Genome-wide algorithm for detecting CNV associations with diseases

SNP genotyping arrays have been developed to characterize single-nucleotide polymorphisms (SNPs) and DNA copy number variations (CNVs). The quality of the inferences about copy number can be affected by many factors including batch effects, DNA sample preparation, signal processing, and analytical approach. Nonparametric and model-based statistical algorithms have been developed to detect CNVs from SNP genotyping data. However, these algorithms lack specificity to detect small CNVs due to the high false positive rate when calling CNVs based on the intensity values. Association tests based on detected CNVs therefore lack power even if the CNVs affecting disease risk are common. In this research, by combining an existing Hidden Markov Model (HMM) and the logistic regression model, a new genome-wide logistic regression algorithm was developed to detect CNV associations with diseases. We showed that the new algorithm is more sensitive and can be more powerful in detecting CNV associations with diseases than an existing popular algorithm, especially when the CNV association signal is weak and a limited number of SNPs are located in the CNV.^

Micro-scale habitat associations of woody plants in a neotropical cloud forest

Species?habitat associations may contribute to the maintenance of species richness in tropical forests, but previous research has been conducted almost exclusively in lowland forests and has emphasized the importance of topography and edaphic conditions. Is the distribution of woody plant species in a Peruvian cloud forest determined by microhabitat conditions? What is the role of environmental characteristics and forest structure in habitat partitioning in a tropical cloud forest? We examined species?habitat associations in three 1-ha plots using the torus-translation method. We used three different criteria to define habitats for habitat partitioning analyses, based on microtopography, forest structure and both sets of factors. The number of species associated either positively or negatively with each habitat was assessed. Habitats defined on the basis of environmental conditions and forest structure discriminated a greater number of positive and negative associations at the scale of our analyses in a tropical cloud forest. Both topographic conditions and forest structure contribute to small-scale microhabitat partitioning of woody plant species in a Peruvian tropical cloud forest. Nevertheless, canopy species were most correlated with the distribution of environmental variables, while understorey species displayed associations with forest structure.

Quantifying pursuit-diving seabirds’ associations with fine-scale physical features in tidal streamenvironments

Acknowledgements James J. Waggitt was funded by a NERC Case studentship supported by OpenHydro Ltd and Marine Scotland Science (NE/J500148/1). Vessel-based transects were funded by a NERC (NE/J004340/1) and a Scottish National Heritage (SNH) grant. FVCOM modelling was funded by a NERC grant (NE/J004316/1). Marine Scotland Science provided time on the FRV Alba-na-Mara as part as the Marine Collaboration Research Forum (MarCRF). The bathymetry data used in hydrodynamic models (HI 1122 Sanday Sound to Westray Firth) was collected by the Maritime & Coastguard Agency (MCA) as part of the UK Civil Hydrography Programme. We wish to thank Christina Bristow, Matthew Finn and Jennifer Norris at the European Marine Energy Centre (EMEC); Marianna Chimienti, Ciaran Cronin, Tim Sykes and Stuart Thomas for performing vessel-based transects; Marine Scotland Science staff Eric Armstrong, Ian Davies, Mike Robertson, Robert Watret and Michael Stewart for their assistance; Shaun Fraser, Pauline Goulet, Alex Robbins, Helen Wade and Jared Wilson for invaluable discussions; Thomas Cornulier, Alex Douglas, James Grecian and Samantha Patrick for their help with statistical analysis; and Gavin Siriwardena, Leigh Torres, Mark Whittingham and Russell Wynn for their constructive comments on earlier versions of this manuscript.

Exome-wide analysis of rare coding variation identifies novel associations with COPD and airflow limitation in MOCS3, IFIT3 and SERPINA12

Funding: British Women’s Heart and Health Study is funded by the Department of Health grant no. 90049 and the British Heart Foundation grant no. PG/09/022. British Regional Heart Study is supported by the British Heart Foundation (grant RG/ 13/16/30528). CB (COPDBEAT) received funding from the Medical Research Council UK (grant no. G0601369), CB (COPDBEAT) and AJW (UKCOPD) were supported by the National Institute for Health Research (NIHR Leicester Biomedical Research Unit). MB (COPDBEAT) received funding from the NIHR (grant no. PDF-2013-06-052). Hertfordshire Cohort Study received support from the Medical Research Council, Arthritis Research UK, the International Osteoporosis Foundation and the British Heart Foundation; NIHR Biomedical Research Centre in Nutrition, University of Southampton; NIHR Musculoskeletal Biomedical Research Unit, University of Oxford. Generation Scotland: Scottish Family Health Study is funded by the Chief Scientist Office, Scottish Government Health Directorates, grant number CZD/16/6 and the Scottish Funding Council grant HR03006. EU COPD Gene Scan is funded by the European Union, grant no. QLG1-CT-2001-01012. English Longitudinal Study of Aging is funded by the Institute of Aging, NIH grant No. AG1764406S1. GoDARTs is funded by the Wellcome Trust grants 072960, 084726 and 104970. MDT has been supported by MRC fellowship G0902313. UK Biobank Lung Exome Variant Evaluation study was funded by a Medical Research Council strategic award to MDT, IPH, DPS and LVW (MC_PC_12010)

Industries and Citizens’ Groups Networks in EU Food Policy: The Emergence of ‘Unholy Alliances’ in Multilevel Governance? Brugges Political Research Paper No. 30, September 2013

Food policy is one the most regulated policy fields at the EU level. ‘Unholy alliances’ are collaborative patterns that temporarily bring together antagonistic stakeholders behind a common cause. This paper deals with such ‘transversal’ co-operations between citizens’ groups (NGOs, consumers associations…) and economic stakeholders (food industries, retailers…), focusing on their ambitions and consequences. This paper builds on two case studies that enable a more nuanced view on the perspectives for the development of transversal networks at the EU level. The main findings are that (i) the rationale behind the adoption of collaborative partnerships actually comes from a case-by-case cost/benefit analysis leading to hopes of improved access to institutions; (ii) membership of a collaborative network leads to a learning process closely linked to the network’s performance; and (iii) coalitions can have a better reception — rather than an automatic better access — depending on several factors independent of the stakeholders themselves.

Prospective associations between meth/amphetamine (speed) and MDMA (ecstasy) use and depressive symptoms in secondary school students

Background Research has raised significant concern regarding the affective consequences of synthetic drug use. However, little evidence from well-controlled longitudinal studies exists on these consequences. The aim of this study was to determine whether use of meth/amphetamine (speed) and 63,4- methylenedioxymethamphetamine (MDMA, ecstasy) is independently predictive of subsequent depressive symptoms in adolescents. Methods A sample of 3880 adolescents from secondary schools in disadvantaged areas of Quebec, Canada, were followed over time (2003e2008). Logistic regression was used to test the association between meth/ amphetamine and MDMA use in grade 10 (ages 15e16 years) and elevated depressive symptoms on an abridged Center for Epidemiologic Studies-Depression scale in grade 11, controlling for pre-existing individual and contextual characteristics. Results After adjustment, both MDMA use (OR 1.7, 95% CI 1.1 to 2.6) and meth/amphetamine use (OR 1.6, 95% CI 1.1 to 2.3) in grade 10 significantly increased the odds of elevated depressive symptoms in grade 11. These relationships did not vary by gender or pre-existing depressive symptoms. Increased risk was particularly observed in concurrent usage (OR 1.9, 95% CI 1.2 to 2.9). Conclusions Adolescent use of meth/amphetamine and MDMA (particularly concurrent use) is independently associated with subsequent depressive symptoms. Further enquiry must determine whether these associations reflect drug-induced neurotoxicity and whether adolescence is a period of increased vulnerability to the hazards of synthetic drug exposure.

Associations among Nosema spp. fungi, Varroa destructor mites, and chemical treatments in honey bees, Apis mellifera

Nosema spp. and Varroa destructor are common parasites of honey bee colonies. Beekeepers routinely treat colonies with the fungicide fumagillin to control Nosema and an array of miticides to control V. destructor. Interactions between these parasites and chemical treatments are poorly understood. We allocated honey bee colonies to distinct chemical treatment regimes and monitored parasite intensities in the subsequent year. Infections of Nosema and infestations of V. destructor were positively correlated. Fumagillin was effective at mitigating Nosema intensities only over the short term, suggesting that biannual application is essential. V. destructor intensities were higher in colonies that had been previously treated with miticides, reasons for this warrant further investigation.

Prospective associations between meth/amphetamine (speed) and MDMA (ecstasy) use and depressive symptoms in secondary school students

Background Research has raised significant concern regarding the affective consequences of synthetic drug use. However, little evidence from well-controlled longitudinal studies exists on these consequences. The aim of this study was to determine whether use of meth/amphetamine (speed) and 63,4- methylenedioxymethamphetamine (MDMA, ecstasy) is independently predictive of subsequent depressive symptoms in adolescents. Methods A sample of 3880 adolescents from secondary schools in disadvantaged areas of Quebec, Canada, were followed over time (2003e2008). Logistic regression was used to test the association between meth/ amphetamine and MDMA use in grade 10 (ages 15e16 years) and elevated depressive symptoms on an abridged Center for Epidemiologic Studies-Depression scale in grade 11, controlling for pre-existing individual and contextual characteristics. Results After adjustment, both MDMA use (OR 1.7, 95% CI 1.1 to 2.6) and meth/amphetamine use (OR 1.6, 95% CI 1.1 to 2.3) in grade 10 significantly increased the odds of elevated depressive symptoms in grade 11. These relationships did not vary by gender or pre-existing depressive symptoms. Increased risk was particularly observed in concurrent usage (OR 1.9, 95% CI 1.2 to 2.9). Conclusions Adolescent use of meth/amphetamine and MDMA (particularly concurrent use) is independently associated with subsequent depressive symptoms. Further enquiry must determine whether these associations reflect drug-induced neurotoxicity and whether adolescence is a period of increased vulnerability to the hazards of synthetic drug exposure.

Production credit associations ... characteristics of loans and member borrowers.

Cover title.

Technology and the neurologically handicapped : a conference cosponsored by the National Aeronautics and Space Administration and the United Cerebral Palsy Foundation, and held at Ames Research Center, Moffett Field, California, September 8-10, 1971

Includes bibliographies

Employer associations engaged in Collective bargaining in New York State; a directory.

Mode of access: Internet.

Prevalence of mixed neuropathologies in autopsied older adults and associations with clinical disease progression

Thesis (Ph.D.)--University of Washington, 2016-06

Associations of location and perceived environmental attributes with walking in neighborhoods

Purpose. Ecological models highlight the importance of environmental influences. We examined associations of coastal versus noncoastal location and perceived environmental attributes with neighborhood walking, total walking, and total activity. Methods. Telephone interviews with 800 faculty and general staff of an Australian university. Results. Men were significantly more likely to walk in their neighborhood if they lived in a coastal location (odds ratio [OR] = 1.66), and they highly rated environmental aesthetics (OR = 1.91), convenience of facilities (OR = 2.20), and access to facilities (OR = 1.98). For women, neighborhood walking was associated with high ratings of convenience (OR = 3.78) but was significantly less likely if they had high ratings for access (OR = 0.48). For total walking and total physical activity, few significant associations emerged. Conclusions. Environmental attributes were related to walking in the neighborhood but not to more general activity indices. Understanding gender-specific environmental correlates of physical activity should be a priority.

Understanding environmental influences on walking - Review and research agenda

Background: Understanding how environmental attributes can influence particular physical activity behaviors is a public health research priority. Walking is the most common physical activity behavior of adults; environmental innovations may be able to influence rates of participation. Method: Review of studies on relationships of objectively assessed and perceived environmental attributes with walking. Associations with environmental attributes were examined separately for exercise and recreational walking, walking to get to and from places, and total walking. Results: Eighteen Studies were identified. Aesthetic attributes, convenience of facilities for walking (sidewalks, trails); accessibility of destinations (stores, park, beach); and perceptions about traffic and busy roads were found to be associated with walking for particular purposes. Attributes associated with walking for exercise were different front those associated with walking to get to and from places. Conclusions: While few studies have examined specific environment-walking relationships, early evidence is promising. Key elements of the research agenda are developing reliable and valid measures of environmental attributes and walking behaviors, determining whether environment-behavior relationships are causal, and developing theoretical models that account for environmental influences and their interactions with other determinants. (C) 2004 American Journal of Preventive Medicine.

The Short-EMBU in Australia, Spain, and Venezuela - Factorial invariance, and associations with sex roles, self-esteem, and Eysenckian personality dimensions

The short(s)-EMBU (Swedish acronym for Egna Minnen Betraffande Uppfostran [My memories of upbringing]) consists of 23 items, is based on the early 81-item EMBU, and was developed out of the necessity of having a brief measure of perceived parental rearing practices when the clinical and/or research context does not adequately permit application of time-consuming test batteries. The s-EMBU comprises three subscales: Rejection., Emotional Warmth, and (Over)Protection. The factorial and/or construct validity and reliability of the s-EMBU were examined in samples comprising a total of 1950 students from Australia, Spain, and Venezuela. The data were presented for the three national groups separately. Findings confirmed the cross-national validity of the factorial structure underlying the s-EMBU. Rejection by fathers and mothers was consistently associated with high trait-neuroticism and low self-esteem in recipients of both sexes in each nation, as was high parental emotional warmth with high femininity (humility). The findings on factorial validity are in keeping with previous ones obtained in East Germany, Greece, Guatemala, Hungary, Italy, and Sweden. The s-EMBU is again recommended for use in several different countries as. a reliable, functional equivalent to the original 81-item EMBU.