In situ micropillar deformation of hydrides in Zircaloy-4

Deformation of hydrided Zircaloy-4 has been examined using in situ loading of hydrided micropillars in the scanning electron microscope and using synchrotron X-ray Laue microbeam diffraction. Results suggest that both the matrix and hydride can co-deform, with storage of deformation defects observed within the hydrides, which were twinned. Hydrides placed at the plane of maximum shear stress showed deformation within the hydride packet, whilst packets in other pillars arrested the propagation of shear bands. X-ray Laue peak broadening, prior to deformation, was associated with the precipitation of hydrides, and during deformation plastic rotation and broadening of both the matrix and hydride peaks were observed. Post-mortem TEM of the deformed pillars has indicated a greater density of dislocations associated with the precipitated hydride packets, while the observed broadening of the hydride electron diffraction spots further suggests that plastic strain gradients were induced in the hydrides by compression

Oldest evidence of tool making hominins in a grassland-dominated ecosystem.

BACKGROUND: Major biological and cultural innovations in late Pliocene hominin evolution are frequently linked to the spread or fluctuating presence of C(4) grass in African ecosystems. Whereas the deep sea record of global climatic change provides indirect evidence for an increase in C(4) vegetation with a shift towards a cooler, drier and more variable global climatic regime beginning approximately 3 million years ago (Ma), evidence for grassland-dominated ecosystems in continental Africa and hominin activities within such ecosystems have been lacking. METHODOLOGY/PRINCIPAL FINDINGS: We report stable isotopic analyses of pedogenic carbonates and ungulate enamel, as well as faunal data from approximately 2.0 Ma archeological occurrences at Kanjera South, Kenya. These document repeated hominin activities within a grassland-dominated ecosystem. CONCLUSIONS/SIGNIFICANCE: These data demonstrate what hitherto had been speculated based on indirect evidence: that grassland-dominated ecosystems did in fact exist during the Plio-Pleistocene, and that early Homo was active in open settings. Comparison with other Oldowan occurrences indicates that by 2.0 Ma hominins, almost certainly of the genus Homo, used a broad spectrum of habitats in East Africa, from open grassland to riparian forest. This strongly contrasts with the habitat usage of Australopithecus, and may signal an important shift in hominin landscape usage

The need to promote behaviour change at the cultural level: one factor explaining the limited impact of the MEMA kwa Vijana adolescent sexual health intervention in rural Tanzania. A process evaluation

Background - Few of the many behavioral sexual health interventions in Africa have been rigorously evaluated. Where biological outcomes have been measured, improvements have rarely been found. One of the most rigorous trials was of the multi-component MEMA kwa Vijana adolescent sexual health programme, which showed improvements in knowledge and reported attitudes and behaviour, but none in biological outcomes. This paper attempts to explain these outcomes by reviewing the process evaluation findings, particularly in terms of contextual factors. Methods - A large-scale, primarily qualitative process evaluation based mainly on participant observation identified the principal contextual barriers and facilitators of behavioural change. Results - The contextual barriers involved four interrelated socio-structural factors: culture (i.e. shared practices and systems of belief), economic circumstances, social status, and gender. At an individual level they appeared to operate through the constructs of the theories underlying MEMA kwa Vijana - Social Cognitive Theory and the Theory of Reasoned Action – but the intervention was unable to substantially modify these individual-level constructs, apart from knowledge. Conclusion - The process evaluation suggests that one important reason for this failure is that the intervention did not operate sufficiently at a structural level, particularly in regard to culture. Recently most structural interventions have focused on gender or/and economics. Complementing these with a cultural approach could address the belief systems that justify and perpetuate gender and economic inequalities, as well as other barriers to behaviour change

Cooperative secretions facilitate host range expansion in bacteria

The majority of emergent human pathogens are zoonotic in origin, that is, they can transmit to humans from other animals. Understanding the factors underlying the evolution of pathogen host range is therefore of critical importance in protecting human health. There are two main evolutionary routes to generalism: organisms can tolerate multiple environments or they can modify their environments to forms to which they are adapted. Here we use a combination of theory and a phylogenetic comparative analysis of 191 pathogenic bacterial species to show that bacteria use cooperative secretions that modify their environment to extend their host range and infect multiple host species. Our results suggest that cooperative secretions are key determinants of host range in bacteria, and that monitoring for the acquisition of secreted proteins by horizontal gene transfer can help predict emerging zoonoses

The Dawn of Open Access to Phylogenetic Data

The scientific enterprise depends critically on the preservation of and open access to published data. This basic tenet applies acutely to phylogenies (estimates of evolutionary relationships among species). Increasingly, phylogenies are estimated from increasingly large, genome-scale datasets using increasingly complex statistical methods that require increasing levels of expertise and computational investment. Moreover, the resulting phylogenetic data provide an explicit historical perspective that critically informs research in a vast and growing number of scientific disciplines. One such use is the study of changes in rates of lineage diversification (speciation - extinction) through time. As part of a meta-analysis in this area, we sought to collect phylogenetic data (comprising nucleotide sequence alignment and tree files) from 217 studies published in 46 journals over a 13-year period. We document our attempts to procure those data (from online archives and by direct request to corresponding authors), and report results of analyses (using Bayesian logistic regression) to assess the impact of various factors on the success of our efforts. Overall, complete phylogenetic data for ~60% of these studies are effectively lost to science. Our study indicates that phylogenetic data are more likely to be deposited in online archives and/or shared upon request when: (1) the publishing journal has a strong data-sharing policy; (2) the publishing journal has a higher impact factor, and; (3) the data are requested from faculty rather than students. Although the situation appears dire, our analyses suggest that it is far from hopeless: recent initiatives by the scientific community -- including policy changes by journals and funding agencies -- are improving the state of affairs

Nebuliser therapy in the intensive care unit

The relationship between identity, lived experience, sexual practices and the language through which these are conveyed has been widely debated in sexuality literature. For example, ‘coming out’ has famously been conceptualised as a ‘speech act’ (Sedgwick 1990) and as a collective narrative (Plummer 1995), while a growing concern for individuals’ diverse identifications in relations to their sexual and gender practices has produced interesting research focusing on linguistic practices among LGBT-identified individuals (Leap 1995; Kulick 2000; Cameron and Kulick 2006; Farqhar 2000). While an explicit focus on language remains marginal to literature on sexualities (Kulick 2000), issue of language use and translation are seldom explicitly addressed in the growing literature on intersectionality. Yet intersectional perspectives ‘reject the separability of analytical and identity categories’ (McCall 2005:1771), and therefore have an implicit stake in the ‘vernacular’ language of the researched, in the ‘scientific’ language of the researcher and in the relationship of continuity between the two. Drawing on literature within gay and lesbian/queer studies and cross-cultural studies, this chapter revisits debates on sexuality, language and intersectionality. I argue for the importance of giving careful consideration to the language we choose to use as researchers to collectively define the people whose experiences we try to capture. I also propose that language itself can be investigated as a productive way to foreground how individual and collective identifications are discursively constructed, and to unpack the diversity of lived experience. I address intersectional complexity as a methodological issue, where methodology is understood not only as the methods and practicalities of doing research, but more broadly as ‘a coherent set of ideas about the philosophy, methods and data that underlie the research process and the production of knowledge’ (McCall 2005:1774). My points are illustrated with examples drawn from my ethnographic study on ‘lesbian’ identity in urban Russia, interspersed with insights from existing literature. In particular, I aim to show that an explicit focus on language can be a productive way to explore the intersections between the global, the national and the local in cross-cultural research on sexuality, while also addressing issues of positionality and accountability to the communities researched

Control and Characterization of Individual Grains and Grain Boundaries in Graphene Grown by Chemical Vapor Deposition

The strong interest in graphene has motivated the scalable production of high quality graphene and graphene devices. Since large-scale graphene films synthesized to date are typically polycrystalline, it is important to characterize and control grain boundaries, generally believed to degrade graphene quality. Here we study single-crystal graphene grains synthesized by ambient CVD on polycrystalline Cu, and show how individual boundaries between coalescing grains affect graphene's electronic properties. The graphene grains show no definite epitaxial relationship with the Cu substrate, and can cross Cu grain boundaries. The edges of these grains are found to be predominantly parallel to zigzag directions. We show that grain boundaries give a significant Raman "D" peak, impede electrical transport, and induce prominent weak localization indicative of intervalley scattering in graphene. Finally, we demonstrate an approach using pre-patterned growth seeds to control graphene nucleation, opening a route towards scalable fabrication of single-crystal graphene devices without grain boundaries.Comment: New version with additional data. Accepted by Nature Material

The Effect of the CO32- to Ca2+ Ion activity ratio on calcite precipitation kinetics and Sr2+ partitioning

<p>Abstract</p> <p>Background</p> <p>A proposed strategy for immobilizing trace metals in the subsurface is to stimulate calcium carbonate precipitation and incorporate contaminants by co-precipitation. Such an approach will require injecting chemical amendments into the subsurface to generate supersaturated conditions that promote mineral precipitation. However, the formation of reactant mixing zones will create gradients in both the saturation state and ion activity ratios (i.e., <inline-formula><m:math name="1467-4866-13-1-i1" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:msub><m:mrow><m:mi>a</m:mi></m:mrow><m:mrow><m:mi>C</m:mi><m:msup><m:mrow><m:msub><m:mrow><m:mi>O</m:mi></m:mrow><m:mrow><m:mn>3</m:mn></m:mrow></m:msub></m:mrow><m:mrow><m:mn>2</m:mn><m:mo class="MathClass-bin">-</m:mo></m:mrow></m:msup></m:mrow></m:msub><m:mo class="MathClass-bin">/</m:mo><m:msub><m:mrow><m:mi>a</m:mi></m:mrow><m:mrow><m:mi>C</m:mi><m:msup><m:mrow><m:mi>a</m:mi></m:mrow><m:mrow><m:mn>2</m:mn><m:mo class="MathClass-bin">+</m:mo></m:mrow></m:msup></m:mrow></m:msub></m:math></inline-formula>). To better understand the effect of ion activity ratios on CaCO₃precipitation kinetics and Sr²⁺co-precipitation, experiments were conducted under constant composition conditions where the supersaturation state (Ω) for calcite was held constant at 9.4, but the ion activity ratio <inline-formula><m:math name="1467-4866-13-1-i2" xmlns:m="http://www.w3.org/1998/Math/MathML"><m:mrow><m:mo class="MathClass-open">(</m:mo><m:mrow><m:mi>r</m:mi><m:mo class="MathClass-rel">=</m:mo><m:msub><m:mrow><m:mi>a</m:mi></m:mrow><m:mrow><m:mi>C</m:mi><m:msup><m:mrow><m:msub><m:mrow><m:mi>O</m:mi></m:mrow><m:mrow><m:mn>3</m:mn></m:mrow></m:msub></m:mrow><m:mrow><m:mn>2</m:mn><m:mo class="MathClass-bin">-</m:mo></m:mrow></m:msup></m:mrow></m:msub><m:mo class="MathClass-bin">/</m:mo><m:msub><m:mrow><m:mi>a</m:mi></m:mrow><m:mrow><m:mi>C</m:mi><m:msup><m:mrow><m:mi>a</m:mi></m:mrow><m:mrow><m:mn>2</m:mn><m:mo class="MathClass-bin">+</m:mo></m:mrow></m:msup></m:mrow></m:msub></m:mrow><m:mo class="MathClass-close">)</m:mo></m:mrow></m:math></inline-formula> was varied between 0.0032 and 4.15.</p> <p>Results</p> <p>Calcite was the only phase observed, by XRD, at the end of the experiments. Precipitation rates increased from 41.3 ± 3.4 μmol m^-2min^-1at <it>r = </it>0.0315 to a maximum rate of 74.5 ± 4.8 μmol m^-2min^-1at <it>r = </it>0.306 followed by a decrease to 46.3 ± 9.6 μmol m^-2min^-1at <it>r </it>= 1.822. The trend was simulated using a simple mass transfer model for solute uptake at the calcite surface. However, precipitation rates at fixed saturation states also evolved with time. Precipitation rates accelerated for low <it>r </it>values but slowed for high <it>r </it>values. These trends may be related to changes in effective reactive surface area. The <inline-formula><m:math xmlns:m="http://www.w3.org/1998/Math/MathML" name="1467-4866-13-1-i1"><m:msub><m:mrow><m:mi>a</m:mi></m:mrow><m:mrow><m:mi>C</m:mi><m:msup><m:mrow><m:msub><m:mrow><m:mi>O</m:mi></m:mrow><m:mrow><m:mn>3</m:mn></m:mrow></m:msub></m:mrow><m:mrow><m:mn>2</m:mn><m:mo class="MathClass-bin">-</m:mo></m:mrow></m:msup></m:mrow></m:msub><m:mo class="MathClass-bin">/</m:mo><m:msub><m:mrow><m:mi>a</m:mi></m:mrow><m:mrow><m:mi>C</m:mi><m:msup><m:mrow><m:mi>a</m:mi></m:mrow><m:mrow><m:mn>2</m:mn><m:mo class="MathClass-bin">+</m:mo></m:mrow></m:msup></m:mrow></m:msub></m:math></inline-formula> ratios did not affect the distribution coefficient for Sr in calcite (D^P_Sr²⁺), apart from the indirect effect associated with the established positive correlation between D^P_Sr²⁺and calcite precipitation rate.</p> <p>Conclusion</p> <p>At a constant supersaturation state (Ω = 9.4), varying the ion activity ratio affects the calcite precipitation rate. This behavior is not predicted by affinity-based rate models. Furthermore, at the highest ion ratio tested, no precipitation was observed, while at the lowest ion ratio precipitation occurred immediately and valid rate measurements could not be made. The maximum measured precipitation rate was 2-fold greater than the minima, and occurred at a carbonate to calcium ion activity ratio of 0.306. These findings have implications for predicting the progress and cost of remediation operations involving enhanced calcite precipitation where mineral precipitation rates, and the spatial/temporal distribution of those rates, can have significant impacts on the mobility of contaminants.</p

No Gold Standard Estimation of the Sensitivity and Specificity of Two Molecular Diagnostic Protocols for Trypanosoma brucei spp. in Western Kenya

African animal trypanosomiasis is caused by a range of tsetse transmitted protozoan parasites includingTrypanosoma vivax, Trypanosoma congolense and Trypansoma brucei. In Western Kenya and other parts of East Africa two subspecies of T. brucei, T.b. brucei and the zoonoticT.b. rhodesiense, co-circulate in livestock. A range of polymerase chain reactions (PCR) have been developed as important molecular diagnostic tools for epidemiological investigations of T. brucei s.l. in the animal reservoir and of its zoonotic potential. Quantification of the relative performance of different diagnostic PCRs is essential to ensure comparability of studies. This paper describes an evaluation of two diagnostic test systems for T. brucei using a T. brucei s.l. specific PCR [1] and a single nested PCR targeting the Internal Transcribed Spacer (ITS) regions of trypanosome ribosomal DNA [2]. A Bayesian formulation of the Hui-Walter latent class model was employed to estimate their test performance in the absence of a gold standard test for detecting T.brucei s.l. infections in ear-vein blood samples from cattle, pig, sheep and goat populations in Western Kenya, stored on Whatman FTA cards. The results indicate that the system employing the T. brucei s.l. specific PCR (Se1 = 0.760) had a higher sensitivity than the ITS-PCR (Se2 = 0.640); both have high specificity (Sp1 = 0.998; Sp2 = 0.997). The true prevalences for livestock populations were estimated (pcattle = 0.091, ppigs = 0.066, pgoats = 0.005, psheep = 0.006), taking into account the uncertainties in the specificity and sensitivity of the two test systems. Implications of test performance include the required survey sample size; due to its higher sensitivity and specificity, the T. brucei s.l. specific PCR requires a consistently smaller sample size than the ITS-PCR for the detection of T. brucei s.l. However the ITS-PCR is able to simultaneously screen samples for other pathogenic trypanosomes and may thus be, overall, a better choice of test in multi-organism studies

Modelling the public health impact of male circumcision for HIV prevention in high prevalence areas in Africa

Background: Recent clinical trials in Africa, in combination with several observational epidemiological studies, have provided evidence that male circumcision can reduce HIV female-to-male transmission risk by 60% or more. However, the public health impact of large-scale male circumcision programs for HIV prevention is unclear. Methods: Two mathematical models were examined to explore this issue: a random mixing model and a compartmental model that distinguishes risk groups associated with sex work. In the compartmental model, two scenarios were developed, one calculating HIV transmission and prevalence in a context similar to the country of Botswana, and one similar to Nyanza Province, in western Kenya. Results: In both models, male circumcision programs resulted in large and sustained declines in HIV prevalence over time among both men and women. Men benefited somewhat more than women, but prevalence among women was also reduced substantially. With 80% male circumcision uptake, the reductions in prevalence ranged from 45% to 67% in the two "countries", and with 50% uptake, from 25% to 41%. It would take over a decade for the intervention to reach its full effect. Conclusion: Large-scale uptake of male circumcision services in African countries with high HIV prevalence, and where male circumcision is not now routinely practised, could lead to substantial reductions in HIV transmission and prevalence over time among both men and women