s thinking has a strong hermeneutic flavor. It is more important to understand than to explain. He does not deny the need for social scientific data, but that they cannot be the exclusive starting point of theology. There are different readings of the world, both scientific and theological. A holistic understanding of the nature of religious experience is needed. Libanio follows the interpretation given by H. C. de Lima Vaz, according to whom the Hegelian dialectic is a rational circulation between the totality and its parts. He also recalls Oscar Cullmann s idea of God s Kingdom that is already and not yet . In other words, there is a continuous mediation of grace into the natural world. This dialectic is reflected in ethics. Faith must be verified in good works. Libanio uses the Thomist fides caritate formata principle and the modern orthopraxis thinking represented by Edward Schillebeeckx. One needs both the ortho of good faith and the praxis of the right action. The mediation of praxis is the mediation of human and divine love. Libanio s theology has strong roots in the Jesuit spirituality that places the emphasis on contemplation in action.

Investing in the future: Norway, climate change, and fossil fuel divestment

The fossil fuel divestment movement has undergone explosive growth over the last few years - expanding from encouraging educational institutions to adopt ethical investment policies to focusing upon cities, pension funds and philanthropic charities. The fossil fuel divestment movement has attained global ambitions - challenging sovereign wealth funds and national governments to engage in fossil fuel divestment, and pushing for fossil fuel divestment at international climate talks - such as the Paris Climate Summit in 2015. By exploring and analysing a key campaign to 'Divest Norway', this chapter considers the efforts to globalise and internationalise the fossil fuel divestment campaign. Part 1 explores the origins of the fossil fuel divestment movement, and the application of such strategies in a variety of contexts. Part 2 looks at the campaign to divest Norway's sovereign wealth fund of fossil fuel investments. There has been much discussion as to whether the bold decision of Norway to engage in coal divestment will encourage and inspire other sovereign wealth funds to engage in fossil fuel divestment. The conclusion considers the efforts to introduce fossil fuel divestment as a policy initiative for nation states as a policy option in international climate law.

Reynolds stress and heat flux in spherical shell convection

Context. Turbulent fluxes of angular momentum and heat due to rotationally affected convection play a key role in determining differential rotation of stars. Aims. We compute turbulent angular momentum and heat transport as functions of the rotation rate from stratified convection. We compare results from spherical and Cartesian models in the same parameter regime in order to study whether restricted geometry introduces artefacts into the results. Methods. We employ direct numerical simulations of turbulent convection in spherical and Cartesian geometries. In order to alleviate the computational cost in the spherical runs and to reach as high spatial resolution as possible, we model only parts of the latitude and longitude. The rotational influence, measured by the Coriolis number or inverse Rossby number, is varied from zero to roughly seven, which is the regime that is likely to be realised in the solar convection zone. Cartesian simulations are performed in overlapping parameter regimes. Results. For slow rotation we find that the radial and latitudinal turbulent angular momentum fluxes are directed inward and equatorward, respectively. In the rapid rotation regime the radial flux changes sign in accordance with earlier numerical results, but in contradiction with theory. The latitudinal flux remains mostly equatorward and develops a maximum close to the equator. In Cartesian simulations this peak can be explained by the strong 'banana cells'. Their effect in the spherical case does not appear to be as large. The latitudinal heat flux is mostly equatorward for slow rotation but changes sign for rapid rotation. Longitudinal heat flux is always in the retrograde direction. The rotation profiles vary from anti-solar (slow equator) for slow and intermediate rotation to solar-like (fast equator) for rapid rotation. The solar-like profiles are dominated by the Taylor-Proudman balance.

Emergent photophenomena in three dimensional van der Waals heterostructures

We report on the fabrication and observation of emergent opto-electronic phenomena in three dimensional, micron-sized van der Waals heterostructures self-assembled from atomic layers of graphene and hexagonal boron nitride in varying ratios.

Prevalencia del carcinoma escamoso ocular y sus precursores en un hato lechero nicaraguense, relacionado con raza, edad y pigmentación

En el presente trabajo se estudió la prevalencia del Carcinoma escamoso ocular bovino y la relación que tiene esta enfermedad con la pigmentación ocular, la raza y la edad en la Empresa Genética “Roberto Alvarado” (Chiltepe). Para esto se estudiaron 4108 animales de los grupos raciales Holstein Friesian (Canadiense), Holstein Friesian (Criollo), Holstein x Pardo, 75% Holstein y Pardo Suizo. Se determinó que la prevalencia total del cáncer en la población analizada es de 2.6%. Además que existe presencia de lesión únicamente cuando existe pigmentación. Se concluyó que hay claras diferencias entre los grupos raciales estudiados siendo el más afectado el Holstein Friesian(Canadiense), y que hay una tendencia a incrementarse la presencia del cáncer a medida la edad.

Caracterización técnica de los sistemas de explotación ganadera de los pequeños y medianos productores en los municipios de Tisma, Nandaime y Granada (Malacatoya)

El presente trabajo se llevó a cabo con el objetivo de realizar una caracterización de los sistemas de producción ganadera en los Municipios de Tisma, Nandaime y granada (Malacatoya.). El estudio se llevo acabo en 4 fases: Realización de la entrevista a los productores en la que se determino la disponibilidad y uso actual de los recursos en las fincas. La segunda fase consistió en la codificación de los datos obtenidos de las entrevistas asignándoles un número para su análisis por medio del programa computarizado y se creo una base de datos ordenada por municipio y de manera general. La tercera fase comprendió en el análisis estadistico de la información recopilada en las entrevistas ordenándose en programas computarizados Microsoft Word, Excel y para el análisis de los datos se utilizo un programa estadístico SPSS (paquete estadístico para ciencias sociales). La cuata fase consistió en la obtención y discusión de resultados. En cada unó de los aspectos de la entrevista se determino lo siguiente: Característica de la población animal. El 73.6% de los productores encuestados saben leer, un 70.5 %sabe escribir, en cuanto al tiempo de trabajo en la finca el 82.2% trabaja tiempo completo en la finca, en lo referente a la edad del productor el promedio es de 50 años, y el números de personas promedio que viven en la finca es de 6 personas. Característica de la finca: En cuanto a la distribución de la tierra el área total promedio en manzana es de 33.75 manzanas, y el área ganadera en promedio es de 24.36 manzana, en lo referente a la tenencia de la tierra el 53.5% de los productores encuestados poseen tierras propias, un 24.8% tienen una forma de tenencia de la tierra propia y alquilada y % restante tienen otra modalidad de tenencia. En lo referente a la infraestructura el 96.1% de los productores poseen corrales, un 66.7% tienen salitreros, un 51.9% cuentan con comederos, apenas un 10.1% poseen mangas, un 55.8% tienen pilas para abrevar su ganado y apenas un 33.3% cuentan con bodegas. Características de la población animal: En promedio de vaquillas es de 2.55, el promedio de vacas en producción es de 6.31, el promedio de vacas secas es de 3.67 y el promedio de toros es de 0.65.Esto es con respecto a las categorías tomadas en cuentas en esta variable. Hablando del tamaño general del hato en promedio es de 24.58 U.A. Manejo sanitario: Con respecto a la desparasitación del ganado en el ultimo año un 94.6% de los productores ha desparasitado. Referente a los que han vacunado en el ultimo año un 87.4% manifestó haber realizado dicha actividad. En cuanto a cuantas veces vacuna al año un 55% manifestaron hacerlo 2 veces al año, hablando de las enfermedades contra las que vacunan el 59.6 % expresaron vacunar contra ántrax y pierna negra. Manejo productivo el promedio de vacas en ordeños fue de 6.31 U.A, la producción de leche en invierno es de 4.61 Lt/v/día y la producción en verano es de 3.24 Lt/v/día, con lo que respecta a la venta de la leche un 50.39 % de los productores venden la leche al contado y en cuanto a la venta de carne un 87..6% de los productores venden al contado. Manejo reproductivo la edad en que son incorporadas las vaquillas es a los 28.13 meses, el intervalo parto-parto en promedio es de 14.67 meses y el promedio de partos por vacas es de 5.7 partos, el 94.6% de los productores utiliza semental para cubrir las hembras. Manejo alimentario con respecto al tipo de pasto suministrados al ganado un 41.8 % de los productores de dan pasto mejorados y naturales, únicamente un 10.9% de los productores le da concentrado a su ganado, el 38 % les dan suplemento al ganado y un 68.2 % de los encuestados dan rastrojo en la alimentación del ganado. Conocimiento tecnológico referente al uso de registro apenas un 32.6 % lleva registros productivos y reproductivos, con lo que respecta a la organización un 44.2 % forma parte de una organización, apenas un 15.5 % de los productores encuestados reciben financiamiento de instituciones y apenas el 30.2 % del total de productores ha recibido capacitaciones sobre el manejo del ganado.

Influencia de la rotación de cultivos y control de malezas sobre la cenosis y el crecimiento, desarrollo y rendimiento del cultivo de la soya (Glycine max (L) Merr) c.v. cristalina

Con el objetivo de determinar la influencia de dos rotaciones y tres métodos de control de malezas sobre el crecimiento, desarrollo y rendimiento de la soya se realizó un estudio en los terrenos de la Hacienda "Las Mercedes" en Managua, sobre un suelo de textura arcillosa. La siembra se realizó el siete de septiembre de 1990, utilizando un diseño en bloques completos al azar en parcelas divididas con cuatro réplicas. Siendo el factor "A": rotación; a3 = maíz, a4 = pepino; y el factor "B": Métodos de control de malezas; b1 = químico, b2 = período crítico, b3=limpia periódica. Los resultados reflejan que el cultivo antecedente maíz representa menor abundancia, cobertura y biomasa de malezas a la cosecha de la soya, siendo la especie más abundante Rottboellia cochinchinensis. El cultivo antecedente pepino presenta la menor diversidad, con mayor abundancia de la especie R. cochinchinensis seguida de Cyperus rotundus. Se obtuvieron diferencias significativas solamente en altura de planta a los 27 y 42 días después de la siembra a favor del cultivo antecedente maíz, también se obtuvo mayor número de plantas 39.4 pta/m2, altura de plantas 63.9 cm, número de vainas por plantas 13.92, número de ramas por planta 1.4, diámetro del tallo 3.98 mm, peso seco de paja 4824.5 kg/ha y rendimiento de grano 2289.42 kg/ha. Respecto a los métodos de control la menor abundancia, cobertura y biomasa de malezas se presentó en limpia periódica y el mayor valor el control químico fomesafén en post-emergencia. La diversidad al momento de la cosecha fue similar en los controles limpia periódica y período crítico. Las variables de crecimiento, desarrollo y rendimiento presentaron diferencias significativas para altura de plantas 67.3 cm a favor del control químico; número de semillas por vaina 2.80 a favor de periodo crítico; número de nódulos por planta en R5 14.25, número de ramas por planta 2.4, número de vainas 24.75, diámetro del tallo 5.0 mm, peso seco de paja 7645.8 kg/ha, peso de 1000 semillas 153 g y rendimiento del grano 4141.5 kg/ha a favor del control limpia periódica. En el control químico se presentó el menor número de semillas por vaina 2.55, vainas por planta 5.5, peso seco de nódulos: R1=0.15 g/pta y R5=0.34 g/pta y rendimiento con 832 kg/ha.