Multiplexed quantitative proteomics using differential metabolic 15N-labeling

There are several advantages of using metabolic labeling in quantitative proteomics. The early pooling of samples compared to post-labeling methods eliminates errors from different sample processing, protein extraction and enzymatic digestion. Metabolic labeling is also highly efficient and relatively inexpensive compared to commercial labeling reagents. However, methods for multiplexed quantitation in the MS-domain (or ‘non-isobaric’ methods), suffer from signal dilution at higher degrees of multiplexing, as the MS/MS signal for peptide identification is lower given the same amount of peptide loaded onto the column or injected into the mass spectrometer. This may partly be overcome by mixing the samples at non-uniform ratios, for instance by increasing the fraction of unlabeled proteins. We have developed an algorithm for arbitrary degrees of nonisobaric multiplexing for relative protein abundance measurements. We have used metabolic labeling with different levels of 15N, but the algorithm is in principle applicable to any isotope or combination of isotopes. Ion trap mass spectrometers are fast and suitable for LC-MS/MS and peptide identification. However, they cannot resolve overlapping isotopic envelopes from different peptides, which makes them less suitable for MS-based quantitation. Fourier-transform ion cyclotron resonance (FTICR) mass spectrometry is less suitable for LC-MS/MS, but provides the resolving power required to resolve overlapping isotopic envelopes. We therefore combined ion trap LC-MS/MS for peptide identification with FTICR LC-MS for quantitation using chromatographic alignment. We applied the method in a heat shock study in a plant model system (A. thaliana) and compared the results with gene expression data from similar experiments in literature.

Aidos

Aidos, an abstraction whose meaning ranges from shame to modesty, is personified in literature (Hani 1980) but not art (Cairns 1996). Homer contrasts aidos, personal shame, with Nemesis, public indignation (Scott 1980).

Aletheia

The abstract concept Aletheia, Truth, is personified in literature as a daughter of Zeus (Pind. Ol. 10.3–4 and fr. 205) and nurse of Apollo (Plut. Symp. 657e).

The child and the letter: Anne Brontë’s The Tenant of Wildfell Hall

This essay engages with the question of childhood in Anne Brontë’s The Tenant of Wildfell Hall. Despite narrating a conflict concerning child custody, childhood is a subject rarely broached by the critics of the text. Indeed, the only instance of the child being addressed in criticism grants it the power to enclose potentially subversive narrative. This is a function attributed to the framing structure of the novel by other critics. This essay returns the child to Brontë’s text as a disruptive rather than containing force. Through a detailed close analysis of the novel I track such disruptions, and the extent to which these point to wider theoretical or methodological difficulties in critical accounts of childhood and absence in literature. The essay makes interventions into psychoanalysis, childhood studies, and the discourse of ‘framing’ within C19th literature.

Organisational semiotics methods to assess organisational readiness for internal use of social media

The paper presents organisational semiotics (OS) as an approach for identifying organisational readiness factors for internal use of social media within information intensive organisations (IIO). The paper examines OS methods, such as organisational morphology, containment analysis and collateral analysis to reveal factors of readiness within an organisation. These models also help to identify the essential patterns of activities needed for social media use within an organisation, which can provide a basis for future analysis. The findings confirmed many of the factors, previously identified in literature, while also revealing new factors using OS methods. The factors for organisational readiness for internal use of social media include resources, organisational climate, processes, motivational readiness, benefit and organisational control factors. Organisational control factors revealed are security/privacy, policies, communication procedures, accountability and fallback.

Issues and benefits of using 3D Interfaces: visual and verbal tasks

Spatial memory is important for locating objects in hierarchical data structures, such as desktop folders. There are, however, some contradictions in literature concerning the effectiveness of 3D user interfaces when compared to their 2D counterparts. This paper uses a task-based approach in order to investigate the effectiveness of adding a third dimension to specific user tasks, i.e. the impact of depth on navigation in a 3D file manager. Results highlight issues and benefits of using 3D interfaces for visual and verbal tasks, and introduces the possible existence of a correlation between aptitude scores achieved on the Guilford- Zimmerman Orientation Survey and Electroencephalography- measured brainwave activity as participants search for targets of variable perceptual salience in 2D and 3D environments.

Revolutionary insurgencies, paradigmatic cases

This essay will examine and compare the production of women's writing during and after the Nicaraguan and Cuban Revolutions, a corpus that includes novels, poetry, and testimonies, but also features considerable generic hybridity. Since both revolutions are separated by some twenty years, each must be understood in the context of the specific ideological conditions that framed women’s participation in culture and revolution, and must also be considered in light of evolving gender discourses, both national and international. As such, these texts respond to both local and transnational paradigms of feminine subjectivity, and highlight the particular problems that arise from women’s insertion into the revolution and its representation in literature. These writers also have to negotiate the evolving context of revolution itself, with its moments of euphoria and disenchantment – and it is here that the greatest contrasts can be found between the two revolutionary instances and their political features: whilst Cuba’s revolutionary process has somehow survived economic crisis and created a level of political stability and continuity (not without its own problems), the Nicaraguan case is characterised by ruptures and resentments which are clearly reflected in the work of writers before, during, and after the Sandinista revolution, and which continue to the present day. This chapter will address the work of the most prominent woman writer of the Nicaraguan revolution, Gioconda Belli, whose main work reflects her involvement in the Sandinista struggle; ex-commander Mónica Baltodano has recently compiled a four volume piece with testimonials of men and women who participated in the organization and actions led by the Frente Sandinista de Liberación Nacional, and Violeta Barrios de Chamorro, former president of Nicaragua, who has recently co-authored an autobiography. There are other women poets to consider, especially under the auspices of the Asociación de Mujeres Nicaraguenses Luisa Amanda Espinoza, such as Vidaluz Meneses, Michele Najlis and Daisy Zamora. The testimonios compiled by Margaret Randall are also important pieces to consider for both Nicaragua and Cuba. The most important voices of the Cuban revolution still resident on the island are poet Nancy Morejón and writers Mirta Yáñez and Aida Bahr, with younger writers such as Adelaida Fernández de Juan and Marilyn Bobes representing a more recent generation.

Sustainable construction: exploring the capabilities of Nigerian construction firms

As the built environment accounts for much of the world's emissions, resource consumption and waste, concerns remain as to how sustainable the sector is. Understanding how such concerns can be better managed is complex, with a range of competing agendas and institutional forces at play. This is especially the case in Nigeria where there are often differing priorities, weak regulations and institutions to deal with this challenge. Construction firms are in competition with each other in a market that is growing in size and sophistication yearly. The business case for sustainability has been argued severally in literature. However, the capability of construction firms with respect to sustainability in Nigeria has not been studied. This paper presents the preliminary findings of an exploratory multi-case study carried out to understand the firm's views on sustainability as a source of competitive advantage. A international firm and a lower medium-sized indigenous firm were selected for this purpose. Qualitative interviews were conducted with top-level management of both firms, with key themes from the sustainable construction and dynamic capabilities literature informing the case study protocol. The interviews were transcribed and analysed with the use of NVivo software. The findings suggest that the multinational firm is better grounded in sustainability knowledge. Although the level of awareness and demand for sustainable construction is generally very poor, few international clients are beginning to stimulate interest in sustainable buildings. This has triggered both firms to build their capabilities in that regard, albeit in an unhurried manner. Both firms agree on the potentials of market-driven sustainability in the long term. Nonetheless, more drastic actions are required to accelerate the sustainable construction agenda in Nigeria.

Collocating satellite-based radar and radiometer measurements — methodology and usage examples

Collocations between two satellite sensors are occasions where both sensors observe the same place at roughly the same time. We study collocations between the Microwave Humidity Sounder (MHS) on-board NOAA-18 and the Cloud Profiling Radar (CPR) on-board CloudSat. First, a simple method is presented to obtain those collocations and this method is compared with a more complicated approach found in literature. We present the statistical properties of the collocations, with particular attention to the effects of the differences in footprint size. For 2007, we find approximately two and a half million MHS measurements with CPR pixels close to their centrepoints. Most of those collocations contain at least ten CloudSat pixels and image relatively homogeneous scenes. In the second part, we present three possible applications for the collocations. Firstly, we use the collocations to validate an operational Ice Water Path (IWP) product from MHS measurements, produced by the National Environment Satellite, Data and Information System (NESDIS) in the Microwave Surface and Precipitation Products System (MSPPS). IWP values from the CloudSat CPR are found to be significantly larger than those from the MSPPS. Secondly, we compare the relation between IWP and MHS channel 5 (190.311 GHz) brightness temperature for two datasets: the collocated dataset, and an artificial dataset. We find a larger variability in the collocated dataset. Finally, we use the collocations to train an Artificial Neural Network and describe how we can use it to develop a new MHS-based IWP product. We also study the effect of adding measurements from the High Resolution Infrared Radiation Sounder (HIRS), channels 8 (11.11 μm) and 11 (8.33 μm). This shows a small improvement in the retrieval quality. The collocations described in the article are available for public use.

On mathematical and physical principles of transformations of the coherent radar backscatter matrix

The congruential rule advanced by Graves for polarization basis transformation of the radar backscatter matrix is now often misinterpreted as an example of consimilarity transformation. However, consimilarity transformations imply a physically unrealistic antilinear time-reversal operation. This is just one of the approaches found in literature to the description of transformations where the role of conjugation has been misunderstood. In this paper, the different approaches are examined in particular in respect to the role of conjugation. In order to justify and correctly derive the congruential rule for polarization basis transformation and properly place the role of conjugation, the origin of the problem is traced back to the derivation of the antenna height from the transmitted field. In fact, careful consideration of the role played by the Green’s dyadic operator relating the antenna height to the transmitted field shows that, under general unitary basis transformation, it is not justified to assume a scalar relationship between them. Invariance of the voltage equation shows that antenna states and wave states must in fact lie in dual spaces, a distinction not captured in conventional Jones vector formalism. Introducing spinor formalism, and with the use of an alternate spin frame for the transmitted field a mathematically consistent implementation of the directional wave formalism is obtained. Examples are given comparing the wider generality of the congruential rule in both active and passive transformations with the consimilarity rule.

Screening of bacteria to produce polyhydroxyalkanoates from xylose

Although xylose is a major constituent of lignocellulosic feedstock and the second most abundant sugar in nature, only 22% of 3,152 screened bacterial isolates showed significant growth in xylose in 24 h. Of those 684, only 24% accumulated polyhydroxyalkanoates after 72 h. A mangrove isolate, identified as Bacillus sp. MA3.3, yielded the best results in literature thus far for Gram-positive strains in experiments with glucose and xylose as the sole carbon source. When glucose or xylose were supplied, poly-3-hydroxybutyrate (PHB) contents of cell dry weight were, respectively, 62 and 64%, PHB yield 0.25 and 0.24 g g(-1) and PHB productivity (P(PHB)) 0.10 and 0.06 g l(-1) h(-1). This 40% P(PHB) difference may be related to the theoretical ATP production per 3-hydroxybutyrate (3HB) monomer calculated as 3 mol mol(-1) for xylose, less than half of the ATP/3HB produced from glucose (7 mol mol(-1)). In PHB production using sugar mixtures, all parameters were strongly reduced due to carbon catabolite repression. PHB production using Gram-positive strains is particularly interesting for medical applications because these bacteria do not produce lipopolysaccharide endotoxins which can induce immunogenic reactions. Moreover, the combination of inexpensive substrates and products of more value may lead to the economical sustainability of industrial PHB production.