Genomic selection and complex trait prediction using a fast EM algorithm applied to genome-wide markers

Background: The information provided by dense genome-wide markers using high throughput technology is of considerable potential in human disease studies and livestock breeding programs. Genome-wide association studies relate individual single nucleotide polymorphisms (SNP) from dense SNP panels to individual measurements of complex traits, with the underlying assumption being that any association is caused by linkage disequilibrium (LD) between SNP and quantitative trait loci (QTL) affecting the trait. Often SNP are in genomic regions of no trait variation. Whole genome Bayesian models are an effective way of incorporating important prior information into modelling. However a full Bayesian analysis is often not feasible due to the amount of data and the computational time involved. Results: This article proposes an expectation-maximization (EM) algorithm called emBayesB which allows only a proportion of SNP to be in LD with QTL and incorporates important prior information about the distribution of SNP effects. The posterior probability of being in LD with at least one QTL is calculated for each SNP along with estimates of the hyperparameters for the mixture prior. A simulated example of genomic selection from an international workshop is used to demonstrate the features of the EM algorithm. The accuracy of prediction is comparable to a full Bayesian analysis but the EM algorithm is considerably faster. The EM algorithm was accurate in locating QTL which explained more than 1% of the total genetic variation. A computational algorithm for very large SNP panels is described. Conclusions: emBayesB is a fast and accurate EM algorithm for implementing genomic selection and predicting complex traits by mapping QTL in genome-wide dense SNP marker data. Its accuracy is similar to Bayesian methods but it takes only a fraction of the time

Children With Persistent Feeding Difficulties: An Observational Analysis of the Feeding Interactions of Problem and Non-Problem Eaters

This study examined the relationship between parent's feeding practices and the feeding behavior of toddlers and preschool-age children with (n = 19) or without (n = 26) persistent feeding difficulties. Specifically, patterns of parent-child interaction were assessed during standardized family mealtime observations in the clinic. Parents also kept observational records of their children's mealtime behavior at home and rated the degree of difficulty they experienced in feeding their child during each meal on a daily basis. Observational results showed that feeding-disordered children engaged in higher levels of disruptive mealtime behavior (food refusal, noncompliance, complaining, oppositional behavior, and playing with food) and lower levels of chewing during mealtime. There were several significant age effects, with younger children (under age 3) engaging in more vomiting and less aversive demanding and verbalizations. Parents of feeding-disordered children were more negative and coercive in their feeding practices and engaged in higher levels of aversive instruction giving, aversive prompting, and negative eating-related comments. There were several significant associations between coercive parental behaviors and children's food refusal and noncompliance in the sample as a whole. Measures of children's disruptiveness at mealtimes in the clinic were significantly correlated with measures of mealtime behavior in the home

Flammability limits, ignition energy, and flame speeds in H₂–CH₄–NH₃–N₂O–O₂–N₂ mixtures

Experiments on flammability limits, ignition energies, and flame speeds were carried out in a 11.25- and a 400-liter combustion vessel at initial pressures and temperatures of 100 kPa and 295 K, respectively. Flammability maps of hydrogen–nitrous oxide–nitrogen, methane–nitrous oxide–nitrogen, ammonia–nitrous oxide–nitrogen, and ammonia–nitrous oxide–air, as well as lean flammability limits of various hydrogen–methane–ammonia–nitrous oxide–oxygen–nitrogen mixtures were determined. Ignition energy bounds of methane–nitrous oxide, ammonia–nitrous oxide, and ammonia–nitrous oxide–nitrogen mixtures have been determined and the influence of small amounts of oxygen on the flammability of methane–nitrous oxide–nitrogen mixtures has been investigated. Flame speeds have been measured and laminar burning velocities have been determined for ammonia–air–nitrous oxide and various hydrogen–methane–ammonia–nitrous oxide–oxygen–nitrogen mixtures. Lower and upper flammability limits (mixing fan on, turbulent conditions) for ignition energies of 8 J are: H₂–N₂O: 4.5 ∼ 5.0% H₂(LFL), 76 ∼ 80% H₂(UFL); CH₄–N₂O: 2.5 ∼ 3.0% CH₄(LFL), 43 ∼ 50% CH₄(UFL); NH₃–N₂O: 5.0 ∼ 5.2% NH₃(LFL), 67.5 ∼ 68% NH₃(UFL). Inerting concentrations are: H₂–N₂O–N₂: 76% N₂; CH₄–N₂O–N₂: 70.5% N₂; NH₃–N₂O–N₂: 61% N₂; NH₃–N₂O–air: 85% air. Flammability limits of methane–nitrous oxide–nitrogen mixtures show no pronounced dependence on small amounts of oxygen (<5%). Generally speaking, flammable gases with large initial amounts of nitrous oxide or ammonia show a strong dependence of flammability limits on ignition energy

Flammability limits, ignition energy, and flame speeds in H₂–CH₄–NH₃–N₂O–O₂–N₂ mixtures

Experiments on flammability limits, ignition energies, and flame speeds were carried out in a 11.25- and a 400-liter combustion vessel at initial pressures and temperatures of 100 kPa and 295 K, respectively. Flammability maps of hydrogen–nitrous oxide–nitrogen, methane–nitrous oxide–nitrogen, ammonia–nitrous oxide–nitrogen, and ammonia–nitrous oxide–air, as well as lean flammability limits of various hydrogen–methane–ammonia–nitrous oxide–oxygen–nitrogen mixtures were determined. Ignition energy bounds of methane–nitrous oxide, ammonia–nitrous oxide, and ammonia–nitrous oxide–nitrogen mixtures have been determined and the influence of small amounts of oxygen on the flammability of methane–nitrous oxide–nitrogen mixtures has been investigated. Flame speeds have been measured and laminar burning velocities have been determined for ammonia–air–nitrous oxide and various hydrogen–methane–ammonia–nitrous oxide–oxygen–nitrogen mixtures. Lower and upper flammability limits (mixing fan on, turbulent conditions) for ignition energies of 8 J are: H₂–N₂O: 4.5 ∼ 5.0% H₂(LFL), 76 ∼ 80% H₂(UFL); CH₄–N₂O: 2.5 ∼ 3.0% CH₄(LFL), 43 ∼ 50% CH₄(UFL); NH₃–N₂O: 5.0 ∼ 5.2% NH₃(LFL), 67.5 ∼ 68% NH₃(UFL). Inerting concentrations are: H₂–N₂O–N₂: 76% N₂; CH₄–N₂O–N₂: 70.5% N₂; NH₃–N₂O–N₂: 61% N₂; NH₃–N₂O–air: 85% air. Flammability limits of methane–nitrous oxide–nitrogen mixtures show no pronounced dependence on small amounts of oxygen (<5%). Generally speaking, flammable gases with large initial amounts of nitrous oxide or ammonia show a strong dependence of flammability limits on ignition energy

From Transit Hub to Major Supplier of Illicit Cigarettes to Argentina and Brazil: The Changing Role of Domestic Production and Transnational Tobacco Companies in Paraguay Between 1960 and 2003

Background&nbsp; Paraguay has reportedly been a major transit hub for illicit tobacco products since the 1960s, initially to supply markets in Argentina and Brazil and, more recently, other regional markets and beyond. However, to date there has been no systematic analysis, notably independent of the tobacco industry, of this trade including the roles of domestic production and transnational tobacco companies (TTCs). This article fills that gap by detailing the history of Paraguay’s illicit cigarette trade to Brazil and Argentina of TTC products and Paraguayan production between 1960 and 2003. The effective control of illicit cigarette flows, under Article 15 of the World Health Organization (WHO) Framework Convention on Tobacco Control (FCTC) and the Protocol to Eliminate the Illicit Trade in Tobacco Products, requires fuller understanding of the changing nature of the illicit trade. Methods&nbsp; We systematically searched internal industry documents to understand the activities and strategies of leading TTCs in Paraguay and subregion over time. We also mapped illicit trade volume and patterns using US government and UN data on the cigarette trade involving Paraguay. We then estimated Paraguay’s cigarette production from 1989 to 2003 using tobacco leaf flows from the United Nations Commodity Trade Statistics Database (UN Comtrade). Results&nbsp; We identify four phases in the illicit tobacco trade involving Paraguay: 1) Paraguay as a transit hub to smuggle BAT and PMI cigarettes from the U.S. into Argentina and Brazil (from the 1960s to the mid-1970s); 2) BAT and PMI competing in north-east Argentina (1989–1994); 3) BAT and PMI competing in southern and southern-east Brazil (mid to late 1990s); and 4) the growth in the illicit trade of Paraguayan manufactured cigarettes (from the mid- 1990s onwards). These phases suggest the illicit trade was seeded by TTCs, and that the system of supply and demand on lower priced brands they developed in the 1990s created a business opportunity for manufacturing in Paraguay. Brazil’s efforts to fight this trade, with a 150% tax on exports to Latin American countries in 1999, further prompted supply of the illicit trade to shift from TTCs to Paraguayan manufacturers. Conclusion&nbsp; This paper extends evidence of the longstanding complicity of TTCs in the illicit trade to this region and the consequent growth of Paraguayan production in the 1990s. Our findings confirm the need to better understand the factors influencing how the illicit tobacco trade has changed over time, in specific regional contexts, and amid tobacco industry globalization. In Paraguay, the changing roles of TTC and domestic production have been central to shifting patterns of illicit supply and distribution since the 1960s. Important questions are raised, in turn, about TTCs efforts to participate as legitimate partners in global efforts to combat the problem, including a leading role in data gathering and analysis

Acceptability of Telerehabilitation for Magnification Devices for the Visually Impaired Using Various Approaches to Facilitate Accessibility

PurposeWe examined different methods to reduce the burden of accessing technology for videoconferencing during telerehabilitation for magnification devices for the visually impaired.MethodsDuring telerehabilitation studies over the past 5 years, vision rehabilitation providers assessed and gave training to visually impaired participants with newly dispensed magnification devices at home who connected to Zoom videoconferencing via loaner tablets or smartphones with assistance from (phase 1; n = 10) investigators by phone, (phase 2; n = 11) local Lions Club volunteers in participants' homes, or (phase 3; n = 24) remote access control software in a randomized controlled trial with 13 usual care controls who received in-office training. All participants completed the same post-telerehabilitation phone survey.ResultsA significantly greater proportion of phase 3 subjects indicated they strongly or mostly agreed that the technology did not interfere with the session (96%) compared to phase 1 (60%; 95% confidence interval [CI], 1.2-12.5; P = 0.03) or phase 2 (55%; 95% CI, 1.8-188; P = 0.01). The majority indicated telerehabilitation was as accurate as in person (68%), they were comfortable with telerehabilitation (91%) and interested in a future session (83%), and their magnifier use improved (79%), with no significant differences in these responses between phases (all P &gt; 0.10), including comparisons of participants randomized to telerehabilitation or in-office training in phase 3 who reported similar overall satisfaction levels (P = 0.84).ConclusionsParticipants across all phases reported high levels of acceptance for telerehabilitation, with least interference from technology using remote access control in phase 3.Translational relevanceWith accommodations for accessibility to videoconferencing technology, telerehabilitation for magnification devices can be a feasible, acceptable, and valuable option in countries with resources to support the technology

Menopausal status, age and management among women living with HIV in the UK

BACKGROUND: There is currently little evidence exploring menopausal status, age at last menstrual period (LMP) and management of menopause among women living with HIV aged 45-60 years in England. METHODS: Socio-demographic, lifestyle and clinical data were collected through a self-completed cross-sectional survey. Longitudinal CD4 count and viral load data were available from linkage to clinical records, if consent was provided. Women were categorised as pre-, peri- or post-menopausal. Factors associated with menopausal stage were examined using ordinal logistic regression adjusting for age. Age at LMP was estimated using Kaplan-Meier survival analysis. RESULTS: The 847 women had a median age of 49 [interquartile range (IQR): 47-52] years. Most were of black ethnicity (81.3%), were born outside the UK (85.0%) and had completed secondary education (88.7%); 177 (20.4%), 373 (43.0%) and 297 (34.2%) were pre-, peri- or post-menopausal, respectively. After adjusting for age, associations of menopausal status with non-cohabiting relationship [adjusted odds ratio = 0.63 (95% confidence interval: 0.43-0.91)], baseline viral load ≥ 100 000 copies/mL [2.67 (1.20-5.94)] and unemployment [1.34 (0.97-1.84)] remained significant. Median (IQR) age at LMP was 54 (51-55) years in the group. In total, 27.9% (233/836) of women reported severe menopausal symptoms; 45.6% of those with somatic symptoms had heard of hormone replacement therapy and 8.7% had used it. Only 5.6% of women with urogenital symptoms had used topical oestrogen. CONCLUSIONS: Our findings highlight the importance of educating both women and their healthcare providers about menopausal symptoms and management options

Introduction: Interrogating the 'everyday' politics of emotions in international relations

The focus on the everyday in this Special Issue reveals different kinds of emotional practices, their political effects and their political contestation within both micro- and macro-politics in international relations. The articles in this Special Issue address the everyday negotiation of emotions, shifting between the reproduction of hegemonic structures of feelings and emancipation from them. In other words, the everyday politics of emotions allows an exploration of who gets to express emotions, what emotions are perceived as (il)legitimate or (un)desirable, how emotions are circulated and under what circumstances. Consequently, we identify two thematic strands which emerge as central to an interrogation of ‘everyday’ emotions in international relations and which run through each of the contributions: first, an exploration of the relationship between individual and collective emotions and, second, a focus on the role of embodiment within emotions research and its relationship with the dynamics and structures of power