bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying Salmon‐Derived Nutrient Loads from the Mortality of Hatchery‐Origin Juvenile Chinook Salmon in the Snake River Basin
Authors: Warren Dana R. , McClure Michelle M.
Published: August 2012

Hatchery supplementation of anadromous salmon is extensive across the Pacific Northwest region with millions of juvenile salmon stocked annually. The influence of hatchery‐origin fish as prey items in recipient ecosystems has been explored, but influences of these fish on broader stream nutrient dynamics has not been well‐studied. Salmon‐derived nutrients (SDN) associated with the mortality of adult anadromous salmon provide key subsidies to freshwater habitats. While a number of studies have estimated current and historic SDN loading from returning wild salmon, SDN contributions from the mortality of hatchery‐origin juveniles (many of which die in the stream prior to emigration) remains largely unknown. We conducted a mass balance analysis of SDN input and export via hatchery activities (stocking and broodstock collection) in the Snake River watershed. Using Chinook salmon Oncorhynchus tshawytscha as a model species, we accounted for yearly SDN input (via hatchery‐origin juvenile fish mortality) and export (via broodstock collections and presmolt growth) over 6 years (2002–2007) in the portion of the Snake River upstream from Lower Granite Dam accessible to anadromous fish. In the year with highest smolt mortality (2003), hatchery‐origin smolt mortality provided a net input of SDN equivalent to approximately 8,100 returning adults. In the year with lowest smolt mortality (2004), hatchery activities collectively yielded a net loss of nutrients. Although the mass of SDN from hatchery‐origin smolts may be presented in adult equivalencies, functional influences of SDN from hatchery smolt mortality are likely to differ. Salmon‐derived nutrients from hatcheries enter food webs through largely piscivorous pathways whereas SDN from adult carcasses enter food webs through multiple pathways at multiple trophic levels. The SDN from hatchery‐origin smolts probably influence different components of the food web more than do adult carcasses and have the potential to more directly affect predator populations.
Long‐term benefits of immunoadsorption in β1‐adrenoceptor autoantibody‐positive transplant candidates with dilated cardiomyopathy
Authors: Dandel Michael , Wallukat Gerd , Englert Angela , Lehmkuhl Hans B. , Knosalla Christoph , Hetzer Roland
Published: August 2012

Aims

Prolongation of waiting times for heart transplantation (HTx) increases the need for new therapies. In short‐term follow‐up studies, immunoadsorption (IA) appeared beneficial in dilated cardiomyopathy (DCM) associated with β1‐adrenoreceptor‐autoantibodies (β1‐AABs). This study aimed to investigate the long‐term benefits of IA in HTx candidates with DCM, patients' responsiveness to IA, and the impact of β1‐AAB removal on IA results.

Methods and results

In a single‐centre retrospective study of prospectively gathered information we evaluated all β1‐AAB‐positive and ‐negative HTx candidates with end‐stage DCM [left ventricular ejection fraction (LVEF) <30%] who underwent IA between 1995 and 2005 (follow‐up thereafter: 5.3–14.7 years). As controls we used all β1‐AAB‐positive DCM patients referred for HTx during the same time period who received no IA therapy. We also looked for differences in efficacy between unspecific IA (unselective antibody removal) and specific IA (selective β1‐AAB removal). The main outcome measures were cardiac function and HTx/ventricular assist device (VAD)‐free patient survival. The probability for 5‐year HTx/VAD‐free survival for the108 β1‐AAB‐positive DCM patients who underwent unspecific IA reached 69.4 ± 4.4% and was significantly higher (P < 0.05) than for both β1‐AAB‐positive DCM patients without IA (25.4 ± 11.4%) and β1‐AAB‐negative DCM patients who also underwent IA (47.4 ± 11.5). In patients with high β1‐AAB levels, unspecific and specific IA showed the same high efficiency in β1‐AAB removal. LVEF and New York Heart Assocation class improved (P < 0.01) after both, but without differences in improvement after specific or unspecific IA. The prevalence of responders to specific and unspecific IA was similar (78.3% vs. 79.6%). In 76% of the patients with β1‐AAB reappearance, redetection of AABs coincided with worsening of cardiac function.

Conclusions

Removal of β1‐AABs by specific or unspecific IA can improve cardiac function allowing long‐term stability in end‐stage DCM, which can spare many patients from HTx or will delay HTx listing for years. In β1‐AAB‐positive DCM patients the benefits of IA appeared to be associated with the removal of these antibodies.
A comparative analysis of marine fish species susceptibilities to discard mortality: effects of environmental factors, individual traits, and phylogeny
Authors: Benoît Hugues P. , Plante Sébastien , Kroiz Molly , Hurlbut Thomas
Published: August 2012

Benoît, H. P., Plante, S., Kroiz, M., and Hurlbut, T. 2013. A comparative analysis of marine fish species susceptibilities to discard mortality: effects of environmental factors, individual traits, and phylogeny. – ICES Journal of Marine Science, 70:99–113. Determining the sustainability of fishing mortality for discards requires information on discard amounts as well as capture and release mortality rates. Formal estimates of these rates are costly and only available for a limited number of species and fisheries. In their absence, proxies for discard mortality could inform risk assessments of fishing mortality sustainability for discarded species. Here, time-to-mortality (TM) was assessed for 48 marine fish species exposed to air following capture during an annual multi-species bottom-trawl survey. Species-specific estimates of TM were related qualitatively to more formal estimates of discard mortality from commercial fisheries, confirming the use of TM as a proxy. The effects on TM of species and individual traits, phylogenetic similarity (proxy for traits not explicitly included in the analysis) and environmental factors related to capture were also assessed. Much of the observed individual variability was explained by intraspecific and interspecific positive relationships between body size and TM. Sedentary species and those lacking a gas bladder or deciduous scales had greater TM. Effects of phylogeny and capture depth and temperature were also found. This study demonstrates how reliable proxies of discard mortality rate can be readily obtained in the field or estimated from relevant covariates.
Physicochemical and Rheological Properties of Chinese Soft Wheat Flours and Their Relationships with Cookie‐Making Quality
Authors: Geng Zhiming , Zhang Pingping , Yao Jinbao , Yang Dan , Ma Hongxiang , Rayas‐Duarte Patricia
Published: August 2012

The relationship of solvent retention capacity (SRC) values with four solvents, alveograph and farinograph properties, and cookie‐baking performance was evaluated with 20 Chinese soft wheat genotypes, including four cultivars and 16 advanced lines grown in the 2009–2010 season. Significant positive correlations were observed between water SRC (WSRC), sodium carbonate SRC (SOSRC), lactic acid SRC, and sucrose SRC (SUSRC) values. WSRC, SUSRC, and SOSRC showed significant positive correlations with farinograph water absorption (WA), alveograph P (tenacity), and P/L (ratio of tenacity to extensibility). Cookie diameter was significantly correlated with wet gluten (r = –0.491, P < 0.05), WSRC (r = –0.882, P < 0.001), SUSRC (r = –0.620, P < 0.01), SOSRC (r = –0.712, P < 0.001), P (r = –0.787, P < 0.001), L (r = 0.616, P < 0.01), P/L (r = –0.766, P < 0.001) and WA (r = –0.620, P < 0.01), respectively. SRC values were effective predictors of cookie quality in Chinese soft wheat. Alveograph parameters were more closely correlated to cookie quality than were farinograph parameters.
Occurrence and Distribution of Triticum mosaic virus in the Central Great Plains
Authors: Byamukama E. , Seifers D. L. , Hein G. L. , De Wolf E. , Tisserat N. A. , Langham M. A. C. , Osborne L. E. , Timmerman A. , Wegulo S. N.
Published: August 2012

Wheat curl mite (WCM)-transmitted viruses—namely, Wheat streak mosaic virus (WSMV), Triticum mosaic virus (TriMV), and the High Plains virus (HPV)—are three of the wheat-infecting viruses in the central Great Plains of the United States. TriMV is newly discovered and its prevalence and incidence are largely unknown. Field surveys were carried out in Colorado, Kansas, Nebraska, and South Dakota in spring and fall 2010 and 2011 to determine TriMV prevalence and incidence and the frequency of TriMV co-infection with WSMV or HPV in winter wheat. WSMV was the most prevalent and was detected in 83% of 185 season–counties (= s-counties), 73% of 420 season–fields (= s-fields), and 35% of 12,973 samples. TriMV was detected in 32, 6, and 6% of s-counties, s-fields, and samples, respectively. HPV was detected in 34, 15, and 4% of s-counties, s-fields, and samples, respectively. TriMV was detected in all four states. In all, 91% of TriMV-positive samples were co-infected with WSMV, whereas WSMV and HPV were mainly detected as single infections. The results from this study indicate that TriMV occurs in winter wheat predominantly as a double infection with WSMV, which will complicate breeding for resistance to WCM-transmitted viruses.
Towards a general life-history model of the superorganism: predicting the survival, growth and reproduction of ant societies
Authors: Shik Jonathan Z. , Hou Chen , Kay Adam , Kaspari Michael , Gillooly James F.
Published: August 2012

Social insect societies dominate many terrestrial ecosystems across the planet. Colony members cooperate to capture and use resources to maximize survival and reproduction. Yet, when compared with solitary organisms, we understand relatively little about the factors responsible for differences in the rates of survival, growth and reproduction among colonies. To explain these differences, we present a mathematical model that predicts these three rates for ant colonies based on the body sizes and metabolic rates of colony members. Specifically, the model predicts that smaller colonies tend to use more energy per gram of biomass, live faster and die younger. Model predictions are supported with data from whole colonies for a diversity of species, with much of the variation in colony-level life history explained based on physiological traits of individual ants. The theory and data presented here provide a first step towards a more general theory of colony life history that applies across species and environments.
Theft in an ultimatum game: chimpanzees and bonobos are insensitive to unfairness
Authors: Kaiser Ingrid , Jensen Keith , Call Josep , Tomasello Michael
Published: August 2012

Humans, but not chimpanzees, punish unfair offers in ultimatum games, suggesting that fairness concerns evolved sometime after the split between the lineages that gave rise to
Homo
and
Pan
. However, nothing is known about fairness concerns in the other
Pan
species, bonobos. Furthermore, apes do not typically offer food to others, but they do react against theft. We presented a novel game, the ultimatum theft game, to both of our closest living relatives. Bonobos and chimpanzee ‘proposers’ consistently stole food from the responders' portions, but the responders did not reject any non-zero offer. These results support the interpretation that the human sense of fairness is a derived trait.
The modelling cycle for collective animal behaviour
Authors: Sumpter David J. T. , Mann Richard P. , Perna Andrea
Published: August 2012

Collective animal behaviour is the study of how interactions between individuals produce group level patterns, and why these interactions have evolved. This study has proved itself uniquely interdisciplinary, involving physicists, mathematicians, engineers as well as biologists. Almost all experimental work in this area is related directly or indirectly to mathematical models, with regular movement back and forth between models, experimental data and statistical fitting. In this paper, we describe how the modelling cycle works in the study of collective animal behaviour. We classify studies as addressing questions at different levels or linking different levels, i.e. as local, local to global, global to local or global. We also describe three distinct approaches—theory-driven, data-driven and model selection—to these questions. We show, with reference to our own research on species across different taxa, how we move between these different levels of description and how these various approaches can be applied to link levels together.
Healable thermoset polymer composite embedded with stimuli-responsive fibres
Authors: Li Guoqiang , Meng Harper , Hu Jinlian
Published: August 2012

Severe wounds in biological systems such as human skin cannot heal themselves, unless they are first stitched together. Healing of macroscopic damage in thermoset polymer composites faces a similar challenge. Stimuli-responsive shape-changing polymeric fibres with outstanding mechanical properties embedded in polymers may be able to close macro-cracks automatically upon stimulation such as heating. Here, a stimuli-responsive fibre (SRF) with outstanding mechanical properties and supercontraction capability was fabricated for the purpose of healing macroscopic damage. The SRFs and thermoplastic particles (TPs) were incorporated into regular thermosetting epoxy for repeatedly healing macroscopic damages. The system works by mimicking self-healing of biological systems such as human skin, close (stitch) then heal, i.e. close the macroscopic crack through the thermal-induced supercontraction of the SRFs, and bond the closed crack through melting and diffusing of TPs at the crack interface. The healing efficiency determined using tapered double-cantilever beam specimens was 94 per cent. The self-healing process was reasonably repeatable.
Turnover of fibrillar collagen in soft biological tissue with application to the expansion of abdominal aortic aneurysms
Authors: Martufi Giampaolo , Gasser T. Christian
Published: August 2012

A better understanding of the inherent properties of vascular tissue to adapt to its mechanical environment is crucial to improve the predictability of biomechanical simulations. Fibrillar collagen in the vascular wall plays a central role in tissue adaptation owing to its relatively short lifetime. Pathological alterations of collagen turnover may fail to result in homeostasis and could be responsible for abdominal aortic aneurysm (AAA) growth at later stages of the disease. For this reason our previously reported multiscale constitutive framework (Martufi, G. & Gasser, T. C. 2011
J. Biomech
.
44
, 2544–2550 (
doi:10.1016/j.jbiomech.2011.07.015
)) has been enriched by a collagen turnover model. Specifically, the framework's collagen fibril level allowed a sound integration of vascular wall biology, and the impact of collagen turnover on the macroscopic properties of AAAs was studied. To this end, model parameters were taken from the literature and/or estimated from clinical follow-up data of AAAs (on average 50.7 mm-large). Likewise, the
in vivo
stretch of the AAA wall was set, such that 10 per cent of collagen fibres were engaged. Results showed that the stretch spectrum, at which collagen fibrils are deposed, is the most influential parameter, i.e. it determines whether the vascular geometry grows, shrinks or remains stable over time. Most importantly, collagen turnover also had a remarkable impact on the macroscopic stress field. It avoided high stress gradients across the vessel wall, thus predicted a physiologically reasonable stress field. Although the constitutive model could be successfully calibrated to match the growth of small AAAs, a rigorous validation against experimental data is crucial to further explore the model's descriptive and predictive capabilities.
Aggregation by depletion attraction in cultures of bacteria producing exopolysaccharide
Authors: Dorken Gary , Ferguson Gail P. , French Chris E. , Poon Wilson C. K.
Published: August 2012

In bacteria, the production of exopolysaccharides—polysaccharides secreted by the cells into their growth medium—is integral to the formation of aggregates and biofilms. These exopolysaccharides often form part of a matrix that holds the cells together. Investigating the bacterium
Sinorhizobium meliloti
, we found that a mutant that overproduces the exopolysaccharide succinoglycan showed enhanced aggregation, resulting in phase separation of the cultures. However, the aggregates did not appear to be covered in polysaccharides. Succinoglycan purified from cultures was applied to different concentrations of cells, and observation of the phase behaviour showed that the limiting polymer concentration for aggregation and phase separation to occur decreased with increasing cell concentration, suggesting a ‘crowding mechanism’ was occurring. We suggest that, as found in colloidal dispersions, the presence of a non-adsorbing polymer in the form of the exopolysaccharide succinoglycan drives aggregation of
S. meliloti
by depletion attraction. This force leads to self-organization of the bacteria into small clusters of laterally aligned cells, and, furthermore, leads to aggregates clustering into biofilm-like structures on a surface.
Microstructural level response of HMX–Estane polymer-bonded explosive under effects of transient stress waves
Authors: Barua A. , Horie Y. , Zhou M.
Published: August 2012

The effect of transient stress waves on the microstructure of HMX–Estane, a polymer-bonded explosive (PBX), is studied. Calculations carried out concern microstructures with HMX grain sizes on the order of 200 μm and grain volume fractions in the range of 0.50–0.82. The microstructural samples analysed have an aspect ratio of 5:1 (15×3 mm), allowing the transient wave propagation process resulting from normal impact to be resolved. Boundary loading is effected by the imposition of impact face velocities of 50–200 m s
−1
. Different levels of grain–binder interface strength are considered. The analysis uses a recently developed cohesive finite element framework that accounts for coupled thermal–mechanical processes involving deformation, heat generation and conduction, failure in the forms of microcracks in both bulk constituents and along grain/matrix interfaces, and frictional heating along crack faces. Results show that the overall wave speed through the microstructures depends on both the grain volume fraction and interface bonding strength between the constituents and that the distance traversed by the stress wave before the initiation of frictional dissipation is independent of the grain volume fraction but increases with impact velocity. Energy dissipated per unit volume owing to fracture is highest near the impact surface and deceases to zero at the stress wavefront. On the other hand, the peak temperature rises are noted to occur approximately 2–3 mm from the impact surface. Scaling laws are developed for the maximum dissipation rate and the highest temperature rise as functions of impact velocity, grain volume fraction and grain–binder interfacial bonding strength.
Predation risk, stoichiometric plasticity and ecosystem elemental cycling
Authors: Leroux Shawn J. , Hawlena Dror , Schmitz Oswald J.
Published: August 2012

It is widely held that herbivore growth and production is limited by dietary nitrogen (N) that in turn constrains ecosystem elemental cycling. Yet, emerging evidence suggests that this conception of limitation may be incomplete, because chronic predation risk heightens herbivore metabolic rate and shifts demand from N-rich proteins to soluble carbohydrate–carbon (C). Because soluble C can be limiting, predation risk may cause ecosystem elemental cycling rates and stoichiometric balance to depend on herbivore physiological plasticity. We report on a stoichiometrically explicit ecosystem model that investigates this problem. The model tracks N, and soluble and recalcitrant C through ecosystem compartments. We evaluate how soluble plant C influences C and N stocks and flows in the presence and absence of predation risk. Without risk, herbivores are limited by N and respire excess C so that plant-soluble C has small effects only on elemental stocks and flows. With predation risk, herbivores are limited by soluble C and release excess N, so plant-soluble C critically influences ecosystem elemental stocks flows. Our results emphasize that expressing ecosystem stoichiometric balance using customary C : N ratios that do not distinguish between soluble and recalcitrant C may not adequately describe limitations on elemental cycling.
Do different ‘magnocellular tasks’ probe the same neural substrate?
Authors: Goodbourn Patrick T. , Bosten Jenny M. , Hogg Ruth E. , Bargary Gary , Lawrance-Owen Adam J. , Mollon J. D.
Published: August 2012

The sensory abnormalities associated with disorders such as dyslexia, autism and schizophrenia have often been attributed to a generalized deficit in the visual magnocellular–dorsal stream and its auditory homologue. To probe magnocellular function, various psychophysical tasks are often employed that require the processing of rapidly changing stimuli. But is performance on these several tasks supported by a common substrate? To answer this question, we tested a cohort of 1060 individuals on four ‘magnocellular tasks’: detection of low-spatial-frequency gratings reversing in contrast at a high temporal frequency (so-called
frequency-doubled
gratings); detection of pulsed low-spatial-frequency gratings on a steady luminance pedestal; detection of coherent motion; and auditory discrimination of temporal order. Although all tasks showed test–retest reliability, only one pair shared more than 4 per cent of variance. Correlations within the set of ‘magnocellular tasks’ were similar to the correlations between those tasks and a ‘non-magnocellular task’, and there was little consistency between ‘magnocellular deficit’ groups comprising individuals with the lowest sensitivity for each task. Our results suggest that different ‘magnocellular tasks’ reflect different sources of variance, and thus are not general measures of ‘magnocellular function’.
Towards an integrated network of coral immune mechanisms
Authors: Palmer C. V. , Traylor-Knowles N.
Published: August 2012

Reef-building corals form bio-diverse marine ecosystems of high societal and economic value, but are in significant decline globally due, in part, to rapid climatic changes. As immunity is a predictor of coral disease and thermal stress susceptibility, a comprehensive understanding of this new field will likely provide a mechanistic explanation for ecological-scale trends in reef declines. Recently, several strides within coral immunology document defence mechanisms that are consistent with those of both invertebrates and vertebrates, and which span the recognition, signalling and effector response phases of innate immunity. However, many of these studies remain discrete and unincorporated into the wider fields of invertebrate immunology or coral biology. To encourage the rapid development of coral immunology, we comprehensively synthesize the current understanding of the field in the context of general invertebrate immunology, and highlight fundamental gaps in our knowledge. We propose a framework for future research that we hope will stimulate directional studies in this emerging field and lead to the elucidation of an integrated network of coral immune mechanisms. Once established, we are optimistic that coral immunology can be effectively applied to pertinent ecological questions, improve current prediction tools and aid conservation efforts.
A novel RNAi protein, Dsh1, assembles RNAi machinery on chromatin to amplify heterochromatic siRNA
Authors: Kawakami Kei , Hayashi Aki , Nakayama Jun-ichi , Murakami Yota
Published: August 2012

In fission yeast, siRNA is generated from pericentromeric noncoding RNA by the RNAi machinery. siRNA synthesis and heterochromatin formation are interdependent, forming a self-reinforcing loop on chromatin. In this system, siRNA is amplified by the RNA-dependent RNA polymerase complex (RDRC) and the endoribonuclease Dcr1, which synthesizes dsRNA and processes the dsRNA, respectively. The amplification is essential for stable heterochromatin formation. Here, a novel gene, dsh1+ (defect of the gene silencing at centromeric heterochromatin), is identified as an essential component of RNAi-directed heterochromatin assembly. Loss of dsh1+ abolishes normal RNAi function and heterochromatic gene silencing at pericentromeres. Dsh1 interacts with Dcr1 and RDRC and couples the reactions of both proteins to the effective production of siRNA in vivo. Dsh1 binds to heterochromatin in the absence of RDRC, while RDRC requires Dsh1 for its chromatin-binding activity, suggesting that Dsh1 recruits RDRC to chromatin. Immunofluorescence analysis shows that Dsh1 forms foci at the nuclear periphery, and some Dsh1 foci colocalize with Dcr1 and RDRC. Dsh1 is required for the colocalization of Dcr1 and RDRC. Moreover, loss of the nuclear periphery localization of Dsh1 abolishes Dsh1 function. Taken together, these results suggest that Dsh1 assembles the RNAi machinery on heterochromatin and forms a perinuclear compartment for amplification of heterochromatic siRNA.
Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1
Authors: Kubicek Karel , Cerna Hana , Holub Peter , Pasulka Josef , Hrossova Dominika , Loehr Frank , Hofr Ctirad , Vanacova Stepanka , Stefl Richard
Published: August 2012

Recruitment of appropriate RNA processing factors to the site of transcription is controlled by post-translational modifications of the C-terminal domain (CTD) of RNA polymerase II (RNAP II). Here, we report the solution structure of the Ser5 phosphorylated (pSer5) CTD bound to Nrd1. The structure reveals a direct recognition of pSer5 by Nrd1 that requires thecisconformation of the upstream pSer5–Pro6 peptidyl-prolyl bond of the CTD. Mutations at the complex interface diminish binding affinity and impair processing or degradation of noncoding RNAs. These findings underpin the interplay between covalent and noncovalent changes in the CTD structure that constitute the CTD code.
The intermediate-activityL597VBRAF mutant acts as an epistatic modifier of oncogenic RAS by enhancing signaling through the RAF/MEK/ERK pathway
Authors: Andreadi Catherine , Cheung Lai-Kay , Giblett Susan , Patel Bipin , Jin Hong , Mercer Kathryn , Kamata Tamihiro , Lee Pearl , Williams Alexander , McMahon Martin , Marais Richard , Pritchard Catrin
Published: August 2012

L597VBRAFmutations are acquired somatically in human cancer samples and are frequently coincident withRASmutations. GermlineL597VBRAFmutations are also found in several autosomal dominant developmental conditions known as RASopathies, raising the important question of how the same mutation can contribute to both pathologies. Using a conditional knock-in mouse model, we show that endogenous expression ofL597VBraf leads to approximately twofold elevated Braf kinase activity and weak activation of the Mek/Erk pathway. This is associated with induction of RASopathy hallmarks including cardiac abnormalities and facial dysmorphia but is not sufficient for tumor formation. We combinedL597VBraf withG12DKras and found thatL597VBraf modifiedG12DKras oncogenesis such that fibroblast transformation and lung tumor development were more reminiscent of that driven by the high-activityV600EBraf mutant. Mek/Erk activation levels were comparable with those driven byV600EBraf in the double-mutant cells, and the gene expression signature was more similar to that induced byV600EBraf thanG12DKras. However, unlikeV600EBraf, Mek/Erk pathway activation was mediated by both Craf and Braf, and ATP-competitive RAF inhibitors induced paradoxical Mek/Erk pathway activation. Our data show that weak activation of the Mek/Erk pathway underpins RASopathies, but in cancer,L597VBraf epistatically modifies the transforming effects of driver oncogenes.
A role for Rho-dependent polarity in gene regulation by a noncoding small RNA
Authors: Bossi Lionello , Schwartz Annie , Guillemardet Benoit , Boudvillain Marc , Figueroa-Bossi Nara
Published: August 2012

Gene regulation by bacterial trans-encoded small RNAs (sRNAs) is generally regarded as a post-transcriptional process bearing exclusively on the translation and/or the stability of target messenger RNA (mRNA). The work presented here revealed the existence of a transcriptional component in the regulation of a bicistronic operon—the chiPQ locus—by the ChiX sRNA in Salmonella. By studying the mechanism by which ChiX, upon pairing near the 5′ end of the transcript, represses the distal gene in the operon, we discovered that the action of the sRNA induces Rho-dependent transcription termination within the chiP cistron. Apparently, by inhibiting chiP mRNA translation cotranscriptionally, ChiX uncouples translation from transcription, causing the nascent mRNA to become susceptible to Rho action. A Rho utilization (rut) site was identified in vivo through mutational analysis, and the termination pattern was characterized in vitro with a purified system. Remarkably, Rho activity at this site was found to be completely dependent on the function of the NusG protein both in vivo and in vitro. The recognition that trans-encoded sRNA act cotranscriptionally unveils a hitherto neglected aspect of sRNA function in bacteria.
Human intron-encoded Alu RNAs are processed and packaged into Wdr79-associated nucleoplasmic box H/ACA RNPs
Authors: Jády Beáta E. , Ketele Amandine , Kiss Tamás
Published: August 2012

Alu repetitive sequences are the most abundant short interspersed DNA elements in the human genome. Full-length Alu elements are composed of two tandem sequence monomers, the left and right Alu arms, both derived from the 7SL signal recognition particle RNA. Since Alu elements are common in protein-coding genes, they are frequently transcribed into pre-mRNAs. Here, we demonstrate that the right arms of nascent Alu transcripts synthesized within pre-mRNA introns are processed into metabolically stable small RNAs. The intron-encoded Alu RNAs, termed AluACA RNAs, are structurally highly reminiscent of box H/ACA small Cajal body (CB) RNAs (scaRNAs). They are composed of two hairpin units followed by the essential H (AnAnnA) and ACA box motifs. The mature AluACA RNAs associate with the four H/ACA core proteins: dyskerin, Nop10, Nhp2, and Gar1. Moreover, the 3′ hairpin of AluACA RNAs carries two closely spaced CB localization motifs, CAB boxes (UGAG), which bind Wdr79 in a cumulative fashion. In contrast to canonical H/ACA scaRNPs, which concentrate in CBs, the AluACA RNPs accumulate in the nucleoplasm. Identification of 348 human AluACA RNAs demonstrates that intron-encoded AluACA RNAs represent a novel, large subgroup of H/ACA RNAs, which are apparently confined to human or primate cells.
Environmental factors regulating the recruitment of walleye Sander vitreus and white bass Morone chrysops in irrigation reservoirs
Authors: DeBoer Jason A. , Pope Kevin L. , Koupal Keith D.
Published: August 2012

Understanding the environmental factors that regulate fish recruitment is essential for effective management of fisheries. Generally, first‐year survival, and therefore recruitment, is inherently less consistent in systems with high intra‐ and interannual variability. Irrigation reservoirs display sporadic patterns of annual drawdown, which can pose a substantial challenge to recruitment of fishes. We developed species‐specific models using an 18‐year data set compiled from state and federal agencies to investigate variables that regulate the recruitment of walleye Sander vitreus and white bass Morone chrysops in irrigation reservoirs in south‐west Nebraska, USA. The candidate model set for walleye included only abiotic variables (water‐level elevation, minimum daily air temperature during winter prior to hatching, annual precipitation, spring warming rate and May reservoir discharge), and the candidate model set for white bass included primarily biotic variables (catch per unit effort (CPUE) of black crappie Pomoxis nigromaculatus, CPUE of age‐0 walleye, CPUE of bluegill Lepomis macrochirus and CPUE of age‐3 and older white bass), each of which had a greater relative importance than the single abiotic variable (minimum daily air temperature during winter after hatching). Our findings improve the understanding of the recruitment of fishes in irrigation reservoirs and the relative roles of abiotic and biotic factors.
Forecasting extinction risk of ectotherms under climate warming: an evolutionary perspective
Authors: Walters Richard J. , Blanckenhorn Wolf U. , Berger David
Published: August 2012

It has been postulated that climate warming may pose the greatest threat species in the tropics, where ectotherms have evolved more thermal specialist physiologies. Although species could rapidly respond to environmental change through adaptation, little is known about the potential for thermal adaptation, especially in tropical species.

In the light of the limited empirical evidence available and predictions from mutation‐selection theory, we might expect tropical ectotherms to have limited genetic variance to enable adaptation. However, as a consequence of thermodynamic constraints, we might expect this disadvantage to be at least partially offset by a fitness advantage, that is, the ‘hotter‐is‐better’ hypothesis.

Using an established quantitative genetics model and metabolic scaling relationships, we integrate the consequences of the opposing forces of thermal specialization and thermodynamic constraints on adaptive potential by evaluating extinction risk under climate warming. We conclude that the potential advantage of a higher maximal development rate can in theory more than offset the potential disadvantage of lower genetic variance associated with a thermal specialist strategy.

Quantitative estimates of extinction risk are fundamentally very sensitive to estimates of generation time and genetic variance. However, our qualitative conclusion that therelativerisk of extinction is likely to be lower for tropical species than for temperate species is robust to assumptions regarding the effects of effective population size, mutation rate and birth rate per capita.

With a view to improving ecological forecasts, we use this modelling framework to review the sensitivity of our predictions to the model's underpinning theoretical assumptions and the empirical basis of macroecological patterns that suggest thermal specialization and fitness increase towards the tropics. We conclude by suggesting priority areas for further empirical research.
Hope in people with cancer: a multivariate analysis from Turkey
Authors: Kavradim Selma Turan , Özer Zeynep Canli , Bozcuk Hakan
Published: August 2012

Aim

The study was planned to determine the hope levels of people with cancer and the variables affecting hope.

Background

Hope is essential for patient well‐being and positively correlated with improved coping skill.

Design

A descriptive and exploratory design.

Methods

The study sample included 240 consecutive patients treated with chemotherapy and attending the Day Chemotherapy Unit of a University Hospital in Turkey. The study was conducted between December 2009–January 2010. Personal Information Form and Herth Hope Scale were used for data collection. The determinants and subscales of hope were evaluated with univariate and multivariate regression analyses.

Results

These mean scores showed high levels of hope among the patients included in the study. It was found that net family income, knowledge level about the disease, feeling of improvement, perception of satisfactory family support by the patient, mouth ulcers, feeling anxious or worried and presence of fear were independently related with the total hope score.

Conclusions

The study results showed high levels of hope among the participating patients. It is concluded that physical, financial and psychological well‐being and information and support needs are directly and independently related with hope in people with cancer. These findings support the need for clinicians to continue to practise and implement hope fostering/hindering interventions among their patients.
Lesbian co‐mothers' experiences of maternity healthcare services
Authors: Cherguit Jasmina , Burns Jan , Pettle Sharon , Tasker Fiona
Published: August 2012

Aim

This article is a report of a study of lesbian co‐mothers' experiences of UK maternity healthcare services.

Background

With the increase in fertility provision to lesbian couples, maternity healthcare services are increasingly coming into contact with lesbian co‐mothers. Literature highlights the need to investigate donor‐conceived lesbian families and an absence of research focusing on the unique experiences of co‐mothers in the maternity process.

Design

The study followed a qualitative design and interpretative phenome‐nological analysis methodology.

Methods

A qualitative study was carried out involving ten lesbian co‐mothers, whose children were conceived via anonymous donor insemination to their partners. Data collection took place between May–September 2009.

Findings

Interpretative phenomenological analysis revealed two main types of co‐mothers' experiences, those connected with maternity service structures and interpersonal experiences with maternity care staff. Co‐mothers felt excluded by heterocentric organizational service structures. However, the co‐mothers' overwhelming experiences with staff were positive and inclusive. Despite this, co‐mothers reported that any ambiguous or non‐inclusive experiences with professionals left them questioning whether these experiences were due to homophobic attitudes or professional incompetence.

Conclusion

The results indicate that these lesbian co‐mothers felt predominantly included and accepted by maternity services. Ambiguous interpersonal experiences, however, evoked doubts in this regard. In addition, organizational heterocentric structural barriers remain. Structural service delivery changes could facilitate co‐mothers' feelings of inclusion and highlight the important role practitioners have in contributing to co‐mothers' experiences.
The dual nature of medical enculturation in postgraduate medical training and practice
Authors: Gordon Jill , Markham Pippa , Lipworth Wendy , Kerridge Ian , Little Miles
Published: August 2012

Medical Education 2012: 46: 894–902

Objectives  Enculturation is a normal and continuing part of human development. This study examined how medical graduates perceive the process of enculturation after graduation.

Methods  We conducted a qualitative study of the values of medical graduates associated with Sydney Medical School to identify processes that contribute to the ongoing process of enculturation.

Results  Two processes contributing to the process of enculturation were identified. Participants were aware of having passively absorbed the explicit and implicit culture of medicine, and of having actively sought to assimilate (or to avoid assimilating) the medical culture. The processes of enculturation were particularly evident in relation to three major concerns: competence; patient‐centredness, and self‐care.

Conclusions  The participants in this study demonstrated the capacity to reflect on and differentiate between two types of enculturation: absorption and assimilation. They were aware of the impacts of enculturation with respect to three main sets of values that are, respectively, epistemic, interpersonal and personal. Faculty development programmes might benefit from paying explicit attention to the process of enculturation and its influence on learning and practice.
More than an education: the hidden curriculum, professional attitudes and career choice
Authors: Phillips Susan P , Clarke Matthew
Published: August 2012

Medical Education 2012: 46: 887–893

Objectives  In this qualitative study we examine how teachers’ egalitarian or discriminatory behaviours and values at odds with those of the individual learner or the institution are perceived and absorbed by students, and how this hidden curriculum shapes the doctors students become.

Methods  During 2011, a total of 120 randomly selected medical students from each class at three Canadian medical schools were electronically asked for examples of teachers’ words, attitudes or behaviours that discriminated against or promoted equality towards a group or groups of doctors or patients. We examined the content of participants’ examples of unexpected messages and their reactions to these. Responses were aggregated, sorted and coded for conceptual themes. An independent qualitative researcher repeated the analytic process and then engaged in discussion with us to reach consensus on themes and meanings.

Results  The 76 (63%) respondents noted that attitudes in keeping with universally held, institutional values of equality towards, for example, homosexuals or marginalised populations were expressed, but also described role‐modelling at odds with this. Patient characteristics such as obesity, drug abuse, mental illness and poverty were presented as signs of individual weakness or moral failing. Some teachers assumed immigrant status based on a student’s or patient’s skin colour or last name. Respondents described how women in medicine were maligned as potential surgeons and were expected to put family before career. Teachers denigrated doctors from specialties other than their own. Students reacted to discordant role‐modelling by challenging, dissociating themselves, with silence or with confusion followed by attempts at individual transformation to realign careers and behaviours with those of teachers.

Conclusions  When teaching contradicts institutional or learners’ values, or is particularly inspiring, students notice and may be influenced to the extent that they rethink personal beliefs and plans to fit their future doctor selves to these models.
Evaluations of situational judgement tests to assess non‐academic attributes in selection
Authors: Patterson Fiona , Ashworth Victoria , Zibarras Lara , Coan Philippa , Kerrin Maire , O’Neill Paul
Published: August 2012

Medical Education 2012: 46: 850–868

Objectives  This paper presents a systematic review of the emerging international research evidence for the use of situational judgement tests (SJTs) for testing important non‐academic attributes (such as empathy, integrity and resilience) in selection processes.

Methods  Several databases (e.g. MEDLINE, PsycINFO, Web of Science) were searched to retrieve empirical studies relating to SJTs published between 1990 and 2010. Personal contact with experts in the field was made to identify any unpublished research or work in progress to obtain the most current material. Finally, reference lists were checked to access other relevant journal articles and further research. All research studies were required to meet specific inclusion criteria selected by two independent reviewers.

Results  Over 1000 citations were identified during the initial literature search; following the review of abstracts, full‐text copies of 76 articles were retrieved and evaluated. A total of 39 articles that adequately met the inclusion criteria were included in the final review. The research evidence shows that, compared with personality and IQ tests, SJTs have good levels of reliability, predictive validity and incremental validity for testing a range of professional attributes, such as empathy and integrity.

Conclusions  SJTs can be designed to test a broad range of non‐academic constructs depending on the selection context. As a relatively low‐fidelity assessment, SJTs are a cost‐efficient methodology compared with high‐fidelity assessments of non‐academic attributes, such as those used in objective structured clinical examinations. In general, SJTs are found to demonstrate less adverse impact than IQ tests and are positively received by candidates. Further research is required to explore theoretical developments and the underlying construct validity of SJTs.
Representing complexity well: a story about teamwork, with implications for how we teach collaboration
Authors: Lingard Lorelei , McDougall Allan , Levstik Mark , Chandok Natasha , Spafford Marlee M , Schryer Catherine
Published: August 2012

Medical Education 2012: 46: 869–877

Objectives  In order to be relevant and impactful, our research into health care teamwork needs to better reflect the complexity inherent to this area. This study explored the complexity of collaborative practice on a distributed transplant team. We employed the theoretical lenses of activity theory to better understand the nature of collaborative complexity and its implications for current approaches to interprofessional collaboration (IPC) and interprofessional education (IPE).

Methods  Over 4 months, two trained observers conducted 162 hours of observation, 30 field interviews and 17 formal interviews with 39 members of a solid organ transplant team in a Canadian teaching hospital. Participants included consultant medical and surgical staff and postgraduate trainees, the team nurse practitioner, social worker, dietician, pharmacist, physical therapist, bedside nurses, organ donor coordinators and organ recipient coordinators. Data collection and inductive analysis for emergent themes proceeded iteratively.

Results  Daily collaborative practice involves improvisation in the face of recurring challenges on a distributed team. This paper focuses on the theme of ‘interservice’ challenges, which represent instances in which the ‘core’ transplant team (those providing daily care for transplant patients) work to engage the expertise and resources of other services in the hospital, such as those of radiology and pathology departments. We examine a single story of the core team’s collaboration with cardiology, anaesthesiology and radiology services to decide whether a patient is appropriate for transplantation and use this story to consider the team’s strategies in the face of conflicting expectations and preferences among these services.

Conclusions  This story of collaboration in a distributed team calls into question two premises underpinning current models of IPC and IPE: the notion that stable professional roles exist, and the ideal of a unifying objective of ‘caring for the patient’. We suggest important elaborations to these premises as they are used to conceptualise and teach IPC in order to better represent the intricacy of everyday collaborative work in health care.