Motif effects in Affymetrix GeneChips seriously affect probe intensities

An Affymetrix GeneChip consists of an array of hundreds of thousands of probes (each a sequence of 25 bases) with the probe values being used to infer the extent to which genes are expressed in the biological material under investigation. In this article, we demonstrate that these probe values are also strongly influenced by their precise base sequence. We use data from >28 000 CEL files relating to 10 different Affymetrix GeneChip platforms and involving nearly 1000 experiments. Our results confirm known effects (those due to the T7-primer and the formation of G-quadruplexes) but reveal other effects. We show that there can be huge variations from one experiment to another, and that there may also be sizeable disparities between batches within an experiment and between CEL files within a batch. © 2012 The Author(s)

Stage-specific histone modification profiles reveal global transitions in the Xenopus embryonic epigenome.

Vertebrate embryos are derived from a transitory pool of pluripotent cells. By the process of embryonic induction, these precursor cells are assigned to specific fates and differentiation programs. Histone post-translational modifications are thought to play a key role in the establishment and maintenance of stable gene expression patterns underlying these processes. While on gene level histone modifications are known to change during differentiation, very little is known about the quantitative fluctuations in bulk histone modifications during development. To investigate this issue we analysed histones isolated from four different developmental stages of Xenopus laevis by mass spectrometry. In toto, we quantified 59 modification states on core histones H3 and H4 from blastula to tadpole stages. During this developmental period, we observed in general an increase in the unmodified states, and a shift from histone modifications associated with transcriptional activity to transcriptionally repressive histone marks. We also compared these naturally occurring patterns with the histone modifications of murine ES cells, detecting large differences in the methylation patterns of histone H3 lysines 27 and 36 between pluripotent ES cells and pluripotent cells from Xenopus blastulae. By combining all detected modification transitions we could cluster their patterns according to their embryonic origin, defining specific histone modification profiles (HMPs) for each developmental stage. To our knowledge, this data set represents the first compendium of covalent histone modifications and their quantitative flux during normogenesis in a vertebrate model organism. The HMPs indicate a stepwise maturation of the embryonic epigenome, which may be causal to the progressing restriction of cellular potency during development

Use of nutritional supplements in the Costa Rican urban population

Objetivo: diversos estudios revelan que el per l de los consumidores de suplementos nutricionales corresponde a individuos con estilos de vida saludables y ambiente sociodemográ co favorable. Sin embargo, en Costa Rica no hay información disponible referente al consumo de suplementos nutricionales a nivel nacional. Esta investigación pretendió analizar el uso y las características sociodemográ cas, antropométricas y de ingesta de los consumidores de suplementos nutricionales, en población urbana costarricense de 15 a 65 años. Métodos: se utilizaron los datos del Estudio Latinoamericano de Nutrición y Salud (ELANS), una investigación observacional, transversal y correlacional, con una muestra de 798 participantes. Adicionalmente, se diseñó y aplicó un cuestionario vía telefónica, seis meses después del primer contacto con los consumidores de suplementos nutricionales, para profundizar en las características y percepciones de uso de estas sustancias. Resultados: un 6 % de la población re rió el uso suplementos nutricionales, principalmente multivitamínicos. No se encontrón diferencias signi cativas según el sexo, edad, nivel socioeconómico, nivel educativo o índice de masa corporal. Los consumidores de suplementos nutricionales presentaron ingestas signi cativamente mayores de calcio en ambos sexos, y vitaminas C y E en mujeres, en comparación con los no consumidores. Los motivos de consumo de suplementos nutricionales se centraron en el bienestar, y aunque se perciben como bene ciosos, en un 58 % de los casos el uso fue descontinuado luego de seis meses. Conclusiones: la prevalencia de consumo de suplementos nutricionales fue menor a la reportada por otros estudios en el campo, y no se halló un patrón de características similar al descrito por la bibliografía.International Life Science Institute (ILSI)-MesoaméricaUCR::Vicerrectoría de Docencia::Salud::Facultad de Medicina::Escuela de Medicin

Optimización del proceso de cierre contable-financiero de una empresa minera sobre la base de COSO 2013 y la ley Sarbanes-Oxley

La empresa minera materia de estudio presenta demoras y reprocesos en el cierre contable-financiero debido a la alta concentración de actividades manuales de control interno implementadas en respuesta al cumplimiento de la Ley Sarbanes-Oxley y el marco conceptual COSO 2013. Las demoras y reprocesos incrementan la posibilidad de errores contables en los reportes financieros, existiendo un mayor riesgo de incumplimiento por parte de la empresa minera materia de estudio con respecto a la L.SOX, la cual tiene como principal objetivo asegurar que los controles internos de información financiera reportados sean correctos en cuanto a su consistencia, exactitud e integridad. El presente trabajo de investigación tuvo como objetivo principal identificar y conocer las causas que originan las demoras y la alta CAM de CI para presentar recomendaciones que aporten soluciones en la optimización del proceso de cierre contable-financiero. Finalmente, con este trabajo de investigación concluimos que las principales causas que originaran las demoras y la alta CAM de CI son (1) la ausencia de una correcta implementación de controles internos manuales relacionados al reporte financiero, (2) la centralización de actividades de control operativas en el contador general, (3) las AC y reportes financieros no automatizados y (4) la ausencia de una correcta implementación del sistema de CI. Las recomendaciones brindadas para la optimización del proceso del cierre-contable se encuentran detalladas en el Capítulo IV, numeral 4 del documento

Impact of meteorological conditions on airborne fine particle composition and secondary pollutant characteristics in urban area during winter-time

The assessment of airborne fine particle composition and secondary pollutant characteristics in the case of Augsburg, Germany, during winter (31 January–12 March 2010) is studied on the basis of aerosol mass spectrometry (3 non-refractory components and organic matter, 3 positive matrix factorizations (PMF) factors), particle size distributions (PSD, 5 size modes, 5 PMF factors), further air pollutant mass concentrations (7 gases and VOC, black carbon, PM10, PM2.5) and meteorological measurements, including mixing layer height (MLH), with one-hourly temporal resolution. Data were subjectively assigned to 10 temporal phases which are characterised by different meteorological influences and air pollutant concentrations. In each phase hierarchical clustering analysis with the Ward method was applied to the correlations of air pollutants, PM components, PM source contributions and PSD modes and correlations of these data with all meteorological parameters. This analysis resulted in different degrees of sensitivities of these air pollutant data to single meteorological parameters. It is generally found that wind speed (negatively), MLH (negatively), relative humidity (positively) and wind direction influence primary pollutant and accumulation mode particle (size range 100–500 nm) concentrations. Temperature (negatively), absolute humidity (negatively) and also relative humidity (positively) are relevant for secondary compounds of PM and particle (PM2.5, PM10) mass concentrations. NO, nucleation and Aitken mode particle and the fresh traffic aerosol concentrations are only weakly dependent on meteorological parameters and thus are driven by emissions. These daily variation data analyses provide new, detailed meteorological influences on air pollutant data with the focus on fine particle composition and secondary pollutant characteristics and can explain major parts of certain PM component and gaseous pollutant exposure

An 11 year study of multipollutant correlations of urban aerosols in Krakow, Poland

Krakow is the most polluted, as far as particulate matter (PM) is concerned, city in Poland. This is an important public concern as Krakow is also the second largest populated Polish city. The specific geomorphological localization of Krakow influences the atmospheric dynamics over the city, resulting in still- or weak-winds promoting air pollution accumulation, especially during the heating season. Seasonal variability in concentrations and multipollutant correlations of gaseous pollutants (i.e. NO2, NO, NOx, SO2) and PM10, 2.5 measured over a period of January 2005 to December 2013 were investigated. Data for the study were obtained from reports published by the Voivodship Inspectorate for Environmental Protection in Krakow. A strong seasonal variation in PM10 concentration revealed that during warm months the European Union annual limit value of 40 µg/m3 was not exceeded, whereas during the heating season, it was exceeded more than twice (Figure 1). Normalized monthly concentration patterns of all investigated pollutants and temperatures revealed that NO2 had the most consistent concentration pattern over the year. Conversely, SO2, PM2.5 and PM10 levels varied greatly (e.g. SO2 concentrations in January were more than 100% greater and 54% lower than the monthly average in May). Moreover SO2 had the strongest negative correlation (r = -0.64) with temperature. Seasonal correlations between pairs of pollutants were the highest between NO and NOx (0.99) and between PM10 and PM2.5 in annual and seasonal terms. The non-heating season (May-August) was characterised by lower coefficients than the heating season (September-April), when coefficients were similar to the annual values. Additionally, the ratios between average concentrations of investigated pollutants were also higher in the heating season. Transmission electron microscopy (TEM) images confirmed that particles were consistent with the known morphology of fly-ash (Brown et al., 2011) and other combustion-derived PM (BéruBé et al., 1999; Figure 2). For example, individual carbonaceous spheres’ forming grape-like bunches of aggregates and agglomerates which are highly-respirable. Natural factors such as geomorphology, climate and weather conditions have been determined to be the perpetrators of air pollution accumulation over the city (Wlodarczyk et al., 2015). The main source of elevated pollution levels were traffic emissions (i.e. nitrogen compounds) during warm months and residential coal-burning during the heating season. In conclusion, high annual levels, especially for PM, are greatly affected by measurements from the heating season. This ‘seasonality’ in PM2.5 concentrations should be taken into account when treating PM2.5 as a proxy in epidemiological studies for Krakow; as people in colder months spend less time outdoors. Further analysis including in vitro toxicology of PM is required to assess its direct effects on human lung biology. Brown, P., Jones, T. and BéruBé, K. (2011). Environmental Pollution 159 (12):3324-3333. BéruBé, K., Williamson, B., Winters, C., et al., (1999). Atmospheric Environment, 33(10):1599-1614

The right to be me: Psychosocial implications of revealing preferences and identities

La búsqueda de la identidad individual es un constante viaje de transformación y autocuidado. Las experiencias a lo largo de este camino influyen en la perspectiva de cada individuo y moldean su personalidad y forma de expresarse. Sin embargo, cuando las personas son marginadas por diversos grupos sociales, familiares o laborales que reprimen actitudes, conductas y patrones que no se ajustan a las normas sociales heteronormadas, esto puede provocar repercusiones psicosociales, desinformación, violencia y discriminación. Este artículo se centra en las experiencias de los estudiantes de Pachuca, Hidalgo, al expresar públicamente su pertenencia a la comunidad LGBTQ+. Utilizando una metodología cualitativa que incluye entrevistas semi estructuradas basadas en ejes clave, se explora la existencia de inestabilidad emocional debido a la falta de redes de apoyo familiar, la ausencia de acompañamiento en el proceso, la desinformación y la falta de visibilidad institucional, entre otros aspectos como conclusión, los resultados de esta investigación resaltan la urgencia de abordar la falta de apoyo familiar, el desinterés institucional, la persistente marginación social y la inestabilidad emocional experimentada por los miembros de la comunidad LGBTQ+.The search for individual identity is a constant journey of transformation and self-care. The experiences along this path influence each individual’s perspective and shape their personality and way of expressing themselves. However, when people are marginalized by various social, family or occupational groups that repress attitudes, behaviors and patterns that do not conform to heteronormative social norms, this can generate psychosocial repercussions, misinformation, violence and discrimination. This article focuses on the experiences of students in Pachuca, Hidalgo, in publicly expressing their belonging to the LGBTQ+ community. Using a qualitative methodology that includes semi-structured interviews based on key axes, it explores the existence of emotional instability due to lack of family support networks, absence of accompaniment in the process, misinformation and lack of institutional visibility, among other aspects. In conclusion, the results of this research highlight the urgency of addressing the lack of family support, institutional disinterest, persistent social marginalization and emotional instability experienced by members of the LGBTQ+ community

Effect of organic and chemical fertilization on the onion crop (Allium cepa L.)

The bulb onion (Allium cepa L.) is a vegetable widely cultivated and in high demand in national and international markets. Due to the risks that the indiscriminate use of agrochemicals represents for human health and the environment, the present study aimed to make a comparative analysis of the effects of organic vs chemical fertilization currently used in the cropping of red hybrid bulb onion (Eureka). Three organic fertilizers (Zumsil®, ComCat® and EcoFungi®) were compared to three chemical fertilizers (15-15-15®, Muriate of Potash® and Nitrofoska®). The response variables were: plant height at 30 and 60 days after transplanting (DAT), length, diameter and average weight of bulbs, yield in tons per hectare and the relationship between height at 30 and 60 DAT. The experiment was carried out under a completely randomized design with four replicates, seven treatments and 28 experimental units. The statistics used include an analysis of variance and a Canonical Biplot that allowed to obtain groups of variables and to determine their correlation with each one of the treatments. Additionally, a marginal analysis of dominant treatments was performed. Positive response of variables was strongly associated with organic fertilizers. From the economic point of view, the ComCat® organic fertilizer represented an ecological alternative with excellent benefits for the producer. This research is in line with the trends for agrochemical-free foods

Source apportionment and the role of meteorological conditions in the assessment of air pollution exposure due to urban emissions

As particulate matter (PM) impacts human health, knowledge about its composition, exposure and source apportionment is required. A study of the urban atmosphere in the case of Augsburg, Germany, during winter (31 January–12 March 2010) is thus presented here. Investigations were performed on the basis of aerosol mass spectrometry and further air pollutants and meteorological measurements, including mixing layer height. Organic matter was separated by source apportionment of PM1 with positive matrix factorization (PMF) in three factors: OOA – oxygenated organic aerosol (secondary organic factor), HOA – hydrocarbon-like organic aerosol (traffic factor or primary organic factor) and WCOA – wood combustion organic aerosol (wood combustion factor), which extend the information from black carbon (BC) measurements. PMF was also applied to the particle size distribution (PSD) data of PM2.5 to determine different source profiles and we assigned them to the particle sources: nucleation aerosol, fresh traffic aerosol, aged traffic aerosol, stationary combustion aerosol and secondary aerosol. Ten different temporal phases were identified on the basis of weather characteristics and aerosol composition and used for correlations of all air pollutants and meteorological parameters. While source apportionment from both organic PM composition and PSD agree and show that the main emission sources of PM exposure are road traffic as well as stationary and wood combustion, secondary aerosol factor concentrations are very often the highest ones. The hierarchical clustering analysis with the Ward method of cross-correlations of each air pollutant and PM component and of the correlations of each pollutant with all meteorological parameters provided two clusters: "secondary pollutants of PM1 and fine particles" and "primary pollutants (including CO and benzene) and accumulation mode particles". The dominant meteorological influences on pollutant concentrations are wind speed and mixing layer height which are coupled with a certain wind direction. The compounds of the cluster "secondary pollutants and fine particles" show a negative correlation with absolute humidity, i.e., low concentrations during high absolute humidity and vice versa. The PM10 limit value exceedances originated not only from the emissions but also in combination with specific meteorological conditions. NC3-10 (number concentration of nucleation mode particles) and NC10-30 (Aitken mode particles), i.e., ultrafine particles and the fresh traffic aerosol, are only weakly dependent on meteorological parameters and thus are driven by emissions. The results of this case study provide information about chemical composition and causes of PM exposure during winter time in urban air pollution