Genome-Wide Survey of Pseudogenes in 80 Fully Re-sequenced Arabidopsis thaliana Accessions

Pseudogenes (Ψs), including processed and non-processed Ψs, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life. However, systematic surveys of non-processed Ψs utilizing genomic information from multiple samples within a species are still rare. Here a systematic comparative analysis was conducted of Ψs within 80 fully re-sequenced Arabidopsis thaliana accessions, and 7546 genes, representing ~28% of the genomic annotated open reading frames (ORFs), were found with disruptive mutations in at least one accession. The distribution of these Ψs on chromosomes showed a significantly negative correlation between Ψs/ORFs and their local gene densities, suggesting a higher proportion of Ψs in gene desert regions, e.g. near centromeres. On the other hand, compared with the non-Ψ loci, even the intact coding sequences (CDSs) in the Ψ loci were found to have shorter CDS length, fewer exon number and lower GC content. In addition, a significant functional bias against the null hypothesis was detected in the Ψs mainly involved in responses to environmental stimuli and biotic stress as reported, suggesting that they are likely important for adaptive evolution to rapidly changing environments by pseudogenization to accumulate successive mutations.

[Castration of calves: a survey among Swiss suckler beef farmers]

In fall 2004, a survey of a representative sample of 1185 Swiss suckler beef farmers was carried out by questionnaire (return rate 51.9%). 32.7% of the respondents castrated their calves without the help of a veterinarian, 37.8% mandated a veterinarian to carry out the castrations and 29.4% did not castrate their bull calves at all. On average, 8 calves were castrated per farm and year at an average age of 7 days when the castration was carried out by a farmer or 34 days when the castration was carried out by a veterinarian. Almost all farmers castrated their calves with the rubber ring, and a majority considered no other method as feasible. 73.9% of the veterinarians used the Burdizzo technique, 14.9% applied rubber rings, and 11.2% performed a surgical procedure. 22.6% of the farmers and 85.4% of the veterinarians used sedation; local anaesthesia was performed in 32.1% of the castrations carried out by farmers and in 84.5% of the castrations carried out by veterinarians. 65.7% of the farmers were concerned by the change of the Swiss Animal Protection Ordinance (2001), when pain relief became mandatory. 47.6% of these farmers changed their castration routine: 53.1% now mandated a veterinarian, 33.0% used sedation or local anaesthesia and 8.9% abandoned castration of their calves. 59.8% of the farmers intended to participate in a future course for laymen, to study and train the technique of local anaesthesia for castration. Castration of their calves is for many suckler beef farmers an inevitable husbandry procedure. The political goal, that all calves shall be castrated with local anaesthesia can only be reached when livestock owners are informed about the distress caused by the castration and convinced of the benefit of the local anaesthesia.Veterinarians are important information carriers in this process. The implementation also produces work, be it the more complex castration procedure or the education of the farmers who want to carry out the local anaesthesia themselves.

Survey:

In June of 2010, at the African American and Juneteenth Festival in Worcester, Massachusetts, Clark University administered a survey directed toward African American residents of the city of Worcester. In the survey, residents who attended the festival were asked to rate the quality of life in the City, public services, and local government and political representation, as well as leadership in the local African-American community. This report presents and analyzes the primary findings of the survey.

Comments on Kevin Stenson’s ‘Governing the Local: Sovereignty, Social Governance and Community Safety’

It is a challenging time to be a social scientist. Many of the concepts and categories we took for granted have been revealed as temporally and geographically specific. It is now widely accepted that the nation-state is no longer the sole container for economic, political and social processes, if indeed it ever was. This is where Kevin Stenson begins his paper. He traces the re-ordering of both state and nation, highlighting recent discussions about the unbundling and rescaling of the state and outlining how increasing ethnic and cultural diversity challenge homogeneous conceptions of the nation. In Stenson’s account these are largely empirical processes that are the basis for the important questions he raises about changing understandings of publics and social order, and their implications for the local governance of community safety. He contrasts two alternative positions; the ‘universal human rights position’ which refuses to privilege the interests of majority populations, and a more ‘communitarian and nationalistic position’ which he argues is most likely to be deployed by right wing politicians and interests groups. Drawing from extensive research in the Thames Valley region of the United Kingdom, he shows how these two understandings have both shaped the local policy response to crime and disorder.

A Targeted Survey for Scrapie in Jos Plateau State, Nigeria

Scrapie, a disease of sheep and goats with a progressive course and fatal outcome, has not been identified in Nigeria. Anecdotal scrapie reports by livestock workers abound. Livestock diseases like scrapie form huddles in livestock economics of countries. For 8 months we surveyed for scrapie targeting emergency/casualty slaughter sheep and goats in Jos, Nigeria. We clinically examined 510 sheep and 608 goats of local breeds, aged from 12 months to 5 years. In total 31 (5.10%) goats and no sheep were clinically suspicious for scrapie. Caudal brainstem tissues of suspect animals collected postmortem were analyzed for the disease specific form of the prion protein, PrPSc, using Bio-Rad’s TeSeE ELISA rapid test kit. No sample was positive for scrapie. Fluorescent antibody test for rabies and H&E staining on samples were carried out for differential diagnosis. These showed no pathological lesions indicative for neurological disease. While our findings do not exclude the presence of scrapie in Jos, we demonstrate that targeted sampling of small ruminants for neuroinfectious disease is feasible in developing countries, pointing to the possibility of implementing such a monitoring scheme in Nigeria to prevent economic losses in small ruminant livestock as scrapie caveats from endemic countries have shown.

Population structure, inbreeding and local adaptation within an endangered riverine specialist: the nase (Chondrostoma nasus)

Chondrostoma nasus is a cyprinid fish with highly specialized, ecologically and geographically distinct, ontogenetic trophic niches. Nase population numbers across their Swiss range have shown massive declines and many localized extinctions. Here we integrate data from different genetic markers with phenotypic and demographic data to survey patterns of neutral and adaptive genetic diversity in all extant (and one extinct) Swiss nase populations, with the aim to delineate intraspecific conservation units (CUs) and to inform future population management strategies. We discovered two major genetically and geographically distinct population groupings. The first population grouping comprises nase inhabiting rivers flowing into Lake Constance; the second comprises nase populations from Rhine drainages below Lake Constance. Within these clusters there is generally limited genetic differentiation among populations. Genomic outlier scans based on 256–377 polymorphic AFLP loci revealed little evidence of local adaptation both within and among population clusters, with the exception of one candidate locus identified in scans involving the inbred Schanzengraben population. However, significant phenotypic differentiation in body shape between certain populations suggests a need for more intensive future studies of local adaptation. Our data strongly suggests that the two major population groups should be treated as distinct CUs, with any supplemental stocking and reintroductions sourced only from within the range of the CU concerned.

Addressing Obesity: Fear of Crime, Perceptions of Disorder and Disaparities in Child and Adolescent Use of Public Parks

Abstract The objectives of this study were: 1) To determine factors which inhibit and facilitate child and adolescent use of outdoor spaces for healthy physical activity by race and ethnicity in four Houston communities and 2) To propose guidelines for encouraging and maintaining child and adolescent outdoor physical activity. Using local health data and Houston Police Department crime statistics, four communities were identified for the study that had the highest concentration of crime and the racial/ ethnic groups of interest. The researchers then identified public parks in the communities. At least two parks were observed in each of the four communities from 2010 to 2011 during spring, summer, fall and winter. The parks were observed for use by children and adolescents and to describe the condition of the park spaces. The communities were Alief (Asian), Sunnyside (Black), Eldridge- West Oaks (White) and Northside- Northline (Hispanic). Observations were made at varying hours of both day and night, weekdays and weekends. Photographs were taken and the condition of the spaces noted in detail. One hundred and twenty persons, 18 years and over, using the spaces or otherwise in these communities were conveniently sampled and interviewed about their health and the extent to which they, or any children or adolescents under their care, used the outdoor spaces of interest. Data were analyzed qualitatively and with basic descriptive statistics. The photographs, journal notes and observation notes of all investigators and key personnel were analyzed. Interview data were also coded to identify patterns and themes in the responses. The findings indicate disparities in the quality and quantity of park equipment and the maintenance of the areas. Where perceptions of disorder were described, there was often visible evidence to support the perceptions. In many cases, residents' perceptions of crime were corroborated by police data. While interview reports did not seem to support the expectation that the condition of the parks was a significant deterrent to their use by children and adolescents, the condition of the parks might be said to limit the extent of that use. Specific reports of disorder that inhibited use included hearing gunfire, seeing drug dependent homeless persons and/or suspected prostitutes in an area.

Cigarette smoking and Ecuadorian adolescents: A cross-sectional survey and policy review

This study investigates the relationship between cigarette smoking and adolescents in Ecuador, South America. Using the Social Learning Theory as a basis, the cross-sectional survey focuses attention on such social influences as the smoking habits of family members and peers as well as, the role of cigarette advertisements. Actual use prevalence, access to cigarettes and knowledge and attitudes about smoking are also obtained.^ The survey was conducted in both urban and rural areas, with 50 schools in 40 different communities participating. Two thousand four hundred and fifty-seven adolescents aged 9 to 15 years completed a self-administered questionnaire. This part of the study was conducted in collaboration with the international health organization Amigos de las Americas (AMIGOS). Staff assigned to the AMIGOS Ecuador projects worked with local health and education officials to implement the cross-sectional survey in the field.^ The key informant survey and subsequent policy review were designed to illuminate the social, cultural and institutional environment for anti-smoking activities and interventions in Ecuador. Key individuals involved with this issue on both national and local levels were interviewed. A review of past legislative efforts and present anti-smoking laws was also conducted.^ The current smoking prevalence among the study population was 8.6 percent. Findings from the cross-sectional survey revealed significant positive associations between the smoking habits of siblings and peers and the smoking behavior of the adolescents surveyed. Significant age and gender differences were also found in association with several different variables.^ The policy review found an unfavorable environment for anti-smoking efforts. Several factors contribute to this including, most importantly, lack of funding and lack of public support. The present anti-smoking law is often vague and lacks important provisions, such as a prohibition on selling tobacco products to minors.^ Together, the two surveys provide comprehensive information for the purpose of designing smoking prevention interventions. Using the results from the two surveys, recommendations for intervention are proposed. ^

People, protected areas and ecosystem services: a qualitative and quantitative analysis of local people's perception and preferences in Côte d'Ivoire

The long-term integrity of protected areas (PAs), and hence the maintenance of related ecosystem services (ES), are dependent on the support of local people. In the present study, local people's perceptions of ecosystem services from PAs and factors that govern local preferences for PAs are assessed. Fourteen study villages were randomly selected from three different protected forest areas and one control site along the southern coast of Côte d'Ivoire. Data was collected through a mixed-method approach, including qualitative semi-structured interviews and a household survey based on hypothetical choice scenarios. Local people's perceptions of ecosystem service provision was decrypted through qualitative content analysis, while the relation between people's preferences and potential factors that affect preferences were analyzed through multinomial models. This study shows that rural villagers do perceive a number of different ecosystem services as benefits from PAs in Côte d'Ivoire. The results based on quantitative data also suggest that local preferences for PAs and related ecosystem services are driven by PAs' management rules, age, and people's dependence on natural resources.

Disclosing and reporting medical errors: Cross-sectional survey of Swiss anaesthesiologists.

BACKGROUND There is limited research on anaesthesiologists' attitudes and experiences regarding medical error communication, particularly concerning disclosing errors to patients. OBJECTIVE To characterise anaesthesiologists' attitudes and experiences regarding disclosing errors to patients and reporting errors within the hospital, and to examine factors influencing their willingness to disclose or report errors. DESIGN Cross-sectional survey. SETTING Switzerland's five university hospitals' departments of anaesthesia in 2012/2013. PARTICIPANTS Two hundred and eighty-one clinically active anaesthesiologists. MAIN OUTCOME MEASURES Anaesthesiologists' attitudes and experiences regarding medical error communication. RESULTS The overall response rate of the survey was 52% (281/542). Respondents broadly endorsed disclosing harmful errors to patients (100% serious, 77% minor errors, 19% near misses), but also reported factors that might make them less likely to actually disclose such errors. Only 12% of respondents had previously received training on how to disclose errors to patients, although 93% were interested in receiving training. Overall, 97% of respondents agreed that serious errors should be reported, but willingness to report minor errors (74%) and near misses (59%) was lower. Respondents were more likely to strongly agree that serious errors should be reported if they also thought that their hospital would implement systematic changes after errors were reported [(odds ratio, 2.097 (95% confidence interval, 1.16 to 3.81)]. Significant differences in attitudes between departments regarding error disclosure and reporting were noted. CONCLUSION Willingness to disclose or report errors varied widely between hospitals. Thus, heads of department and hospital chiefs need to be aware of the importance of local culture when it comes to error communication. Error disclosure training and improving feedback on how error reports are being used to improve patient safety may also be important steps in increasing anaesthesiologists' communication of errors.

Local Interstellar Medium: Six Years of Direct Sampling by IBEX

The Interstellar Boundary Explorer (IBEX) has been directly observing neutral atoms from the local interstellar medium for the last six years (2009–2014). This paper ties together the 14 studies in this Astrophysical Journal Supplement Series Special Issue, which collectively describe the IBEX interstellar neutral results from this epoch and provide a number of other relevant theoretical and observational results. Interstellar neutrals interact with each other and with the ionized portion of the interstellar population in the “pristine” interstellar medium ahead of the heliosphere. Then, in the heliosphereʼs close vicinity, the interstellar medium begins to interact with escaping heliospheric neutrals. In this study, we compare the results from two major analysis approaches led by IBEX groups in New Hampshire and Warsaw. We also directly address the question of the distance upstream to the pristine interstellar medium and adjust both sets of results to a common distance of ~1000 AU. The two analysis approaches are quite different, but yield fully consistent measurements of the interstellar He flow properties, further validating our findings. While detailed error bars are given for both approaches, we recommend that for most purposes, the community use “working values” of ~25.4 km s⁻¹, ~75°7 ecliptic inflow longitude, ~−5°1 ecliptic inflow latitude, and ~7500 K temperature at ~1000 AU upstream. Finally, we briefly address future opportunities for even better interstellar neutral observations to be provided by the Interstellar Mapping and Acceleration Probe mission, which was recommended as the next major Heliophysics mission by the NRCʼs 2013 Decadal Survey.

A survey of the implementation status of environmental management systems in U.S. colleges and universities, and, An environmental management system implementation model for U.S. colleges and universities

A census of 925 U.S. colleges and universities offering masters and doctorate degrees was conducted in order to study the number of elements of an environmental management system as defined by ISO 14001 possessed by small, medium and large institutions. A 30% response rate was received with 273 responses included in the final data analysis. Overall, the number of ISO 14001 elements implemented among the 273 institutions ranged from 0 to 16, with a median of 12. There was no significant association between the number of elements implemented among institutions and the size of the institution (p = 0.18; Kruskal-Wallis test) or among USEPA regions (p = 0.12; Kruskal-Wallis test). The proportion of U.S. colleges and universities that reported having implemented a structured, comprehensive environmental management system, defined by answering yes to all 16 elements, was 10% (95% C.I. 6.6%–14.1%); however 38% (95% C.I. 32.0%–43.8%) reported that they had implemented a structured, comprehensive environmental management system, while 30.0% (95% C.I. 24.7%–35.9%) are planning to implement a comprehensive environmental management system within the next five years. Stratified analyses were performed by institution size, Carnegie Classification and job title. ^ The Osnabruck model, and another under development by the South Carolina Sustainable Universities Initiative, are the only two environmental management system models that have been proposed specifically for colleges and universities, although several guides are now available. The Environmental Management System Implementation Model for U.S. Colleges and Universities developed is an adaptation of the ISO 14001 standard and USEPA recommendations and has been tailored to U.S. colleges and universities for use in streamlining the implementation process. In using this implementation model created for the U.S. research and academic setting, it is hoped that these highly specialized institutions will be provided with a clearer and more cost-effective path towards the implementation of an EMS and greater compliance with local, state and federal environmental legislation. ^

Smoke free restaurant ordinance, compliance with the regulation to reduce exposure to environmental tobacco smoke while dining at local restaurants in San Antonio, Texas

This study is a secondary analysis of a survey developed by Dr. Jimmy Perkins and administered by San Antonio/Bexar County Metropolitan Health District. The survey was developed subsequent to the implementation of the city smoking ordinance effective January 1, 2004. The survey had a multi-purpose plan to establish the number of restaurants having smoke free status prior to and following the ordinance, determine compliance as it relates to a necessary smoking section and proper signage, and expose the rationale for restaurants to become smoke free. The data resulting from the survey was presented to the San Antonio/Bexar County Metropolitan Health District. The summary presented the types of establishments surveyed, smoking status of the establishment, reasons for the establishment becoming smoke free, compliance with smoking sections, compliance with signage requirements, awareness of ordinance, and chain status of the establishment. ^ The results of this study display the relationships among the variables previously mentioned. The following relationships have been examined and the outcomes have determined whether each is significant. After careful analysis, knowledge translates into compliance with signage regulations, which then translate into ordinance compliance. Size does matter as it relates to an establishment's number of employees and seating capacity. The smaller the establishment the more likely the establishment is to have become smoke free before the ordinance went into effect. Restaurants, rather than fast food establishments most commonly cited their reason for becoming smoke free was to comply with the ordinance and only ten percent of restaurants gave policy as the main reason for becoming smoke free. ^ This study is important for public health because the negative health effects of environmental tobacco smoke (ETS) are still an overwhelming problem in the United States (3). ETS is a Known Human Group A Carcinogen (5). The Environmental Protection Agency (EPA) has estimated that around 3,000 non-smoking Americans die every year from lung cancer caused by ETS (6). This information illustrates the importance of providing smoke free establishments, especially to non-smoking patrons. ^

Environmental influences on self-reported leisure-time physical activity in the Austin/Travis County STEPS survey 2005--2009

This study was an examination of environmental and social correlates of physical inactivity in a socio-economically disadvantaged community. This study was a secondary analysis of data collected by the Austin/Travis County Department of Health and Human Services. The study included an analysis of perceived environmental influences (e.g. access to physical support features like sidewalks and streetlights). This study also investigated several features of the social environment (e.g. perceived neighborhood crime and social influence). Participants’ beliefs and attitudes about the neighborhood were investigated. Results included estimates of the association between neighborhood factors and physical inactivity controlling for age, gender and education. This study found significant associations for social and environmental variables with physical inactivity. The goal of this work was to identify factors that contribute to inactivity and address a number of environmental and neighborhood risk factors that contribute to sedentary behaviors in a population of relative social and economic disadvantage.^

Ordenamiento territorial y desarrollo local : provincia Cercado, Tarija, Bolivia

El proceso de ordenamiento territorial en Bolivia es relativamente nuevo y por tal razón el avance es mínimo si se piensa en los objetivos alcanzados hasta ahora. El presente trabajo pretende mostrar el avance logrado en uno de los departamentos de Bolivia, Tarija, donde en 5 años, se ha logrado elaborar un plan departamental de ordenamiento territorial y mediante la coordinación interinstitucional (prefectura y gobiernos municipales) se ha iniciado el mismo proceso de a nivel municipal. A partir de estos planes municipales se induce a municipios predominantemente urbanos a trabajar planes de ordenamiento territorial a partir de lineamientos planteados desde la prefectura, con el fin de iniciar los procesos de planificación urbana, actualizar la normativa y elaborar proyectos de desarrollo local. El objetivo del presente trabajo, es mostrar los avances a los que se pretende arribar gracias a un proceso metodológico de ordenamiento territorial incorporado a una dinámica urbana que interactúa constantemente con su área de influencia que en el caso boliviano es normalmente rural; pero además demostrar que el componente interdisciplinario en el caso de la planificación urbana es imprescindible considerando que hasta hace unos años este era un trabajo especifico de los colegas urbanistas y que en una realidad como la latinoamericana casi siempre quedaba en planos y en un viejo anaquel. Por lo tanto a partir de una interdisciplinariedad se puede lograr desarrollo local articulando y optimizando relaciones urbano-rurales que basan su desarrollo en un proceso metodológico como es el caso del ordenamiento territorial. El trabajo, se apoya en la guía metodológica para la elaboración de planes elaboradas por el Ministerio de Desarrollo Sostenible del gobierno boliviano, pero como tal cual su nombre expresa es una guía susceptible a ser adecuada a las exigencias del área de estudio, en este sentido sobre esa base es que se incorporan algunas variables de estudio que permitirán mejorar el producto a nivel de propuesta una vez concluido el trabajo. Contempla varias etapas donde la incorporación de los diferentes actores sociales será una clave para lograr resultados exitosos en la etapa de implementación. Actualmente el plan municipal de la provincia Cercado, es un proyecto a encarar en los próximos meses una vez cumplidos con los requisitos administrativos para iniciar el trabajo técnico que comprenderá un trabajo de campo, para el relevamiento de datos, la elaboración de un diagnóstico integral con dos ámbitos territoriales rural y urbano, para luego proceder al análisis territorial y el planteamiento de propuesta que incluirán políticas, estrategias, acciones y proyectos, pero no solo generará bases para el uso de suelo y la ocupación del territorio, a escala urbana se plantearan los lineamientos para el diseño y la normativa urbana. A partir del cual se definirán proyectos de desarrollo local que nos permita orientarnos hacia la imagen objetivo planteada en la visión del proyecto, este trabajo incluye el aspecto institucional para fortalecer al proceso que hasta esta ahora se encuentra desarticulado; se pretende consolidar el proceso de ordenamiento y dar inicio a otros en escalas de mayor detalle permitiendo la optimización de recursos y el aprovechamiento de las potencialidades y recursos naturales para mejorar la calidad de vida.