caCORRECT2: Improving the accuracy and reliability of microarray data in the presence of artifacts

© 2011 Moffitt et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.DOI: 10.1186/1471-2105-12-383Background. In previous work, we reported the development of caCORRECT, a novel microarray quality control system built to identify and correct spatial artifacts commonly found on Affymetrix arrays. We have made recent improvements to caCORRECT, including the development of a model-based data-replacement strategy and integration with typical microarray workflows via caCORRECT's web portal and caBIG grid services. In this report, we demonstrate that caCORRECT improves the reproducibility and reliability of experimental results across several common Affymetrix microarray platforms. caCORRECT represents an advance over state-of-art quality control methods such as Harshlighting, and acts to improve gene expression calculation techniques such as PLIER, RMA and MAS5.0, because it incorporates spatial information into outlier detection as well as outlier information into probe normalization. The ability of caCORRECT to recover accurate gene expressions from low quality probe intensity data is assessed using a combination of real and synthetic artifacts with PCR follow-up confirmation and the affycomp spike in data. The caCORRECT tool can be accessed at the website: http://cacorrect.bme.gatech.edu webcite. Results. We demonstrate that (1) caCORRECT's artifact-aware normalization avoids the undesirable global data warping that happens when any damaged chips are processed without caCORRECT; (2) When used upstream of RMA, PLIER, or MAS5.0, the data imputation of caCORRECT generally improves the accuracy of microarray gene expression in the presence of artifacts more than using Harshlighting or not using any quality control; (3) Biomarkers selected from artifactual microarray data which have undergone the quality control procedures of caCORRECT are more likely to be reliable, as shown by both spike in and PCR validation experiments. Finally, we present a case study of the use of caCORRECT to reliably identify biomarkers for renal cell carcinoma, yielding two diagnostic biomarkers with potential clinical utility, PRKAB1 and NNMT. Conclusions. caCORRECT is shown to improve the accuracy of gene expression, and the reproducibility of experimental results in clinical application. This study suggests that caCORRECT will be useful to clean up possible artifacts in new as well as archived microarray data

Inflation and Brane Gases

We investigate a new way of realizing a period of cosmological inflation in the context of brane gas cosmology. It is argued that a gas of co-dimension one branes, out of thermal equilibrium with the rest of the matter, has an equation of state which can - after stabilization of the dilaton - lead to power-law inflation of the bulk. The most promising implementation of this mechanism might be in Type IIB superstring theory, with inflation of the three large spatial dimensions triggered by ``stabilized embedded 2-branes''. Possible applications and problems with this proposal are discussed.Comment: 7 pages, uses REVTeX, version to appear in Phys. Rev.

Engineering Rubisco to change its catalytic properties

Abstract The initial steps of carbon assimilation and photorespiration are catalysed by ribulose-1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39). Natural variation in the kinetic properties of the enzyme suggest that it is possible to alter the enzyme to favour the carboxylation activity relative to oxygenation. Mutagenesis in vitro of the gene encoding the large subunit of the enzyme from Anacystis nidulans has been used to modify catalytic properties. Residues at the C-terminal end of loop 6 of the β/α barrel structure of the large subunit influence specificity towards the gaseous substrates, CO2 and O2. None of the residues altered by mutagenesis appear to interact directly with the transition state analogue and their effect on the reaction of the enediolate intermediate with the gaseous substrates and stabilization of the resulting transition state intermediates by lysine 334 must be indirect. Interactions with other parts of the enzyme must also be important in determining substrate specificity. Backbone carbonyl groups close to lysine 334 interact with lysine 128; mutation of lysine 128 to residues of less positive polarity reduces enzyme activity and favours oxygenation relative to carboxylation. The likely effects on assimilation rates of altering the kinetic properties of Rubisco have been modelled. A leaf with cyanobacterial Rubisco may out-perform a higher plant Rubisco at elevated CO2 and cool temperatures.</jats:p

Can a key boreal Calanus copepod species now complete its life-cycle in the Arctic? Evidence and implications for Arctic food-webs

The changing Arctic environment is affecting zooplankton that support its abundant wildlife. We examined how these changes are influencing a key zooplankton species, Calanus finmarchicus, principally found in the North Atlantic but expatriated to the Arctic. Close to the ice-edge in the Fram Strait, we identified areas that, since the 1980s, are increasingly favourable to C. finmarchicus. Field-sampling revealed part of the population there to be capable of amassing enough reserves to overwinter. Early developmental stages were also present in early summer, suggesting successful local recruitment. This extension to suitable C. finmarchicus habitat is most likely facilitated by the long-term retreat of the ice-edge, allowing phytoplankton to bloom earlier and for longer and through higher temperatures increasing copepod developmental rates. The increased capacity for this species to complete its life-cycle and prosper in the Fram Strait can change community structure, with large consequences to regional food-webs

(Un)twisted: talking back to media representations of eating disorders

In 2014-15, there were several news reports about a rise in the diagnoses and treatment of eating disorders (EDs), as attributed to the use of image-driven social media. Such coverage can be situated within a long history of concern in which those diagnosed with an ED are constructed as ‘especially vulnerable’ to the power of media images – a subjectivity which is pathologised and devalued precisely through its association with femininity. The most incisive objections to EDs being presented as a response to the ‘weight’ of media representation have come from Abigail Bray (2005) in her work on how anorexia is constructed as a reading as well as an eating disorder. Indeed, there is a whole history of empirical work in Feminist Media Studies and Girlhood Studies which has challenged the pernicious construction of female subjectivity as ‘excessively’ invested in, and ‘damaged’ by, the consumption of mass mediated forms. Yet the media consumption practices of those with experience of an ED have not been subject to similar feminist re-evaluation – an omission which this research seeks to address. In exploring the results of 17 semi-structured interviews with people who have experience of an ED discussing their encounters with media representations of EDs (material that is often co-opted into debates about the ‘toxic’ nature of media culture in this regard), this article seeks to intervene in how such imagined media consumption practices are often defined. In seeking to speak back to historically pathologising constructions, the article seeks to explore the qualitative responses in the context of more ‘every day’ understandings of media engagement, thus working against the gendered othering which has persistently occurred

The Intentional Use of Service Recovery Strategies to Influence Consumer Emotion, Cognition and Behaviour

Service recovery strategies have been identified as a critical factor in the success of. service organizations. This study develops a conceptual frame work to investigate how specific service recovery strategies influence the emotional, cognitive and negative behavioural responses of . consumers., as well as how emotion and cognition influence negative behavior. Understanding the impact of specific service recovery strategies will allow service providers' to more deliberately and intentionally engage in strategies that result in positive organizational outcomes. This study was conducted using a 2 x 2 between-subjects quasi-experimental design. The results suggest that service recovery has a significant impact on emotion, cognition and negative behavior. Similarly, satisfaction, negative emotion and positive emotion all influence negative behavior but distributive justice has no effect

The facilitating factors and barriers encountered in the adoption of a humanized birth care approach in a highly specialized university affiliated hospital

<p>Abstract</p> <p>Background</p> <p>Considering the fact that a significant proportion of high-risk pregnancies are currently referred to tertiary level hospitals; and that a large proportion of low obstetric risk women still seek care in these hospitals, it is important to explore the factors that influence the childbirth experience in these hospitals, particularly, the concept of humanized birth care.</p> <p>The aim of this study was to explore the organizational and cultural factors, which act as barriers or facilitators in the provision of humanized obstetrical care in a highly specialized, university-affiliated hospital in Quebec province, in Canada.</p> <p>Methods</p> <p>A single case study design was chosen. The study sample included 17 professionals and administrators from different disciplines, and 157 women who gave birth in the hospital during the study. The data was collected through semi-structured interviews, field notes, participant observations, a self-administered questionnaire, documents, and archives. Both descriptive and qualitative deductive content analyses were performed and ethical considerations were respected.</p> <p>Results</p> <p>Both external and internal dimensions of a highly specialized hospital can facilitate or be a barrier to the humanization of birth care practices in such institutions, whether independently, or altogether. The greatest facilitating factors found were: caring and family- centered model of care, professionals' and administrators' ambient for the provision of humanized birth care besides the medical interventional care which is tailored to improve safety, assurance, and comfort for women and their children, facilities to provide a pain-free birth, companionship and visiting rules, dealing with the patients' spiritual and religious beliefs. The most cited barriers were: the shortage of health care professionals, the lack of sufficient communication among the professionals, the stakeholders' desire for specialization rather than humanization, over estimation of medical performance, finally the training environment of the hospital leading to the presence of too many health care professionals, and consequently, a lack of privacy and continuity of care.</p> <p>Conclusion</p> <p>The argument of medical intervention and technology at birth being an opposing factor to the humanization of birth was not seen to be an issue in the studied highly specialized university affiliated hospital.</p

Evaluating the use of dominant microbial consumers (testate amoebae) as indicators of blanket peatland restoration

Peatlands represent globally-important ecosystems and carbon stores. However, large areas of peatland have been drained for agriculture, or peat has been harvested for use as fuel or in horticulture. Increasingly, these landscapes are being restored through ditch blocking and rewetting primarily to improve biodiversity and promote peat accumulation. To date we have little knowledge of how these interventions influence the microbial communities in peatlands. We compared the responses of dominant microbial consumers (testate amoebae) to drainage ditch restoration relative to unblocked ditches in a UK upland blanket peatland (Migneint, North Wales). Two techniques were used for restoration: (i) dammed ditches with re-profiling; and (ii) dammed ditches with pools of open water behind each dam. Testate communities in the inter-ditch areas changed markedly over time and between treatments illustrating the potential of this group of organisms as indicators of blanket peatland restoration status. However, the responses of testate amoebae to peat rewetting associated with restoration were partially obscured by inter-annual variability in weather conditions through the course of the experiment. Although there was considerable variability in the response of testate amoebae communities to peatland drain blocking, there were clearly more pronounced changes in samples from the dammed and reprofiled treatments including an increase in diversity, and the appearance of unambiguous wet-indicator species in relatively high abundances (including Amphitrema stenostoma, Archerella flavum, Arcella discoides type, Difflugia bacillifera and Difflugia bacillarium). This reflects a shift towards overall wetter conditions across the site and the creation of new habitats. However, water-table was not a significant control on testate amoebae in this case, suggesting a poor relationship between water table and surface moisture in this sloping blanket peatland. Our findings highlight the potential of testate amoebae as bioindicators of peatland restoration success; however, there is a need for caution as mechanisms driving change in the microbial communities may be more complex than first assumed. Several factors need to be taken into account when implementing biomonitoring studies in peatlands including: (i) the natural variability of the peatland ecosystem under changing weather conditions; (ii) any disturbance connected with the restoration procedures; and (iii) the timescales over which the ecosystem responds to the management intervention. Our results also suggest an indicator species approach based on population dynamics may be more appropriate for biomonitoring peatland restoration than examining changes at the community level

Can forest management based on natural disturbances maintain ecological resilience?

Given the increasingly global stresses on forests, many ecologists argue that managers must maintain ecological resilience: the capacity of ecosystems to absorb disturbances without undergoing fundamental change. In this review we ask: Can the emerging paradigm of natural-disturbance-based management (NDBM) maintain ecological resilience in managed forests? Applying resilience theory requires careful articulation of the ecosystem state under consideration, the disturbances and stresses that affect the persistence of possible alternative states, and the spatial and temporal scales of management relevance. Implementing NDBM while maintaining resilience means recognizing that (i) biodiversity is important for long-term ecosystem persistence, (ii) natural disturbances play a critical role as a generator of structural and compositional heterogeneity at multiple scales, and (iii) traditional management tends to produce forests more homogeneous than those disturbed naturally and increases the likelihood of unexpected catastrophic change by constraining variation of key environmental processes. NDBM may maintain resilience if silvicultural strategies retain the structures and processes that perpetuate desired states while reducing those that enhance resilience of undesirable states. Such strategies require an understanding of harvesting impacts on slow ecosystem processes, such as seed-bank or nutrient dynamics, which in the long term can lead to ecological surprises by altering the forest's capacity to reorganize after disturbance

Global-scale climate impact functions: the relationship between climate forcing and impact

Although there is a strong policy interest in the impacts of climate change corresponding to different degrees of climate change, there is so far little consistent empirical evidence of the relationship between climate forcing and impact. This is because the vast majority of impact assessments use emissions-based scenarios with associated socio-economic assumptions, and it is not feasible to infer impacts at other temperature changes by interpolation. This paper presents an assessment of the global-scale impacts of climate change in 2050 corresponding to defined increases in global mean temperature, using spatially-explicit impacts models representing impacts in the water resources, river flooding, coastal, agriculture, ecosystem and built environment sectors. Pattern-scaling is used to construct climate scenarios associated with specific changes in global mean surface temperature, and a relationship between temperature and sea level used to construct sea level rise scenarios. Climate scenarios are constructed from 21 climate models to give an indication of the uncertainty between forcing and response. The analysis shows that there is considerable uncertainty in the impacts associated with a given increase in global mean temperature, due largely to uncertainty in the projected regional change in precipitation. This has important policy implications. There is evidence for some sectors of a non-linear relationship between global mean temperature change and impact, due to the changing relative importance of temperature and precipitation change. In the socio-economic sectors considered here, the relationships are reasonably consistent between socio-economic scenarios if impacts are expressed in proportional terms, but there can be large differences in absolute terms. There are a number of caveats with the approach, including the use of pattern-scaling to construct scenarios, the use of one impacts model per sector, and the sensitivity of the shape of the relationships between forcing and response to the definition of the impact indicator