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.

The separation of americium(III) from europium(III) by two new 6,6'-bistriazinyl-2,2'-bipyridines in different diluents

The synthesis and extraction of americium(III) and europium(III) from aqueous nitric acid solutions by the new BTBP ligands 6,6’-bis(5,5,7,7- tetramethyl-5,7-dihydrofuro[3,4-e]-1,2,4-triazin-3-yl)-2,2’-bipyridine (Cy5-O-Me4-BTBP), and 6,6’-bis(5,5,7,7-tetramethyl-5,7-dihydrothieno[3,4-e]-1,2,4-triazin-3-yl)- 2,2’-bipyridine (Cy5-S-Me4-BTBP) is described. The affinity for Am(III) and the selectivity for Am(III) over Eu(III) of Cy5-S-Me4-BTBP were generally higher than for Cy5-O-Me4-BTBP. For both ligands, the extraction of Am(III) and Eu(III) from 3 M HNO3 into 3 mM organic solutions varied with the diluent used. The highest distribution ratios and separation factors observed were in cyclohexanone and 2-methylcyclohexanone, respectively. For Cy5-S-Me4-BTBP, there is a strong correlation between the distribution ratio for Am(III) and the permittivity of the diluent used. With 1-octanol as the diluent, low distribution ratios (D(Am) < 1) were observed for Cy5-S-Me4-BTBP although this ligand extracts Am(III) selectively (SFAm/Eu = 16-46 from 1-4 M HNO3). For Cy5-S-Me4-BTBP, Am(III) is extracted as the disolvate. The distribution ratios for Am(III), and the separation factors for Am(III) over Eu(III) are both significantly higher for CyMe4-BTBP than they are for Cy5-O-Me4-BTBP and Cy5-S-Me4-BTBP in cyclohexanone. Changing the diluent from cyclohexanone to 2-methylcyclohexanone leads to a decrease in D(Am) but an increase in SFAm/Eu for Cy5-S-Me4-BTBP.

‘Inherited commitments’: do changes in ownership affect corporate social responsibility (CSR) at African gold mines?

This paper critically examines the issue of ‘inherited corporate social responsibility’ in the gold mining industry, focusing specifically on the case of sub-Saharan Africa, a region plagued with excessive corruption, rampant poverty and weak governance. Whilst there appears to be little incentive to proactively engage with communities and implement cutting-edge environmental policies in the region, mine managers argue otherwise, highlighting a number of reasons for embracing corporate social responsibility (CSR). After briefly reviewing the philosophical underpinnings of CSR, the paper provides an in-depth analysis of these arguments, in the process, underscoring how tenuous the case for CSR in the extractive industries, and gold mining more specifically, is in the context of sub-Saharan Africa. Following a change in ownership, new management faces few pressures to embrace CSR in its entirety and therefore, more often than not, finds itself in a position to implement programs and policies of its choice. More research is needed that further popularizes the issue of ‘inherited CSR’ in the gold mining sector and extractive industries more generally.

Perspectives on community representation within the Extractive Industries Transparency Initiative: experiences from south-east Madagascar

This article critically examines the nature and quality of governance in community representation and civil society engagement in the context of trans-national large-scale mining, drawing on experiences in the Anosy Region of south-east Madagascar. An exploration of functional relationships between government, mining business and civil society stakeholders reveals an equivocal legitimacy of certain civil society representatives, created by state manipulation, which contributes to community disempowerment. The appointment of local government officials, rather than election, creates a hierarchy of upward dependencies and a culture where the majority of officials express similar views and political alliances. As a consequence, community resistance is suppressed. Voluntary mechanisms such as Corporate Social Responsibility (CSR) and the Extractive Industries Transparency Initiative (EITI) advocate community stakeholder engagement in decision making processes as a measure to achieve public accountability. In many developing countries, where there is a lack of transparency and high levels of corruption, the value of this engagement, however, is debatable. Findings from this study indicate that the power relationships which exist between stakeholders in the highly lucrative mining industry override efforts to achieve "good governance" through voluntary community engagement. The continuing challenge lies in identifying where the responsibility sits in order to address this power struggle to achieve fair representation.

Non-uniform data distribution for communication-efficient parallel clustering

Global communicationrequirements andloadimbalanceof someparalleldataminingalgorithms arethe major obstacles to exploitthe computational power of large-scale systems. This work investigates how non-uniform data distributions can be exploited to remove the global communication requirement and to reduce the communication costin parallel data mining algorithms and, in particular, in the k-means algorithm for cluster analysis. In the straightforward parallel formulation of the k-means algorithm, data and computation loads are uniformly distributed over the processing nodes. This approach has excellent load balancing characteristics that may suggest it could scale up to large and extreme-scale parallel computing systems. However, at each iteration step the algorithm requires a global reduction operationwhichhinders thescalabilityoftheapproach.Thisworkstudiesadifferentparallelformulation of the algorithm where the requirement of global communication is removed, while maintaining the same deterministic nature ofthe centralised algorithm. The proposed approach exploits a non-uniform data distribution which can be either found in real-world distributed applications or can be induced by means ofmulti-dimensional binary searchtrees. The approachcanalso be extended to accommodate an approximation error which allows a further reduction ofthe communication costs. The effectiveness of the exact and approximate methods has been tested in a parallel computing system with 64 processors and in simulations with 1024 processing element

Rule Type Identification using TRCM for trend analysis in Twitter

This paper considers the use of Association Rule Mining (ARM) and our proposed Transaction based Rule Change Mining (TRCM) to identify the rule types present in tweet’s hashtags over a specific consecutive period of time and their linkage to real life occurrences. Our novel algorithm was termed TRCM-RTI in reference to Rule Type Identification. We created Time Frame Windows (TFWs) to detect evolvement statuses and calculate the lifespan of hashtags in online tweets. We link RTI to real life events by monitoring and recording rule evolvement patterns in TFWs on the Twitter network.

Online persuasion for e-commerce websites

The persuasive design of e-commerce websites has been shown to support people with online purchases. Therefore, it is important to understand how persuasive applications are used and assimilated into e-commerce website designs. This paper demonstrates how the PSD model’s persuasive features could be used to build a bridge supporting the extraction and evaluation of persuasive features in such e-commerce websites; thus practically explaining how feature implementation can enhance website persuasiveness. To support a deeper understanding of persuasive e-commerce website design, this research, using the Persuasive Systems Design (PSD) model, identifies the distinct persuasive features currently assimilated in ten successful e-commerce websites. The results revealed extensive use of persuasive features; particularly features related to dialogue support, credibility support, and primary task support; thus highlighting weaknesses in the implementation of social support features. In conclusion we suggest possible ways for enhancing persuasive feature implementation via appropriate contextual examples and explanation.

Twentieth-century global-mean sea-level rise: is the whole greater than the sum of the parts?

Confidence in projections of global-mean sea level rise (GMSLR) depends on an ability to account for GMSLR during the twentieth century. There are contributions from ocean thermal expansion, mass loss from glaciers and ice sheets, groundwater extraction, and reservoir impoundment. Progress has been made toward solving the “enigma” of twentieth-century GMSLR, which is that the observed GMSLR has previously been found to exceed the sum of estimated contributions, especially for the earlier decades. The authors propose the following: thermal expansion simulated by climate models may previously have been underestimated because of their not including volcanic forcing in their control state; the rate of glacier mass loss was larger than previously estimated and was not smaller in the first half than in the second half of the century; the Greenland ice sheet could have made a positive contribution throughout the century; and groundwater depletion and reservoir impoundment, which are of opposite sign, may have been approximately equal in magnitude. It is possible to reconstruct the time series of GMSLR from the quantified contributions, apart from a constant residual term, which is small enough to be explained as a long-term contribution from the Antarctic ice sheet. The reconstructions account for the observation that the rate of GMSLR was not much larger during the last 50 years than during the twentieth century as a whole, despite the increasing anthropogenic forcing. Semiempirical methods for projecting GMSLR depend on the existence of a relationship between global climate change and the rate of GMSLR, but the implication of the authors' closure of the budget is that such a relationship is weak or absent during the twentieth century.

New-on-line method for water isotope analysis of speleothem fluid inclusions using laser absorption spectroscopy (WS-CRDS)

A new online method to analyse water isotopes of speleothem fluid inclusions using a wavelength scanned cavity ring down spectroscopy (WS-CRDS) instrument is presented. This novel technique allows us simultaneously to measure hydrogen and oxygen isotopes for a released aliquot of water. To do so, we designed a new simple line that allows the online water extraction and isotope analysis of speleothem samples. The specificity of the method lies in the fact that fluid inclusions release is made on a standard water background, which mainly improves the δ D robustness. To saturate the line, a peristaltic pump continuously injects standard water into the line that is permanently heated to 140 °C and flushed with dry nitrogen gas. This permits instantaneous and complete vaporisation of the standard water, resulting in an artificial water background with well-known δ D and δ18O values. The speleothem sample is placed in a copper tube, attached to the line, and after system stabilisation it is crushed using a simple hydraulic device to liberate speleothem fluid inclusions water. The released water is carried by the nitrogen/standard water gas stream directly to a Picarro L1102-i for isotope determination. To test the accuracy and reproducibility of the line and to measure standard water during speleothem measurements, a syringe injection unit was added to the line. Peak evaluation is done similarly as in gas chromatography to obtain &delta D; and δ18O isotopic compositions of measured water aliquots. Precision is better than 1.5 ‰ for δ D and 0.4 ‰ for δ18O for water measurements for an extended range (−210 to 0 ‰ for δ D and −27 to 0 ‰ for δ18O) primarily dependent on the amount of water released from speleothem fluid inclusions and secondarily on the isotopic composition of the sample. The results show that WS-CRDS technology is suitable for speleothem fluid inclusion measurements and gives results that are comparable to the isotope ratio mass spectrometry (IRMS) technique.

Geotechnical systems that evolve with ecological processes

Geotechnical systems, such as landfills, mine tailings storage facilities (TSFs), slopes, and levees, are required to perform safely throughout their service life, which can span from decades for levees to “in perpetuity” for TSFs. The conventional design practice by geotechnical engineers for these systems utilizes the as-built material properties to predict its performance throughout the required service life. The implicit assumption in this design methodology is that the soil properties are stable through time. This is counter to long-term field observations of these systems, particularly where ecological processes such as plant, animal, biological, and geochemical activity are present. Plant roots can densify soil and/or increase hydraulic conductivity, burrowing animals can increase seepage, biological activity can strengthen soil, geochemical processes can increase stiffness, etc. The engineering soil properties naturally change as a stable ecological system is gradually established following initial construction, and these changes alter system performance. This paper presents an integrated perspective and new approach to this issue, considering ecological, geotechnical, and mining demands and constraints. A series of data sets and case histories are utilized to examine these issues and to propose a more integrated design approach, and consideration is given to future opportunities to manage engineered landscapes as ecological systems. We conclude that soil scientists and restoration ecologists must be engaged in initial project design and geotechnical engineers must be active in long-term management during the facility’s service life. For near-surface geotechnical structures in particular, this requires an interdisciplinary perspective and the embracing of soil as a living ecological system rather than an inert construction material.

Contractual restrictions on lawful use of information: sole-source databases protected by the back door?

This article is concerned with the risks associated with the monopolisation of information that is available from a single source only. Although there is a longstanding consensus that sole-source databases should not receive protection under the EU Database Directive, and there are legislative provisions to ensure that lawful users have access to a database’s contents, Ryanair v PR Aviation challenges this assumption by affirming that the use of non-protected databases can be restricted by contract. Owners of non-protected databases can contractually exclude lawful users from taking the benefit of statutorily permitted uses, because such databases are not covered from the legislation that declares this kind of contract null and void. We argue that this judgment is not consistent with the legislative history and can have a profound impact on the functioning of the digital single market, where new information services, such as meta-search engines or price-comparison websites, base their operation on the systematic extraction and re-utilisation of materials available from online sources. This is an issue that the Commission should address in a forthcoming evaluation of the Database Directive.

An assessment of the impact of trees upon archaeology within a relict wetland

An evaluation of a surviving stretch of the Abbot's Way, in the Somerset Levels and Moors, was undertaken to assess the consequences of the previous management regime and inform future management of the site. The scheduled site appeared to have been dewatered and desiccated as a consequence of tree planting and the effects of a deep, adjacent drainage ditch during the previous decade. The evaluation considered the condition of the Neolithic timbers and associated palaeoenvironmental record from three trenches and, where possible, compared the results with those obtained form the 1974 excavation (Girling, 1976). The results of this analysis suggest that the hydrological consequences of tree planting and colonization had a detrimental effect on both the condition of the timbers and insect remains. However, pollen and plant macro-fossils survived well although there was modern contamination. A trench opened outside the scheduled area. where the ground was waterlogged and supported a wet acid grassland flora, revealed similar problems of survival and condition. This almost certainly reflects a period of peat extraction and an associated seasonally fluctuating water table in the 1950s and 1960s; in fact pollen survived better in the scheduled dewatered area. These results are compared with those recovered from the Sweet Track which was evaluated in 1996. Both sites have been subject to recent tree growth but the Sweet Track has been positively managed in terms of hydrology. The most notable difference between the two sites is that insects and wood survived better at the Sweet Track sites than at the Abbot's Way. Insects seem to be a more sensitive indicator of site desiccation than plant remains. It is recommended that any programme of management of wetland for archaeology should avoid deliberate tree planting and natural scrub and woodland generation. It should also take into account past as well as present land use.

Castoraeschna corbeti sp nov from Floresta Nacional de Carajas, Para state, Brazil (Odonata: Aeshnidae)

Castoraeschna corbeti sp. nov. is described and diagnosed based on four males (holotype: Brazil, Para State, Floresta Nacional cle Carajas [6 degrees 06`13.9 `` S, 50 degrees 08`13.1 `` W, ca 600 m a.s.l.], 28 ix 2007 to be deposited in Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro). This species is similar to C. longfieldae and C. coronata but can be distinguished mainly by the absence of medio-dorsal spots on S8; postero-dorsal spots on S8-9 very narrow; cerci external margin almost straight in lateral view, without a distinct angulation between stern and base of lamina; cerci apex blunt. The probable ultimate stadium larva is described based on two individuals, male and female, collected at the type locality. Adults were observed flying along margins of a small shaded second-order stream where the larvae were taken. The surrounding forest is under impact of iron ore extraction and will probably disappear in the next years.

A novel approach for distributed application scheduling based on prediction of communication events

The evolution of commodity computing lead to the possibility of efficient usage of interconnected machines to solve computationally-intensive tasks, which were previously solvable only by using expensive supercomputers. This, however, required new methods for process scheduling and distribution, considering the network latency, communication cost, heterogeneous environments and distributed computing constraints. An efficient distribution of processes over such environments requires an adequate scheduling strategy, as the cost of inefficient process allocation is unacceptably high. Therefore, a knowledge and prediction of application behavior is essential to perform effective scheduling. In this paper, we overview the evolution of scheduling approaches, focusing on distributed environments. We also evaluate the current approaches for process behavior extraction and prediction, aiming at selecting an adequate technique for online prediction of application execution. Based on this evaluation, we propose a novel model for application behavior prediction, considering chaotic properties of such behavior and the automatic detection of critical execution points. The proposed model is applied and evaluated for process scheduling in cluster and grid computing environments. The obtained results demonstrate that prediction of the process behavior is essential for efficient scheduling in large-scale and heterogeneous distributed environments, outperforming conventional scheduling policies by a factor of 10, and even more in some cases. Furthermore, the proposed approach proves to be efficient for online predictions due to its low computational cost and good precision. (C) 2009 Elsevier B.V. All rights reserved.

Chemical variability within the marine sponge Aplysina fulva

Dibromotyrosine-derived metabolites are of common occurrence within marine sponges belonging to the order Verongida. However, previous chemical analysis of crude extracts obtained from samples of the verongid sponge Aplysina fulva collected in Brazil did not provide any dibromotyrosine-derived compounds. In this investigation, five samples of A. fulva from five different locations along the Brazilian coastline and one sample from a temperate reef in the South Atlantic Bight (SAB) (Georgia, USA) were investigated for the presence of bromotyrosine-derived compounds. All six samples collected yielded dibromotyrosine-derived compounds, including a new derivative, named aplysinafulvin, which has been identified by. analysis of spectroscopic data. These results confirm previous assumptions that dibromotyrosine-derived metabolites can be considered as chemotaxonomic markers of verongid sponges. The isolation of aplysinafulvin provides additional support for a biogenetic pathway involving an arene oxide intermediate in the biosynthesis of Verongida metabolites. It cannot yet be established if the chemical variability observed among the six samples of A.fulva collected in Brazil and the SAB is the result of different environmental factors, distinct chemical extraction and isolation protocols, or a consequence of hidden genetic diversity within the postulated morphological plasticity of this species. (C) 2007 Elsevier Ltd. All rights reserved.