Detection of 5′- and 3′-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli

Evidence is accumulating that small, noncoding RNAs are important regulatory molecules. Computational and experimental searches have led to the identification of ∼60 small RNA genes in Escherichia coli. However, most of these studies focused on the intergenic regions and assumed that small RNAs were >50 nt. Thus, the previous screens missed small RNAs encoded on the antisense strand of protein-coding genes and small RNAs of <50 nt. To identify additional small RNAs, we carried out a cloning-based screen focused on RNAs of 30–65 nt. In this screen, we identified RNA species corresponding to fragments of rRNAs, tRNAs and known small RNAs. Several of the small RNAs also corresponded to 5′- and 3′-untranslated regions (UTRs) and internal fragments of mRNAs. Four of the 3′-UTR-derived RNAs were highly abundant and two showed expression patterns that differed from the corresponding mRNAs, suggesting independent functions for the 3′-UTR-derived small RNAs. We also detected three previously unidentified RNAs encoded in intergenic regions and RNAs from the long direct repeat and hok/sok elements. In addition, we identified a few small RNAs that are expressed opposite protein-coding genes and could base pair with 5′ or 3′ ends of the mRNAs with perfect complementarity

Stiffness and Slip in Multi-dowel Timber Connections with Slotted-in Steel Plates

Large multi-dowel connections can provide the strength and ductility required for large, highly-loaded timber structures, but their slip under load is not well understood. This is an important gap in knowledge, because accumulated local displacements at connections represent a large part of the deformation of a timber structure. The empirical relationships used in design codes commonly scale a single-dowel stiffness by the number of dowels, so do not capture the dowel interaction effects of the multi-dowel connections used in larger structures. We present the results of an experimental test series, elastic model and probabilistic numerical analysis investigating the development of stiffness in multi-dowel timber connections with slotted-in steel plates. Novel test methods record the development of stiffness due to each individual connector to show that the stiffness of the complete connection is not proportional to the number of dowels. An elastic stress-function model shows that this is partly due to interaction of the stress field around the dowels. For the first time, this work quantitatively considers the influence of misalignment of dowels due to manufacturing tolerances, and it is shown that this may greatly reduce the overall stiffness of a multi-dowel connection. The test series is used to validate a probabilistic model of this misalignment for the stiffness of such a connection. The model incorporates the nonlinear stiffness and hole opening observed in single-dowel connections to predict the behaviour of the group. The study shows that the random misalignment of dowels in multi-dowel connections reduces the range of displacements over which the connection displays zero stiffness slightly, but that this zone is not eliminated as a result of irreversible hole opening under load, even for a connection with 35 dowels and three steel plates. We conclude that two parameters are important for the design of these connections: the unload-reload stiffness and the zero-stiffness region measured between the zero load intercept of the unload-reload linear fit. With these, a reasonable estimate can be made of the displacement at any serviceability load level in either tension or compression

Food and vulnerability in Aotearoa/New Zealand: A review and theoretical reframing of food insecurity, income and neoliberalism

The incidence of food insecurity in rich countries has remained stubbornly consistent in recent decades, even as rates of undernourishment in poorer countries have dived since 1990 (United Nations, 2015). This article addresses this apparent contradiction through a theoretical reframing of food insecurity in rich liberal democracies, built on a review of key literature and data. We draw a broad distinction between critical social science approaches to engaging with food insecurity and more empirical, policy-oriented approaches. These produce research that emphasises, respectively, the determinate role of economic class and neoliberalism in generating food insecurity, and the wide array of other factors associated with suffering food insecurity. We argue that both offer useful but analytically confined accounts of food insecurity and its drivers in rich liberal democracies. We proceed, seeking to broaden rather than abandon the strengths of these two accounts, with a review of data on incomes and the incidence of food insecurity in the Aotearoa/New Zealand case. Our review reveals patterns of socio-political deprivation beyond class with parallels across both data sets, significantly along lines of gender and ethnicity. This both offers texturing specifics to a 'monolithic' generic view of neoliberalism and contextualises demographic trends of food insecurity within the neoliberalised "contours of contemporary political-economic power" (Peck and Tickell, 2002, pp.381-382). We subsequently argue for the utility of vulnerability as a concept to capture socio-political dynamics and engage with food insecurity in rich liberal democracies. The framing work done by the concept of vulnerability offers the opportunity to: (1) align the strengths of research approaches emphasising theoretically derived context and empirically founded complexity; (2) account for the consistencies and complexities observed in the relationship between the political-economic landscape of rich liberal democracies following the neoliberal turn and the incidence of food insecurity; and (3) reconsider the relationship between political-economic and socio-political contexts of rich liberal democracies that consistently produce food insecurity and groups of people who live and consistently suffer food insecurity in these countries, for example as "structural violence" (Shepherd, 2012, p.206)

Allele Frequencies of 15 STR Loci (Identifiler™ Kit) in Basque-Americans

Individuals with Basque ancestry form a historically and culturally important minority of the population of the western United States. Allele frequencies for the 15 autosomal STRs in the AmpFlSTR® Identifiler® PCR Amplification Kit (Applied Biosystems) from 156 unrelated self-identified Basque individuals born in the United States are presented. Allele frequencies were used to calculate parameters commonly used in genetics and forensics including power of discrimination (PD), power of exclusion (PE), polymorphic information content (PIC), and expected heterozygosity (He). The sample population was also compared with the European Basque population and the major American ethnicities

New Zealand’s Food Waste: Estimating the Tonnes, Value, Calories and Resources Wasted

We used macro-economic data and aggregated waste data to estimate that, in 2011, New Zealand households generated over 224,000 tonnes of food waste, and New Zealand industry generated over 103,000 tonnes of food waste. We split New Zealand’s food waste into 14 food-waste categories and found that 7% is related to “fresh” produce, and 93% “processed” food waste. The value of New Zealand’s food waste in 2011 is estimated to be NZ $568 million, or$131 per person. Furthermore, New Zealand’s food waste represents 163 ˆ 109 calories in total, and avoidable food waste would be able to feed between 50,000 and 80,000 people a year. New Zealand food waste embodies 4.2 ˆ 106 tonnes of CO2-e, 4.7 ˆ 109 m3 of water, and 29 ˆ 103 TJ of energy. Nonetheless, we find that, compared to other nations, New Zealanders waste less food per capita by weight, value and calorie

Stiffness and slip in multi-dowel flitch-plate timber connections

Large multi-dowel connections can provide the strong and ductile connections required for large, highly-loaded timber structures, but their slip under load is not well understood. This is important because accumulated local displacements at connections can have significant implications for overall building serviceability. Empirical relationships for the slip of a single-dowel connection do not capture the dowel interaction effects of the multi-dowel connections used in larger structures. We present the results of an experimental test series and probabilistic numerical analysis investigating the development of stiffness in multi-dowel timber flitch plate connections. The influence of the diameter and number of dowels on the stiffness of the connection are investigated, including the influence of off-centring of dowels due to manufacturing tolerances. The test series is used to validate a probabilistic model for the stiffness of such a connection. The model incorporates the nonlinear stiffness and hole opening observed in single-dowel connections to predict the behaviour of the group. The study shows that the random off-centring of dowels in multi-dowel connections reduces the range of displacements over which the connection displays zero stiffness, but that this zone is not eliminated as a result of irreversible hole opening under load

Embryo movement is more frequent in avian brood parasites than birds with parental reproductive strategies.

Funder: Tanzanian Commission for Science and TechnologyFunder: Tanzania Wildlife Research InstituteFunder: NERCFunder: National Science FoundationFunder: Ministry of EducationFunder: German Academic Exchange ServiceFunder: University of Cape TownFunder: Max-Planck-GesellschaftMovement of the embryo is essential for musculoskeletal development in vertebrates, yet little is known about whether, and why, species vary. Avian brood parasites exhibit feats of strength in early life as adaptations to exploit the hosts that rear them. We hypothesized that an increase in embryonic movement could allow brood parasites to develop the required musculature for these demands. We measured embryo movement across incubation for multiple brood-parasitic and non-parasitic bird species. Using a phylogenetically controlled analysis, we found that brood parasites exhibited significantly increased muscular movement during incubation compared to non-parasites. This suggests that increased embryo movement may facilitate the development of the stronger musculoskeletal system required for the demanding tasks undertaken by young brood parasites

Does publication bias inflate the apparent efficacy of psychological treatment for major depressive disorder? A systematic review and meta-analysis of US national institutes of health-funded trials

Background The efficacy of antidepressant medication has been shown empirically to be overestimated due to publication bias, but this has only been inferred statistically with regard to psychological treatment for depression. We assessed directly the extent of study publication bias in trials examining the efficacy of psychological treatment for depression. Methods and Findings We identified US National Institutes of Health grants awarded to fund randomized clinical trials comparing psychological treatment to control conditions or other treatments in patients diagnosed with major depressive disorder for the period 1972–2008, and we determined whether those grants led to publications. For studies that were not published, data were requested from investigators and included in the meta-analyses. Thirteen (23.6%) of the 55 funded grants that began trials did not result in publications, and two others never started. Among comparisons to control conditions, adding unpublished studies (Hedges’ g = 0.20; CI95% -0.11~0.51; k = 6) to published studies (g = 0.52; 0.37~0.68; k = 20) reduced the psychotherapy effect size point estimate (g = 0.39; 0.08~0.70) by 25%. Moreover, these findings may overestimate the "true" effect of psychological treatment for depression as outcome reporting bias could not be examined quantitatively. Conclusion The efficacy of psychological interventions for depression has been overestimated in the published literature, just as it has been for pharmacotherapy. Both are efficacious but not to the extent that the published literature would suggest. Funding agencies and journals should archive both original protocols and raw data from treatment trials to allow the detection and correction of outcome reporting bias. Clinicians, guidelines developers, and decision makers should be aware that the published literature overestimates the effects of the predominant treatments for depression

Bubbles in Planetary Nebulae and Clusters of Galaxies: Jet Properties

I derive constraints on jet properties for inflating pairs of bubbles in planetary nebulae and clusters of galaxies. This work is motivated by the similarity in morphology and some non-dimensional quantities between X-ray-deficient bubbles in clusters of galaxies and the optical-deficient bubbles in planetary nebulae, which was pointed out in an earlier work. In the present paper I find that for inflating fat bubbles, the opening angle of the jets must be large, i.e., the half opening angle measured from the symemtry axis of the jets should typically be larger than 40 degrees. Narrow jets will form elongated lobes rather than fat bubbles. I emphasize the need to include jets with large opening angle in simulating bubble inflation in both planetary nebulae and (cooling flow) clusters of galaxies.Comment: submitted to AA; a second in a series of 3 paper

Attitudes and delivering brief interventions for heavy drinking in primary health care: analyses from the ODHIN five country cluster randomized factorial trial

Contains fulltext : 170028.pdf (publisher's version ) (Open Access)In this paper, we test path models that study the interrelations between primary health care provider attitudes towards working with drinkers, their screening and brief advice activity, and their receipt of training and support and financial reimbursement. Study participants were 756 primary health care providers from 120 primary health care units (PHCUs) in different locations throughout Catalonia, England, The Netherlands, Poland, and Sweden. Our interventions were training and support and financial reimbursement to providers. Our design was a randomized factorial trial with baseline measurement period, 12-week implementation period, and 9-month follow-up measurement period. Our outcome measures were: attitudes of individual providers in working with drinkers as measured by the Short Alcohol and Alcohol Problems Perception Questionnaire; and the proportion of consulting adult patients (age 18+ years) who screened positive and were given advice to reduce their alcohol consumption (intervention activity). We found that more positive attitudes were associated with higher intervention activity, and higher intervention activity was then associated with more positive attitudes. Training and support was associated with both positive changes in attitudes and higher intervention activity. Financial reimbursement was associated with more positive attitudes through its impact on higher intervention activity. We conclude that improving primary health care providers' screening and brief advice activity for heavy drinking requires a combination of training and support and on-the-job experience of actually delivering screening and brief advice activity