Comparison of bottom-up protein identification methods

With the rapid development of proteomics, a number of different methods appeared for the basic task of protein identification. We made a simple comparison between a common liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflow using an ion trap mass spectrometer and a combined LC-MS and LC-MS/MS method using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry and accurate peptide masses. To compare the two methods for protein identification, we grew and extracted proteins from E. coli using established protocols. Cystines were reduced and alkylated, and proteins digested by trypsin. The resulting peptide mixtures were separated by reversed-phase liquid chromatography using a 4 h gradient from 0 to 50% acetonitrile over a C18 reversed-phase column. The LC separation was coupled on-line to either a Bruker Esquire HCT ion trap or a Bruker 7 tesla APEX-Qe Qh-FTICR hybrid mass spectrometer. Data-dependent Qh-FTICR-MS/MS spectra were acquired using the quadrupole mass filter and collisionally induced dissociation into the external hexapole trap. Proteins were in both schemes identified by Mascot MS/MS ion searches and the peptides identified from these proteins in the FTICR MS/MS data were used for automatic internal calibration of the FTICR-MS data, together with ambient polydimethylcyclosiloxane ions.

The roles of feature-specific task set and bottom-up salience in attentional capture: An ERP study

We investigated the roles of top-down task set and bottom-up stimulus salience for feature-specific attentional capture. Spatially nonpredictive cues preceded search arrays that included a color-defined target. For target-color singleton cues, behavioral spatial cueing effects were accompanied by cueinduced N2pc components, indicative of attentional capture. These effects were only minimally attenuated for nonsingleton target-color cues, underlining the dominance of top-down task set over salience in attentional capture. Nontarget-color singleton cues triggered no N2pc, but instead an anterior N2 component indicative of top-down inhibition. In Experiment 2, inverted behavioral cueing effects of these cues were accompanied by a delayed N2pc to targets at cued locations, suggesting that perceptually salient but task-irrelevant visual events trigger location-specific inhibition mechanisms that can delay subsequent target selection.

Bottom-up, not top-down, modulation of imitation by human and robotic models

Visual observation of human actions provokes more motor activation than observation of robotic actions. We investigated the extent to which this visuomotor priming effect is mediated by bottom-up or top-down processing. The bottom-up hypothesis suggests that robotic movements are less effective in activating the ‘mirror system’ via pathways from visual areas via the superior temporal sulcus to parietal and premotor cortices. The top-down hypothesis postulates that beliefs about the animacy of a movement stimulus modulate mirror system activity via descending pathways from areas such as the temporal pole and prefrontal cortex. In an automatic imitation task, subjects performed a prespecified movement (e.g. hand opening) on presentation of a human or robotic hand making a compatible (opening) or incompatible (closing) movement. The speed of responding on compatible trials, compared with incompatible trials, indexed visuomotor priming. In the first experiment, robotic stimuli were constructed by adding a metal and wire ‘wrist’ to a human hand. Questionnaire data indicated that subjects believed these movements to be less animate than those of the human stimuli but the visuomotor priming effects of the human and robotic stimuli did not differ. In the second experiment, when the robotic stimuli were more angular and symmetrical than the human stimuli, human movements elicited more visuomotor priming than the robotic movements. However, the subjects’ beliefs about the animacy of the stimuli did not affect their performance. These results suggest that bottom-up processing is primarily responsible for the visuomotor priming advantage of human stimuli.

Bottom-up planning and the future of planning education in India

The article discusses normative guidelines for reorienting planning education in India within the context of the immensely influential Constitutional Amendment Act of 1993. First, it briefly sketches the status of planning education at present in India, in relation to the role of planners in planning practice. It then descibes the changes that have taken place in general, following the Constitutional Amendment Act, dwelling more on the specific changes within the State of Kerala. The implications of these for planning education in general are then discussed normatively, highlighting three areas that need immediate attention from the planning academic community.

Joined-up archaeology at Old Scatness, Shetland: thin section analysis of the site and hinterland

Excavations on the multi-period settlement at Old Scatness, Shetland have uncovered a number of Iron Age structures with compacted, floor-like layers. Thin section analysis was undertaken in order to investigate and compare the characteristics of these layers. The investigation also draws on earlier analyses of the Iron Age agricultural soil around the settlement and the midden deposits that accumulated within the settlement, to create a 'joined-up' analysis which considers the way material from the settlement was used and then recycled as fertiliser for the fields. Peat was collected from the nearby uplands and was used for fuel and possibly also for flooring. It is suggested that organic-rich floors from the structures were periodically removed and the material was spread onto the fields as fertilisers. More organic-rich material may have been used selectively for fertiliser, while the less organic peat ash was allowed to accumulate in middens. Several of the structures may have functioned as byres, which suggests a prehistoric plaggen system.

Incorporating technology buying behaviour into UK-based long term domestic stock energy models to provide improved policy analysis

The UK has a target for an 80% reduction in CO2 emissions by 2050 from a 1990 base. Domestic energy use accounts for around 30% of total emissions. This paper presents a comprehensive review of existing models and modelling techniques and indicates how they might be improved by considering individual buying behaviour. Macro (top-down) and micro (bottom-up) models have been reviewed and analysed. It is found that bottom-up models can project technology diffusion due to their higher resolution. The weakness of existing bottom-up models at capturing individual green technology buying behaviour has been identified. Consequently, Markov chains, neural networks and agent-based modelling are proposed as possible methods to incorporate buying behaviour within a domestic energy forecast model. Among the three methods, agent-based models are found to be the most promising, although a successful agent approach requires large amounts of input data. A prototype agent-based model has been developed and tested, which demonstrates the feasibility of an agent approach. This model shows that an agent-based approach is promising as a means to predict the effectiveness of various policy measures.

Analysis and modeling of ants’ behavior from single to multi-body

In order to shed light on the collective behavior of social insects, we analyzed the behavior of ants from single to multi-body. In an experimental set-up, ants are placed in hemisphere without a nest and food. Trajectory of ants is recorded. From this bottom-up approach, we found that collective behavior of ants as follows: 1. Activity of single ant increases and decreases periodically. 2. Spontaneous meeting process is observed between two ants and meeting spot of two ants is localized in hemisphere. 3. Result on division of labor is obtained between two ants.

Analysis and modeling of Diacamma workers’ behavior

It is well-known that social insects such as ants show interesting collective behaviors. How do they organize such behaviors? To expand understanding of collective behaviors of social insects, we focused on ants, Diacamma, and analyzed the behavior of a few individuals. In an experimental set-up, ants are placed in hemisphere without a nest and food and the trajectory of ants is recorded. From this bottom-up approach, we found following characteristics: 1. Activity of individuals increases and decreases periodically. 2. Spontaneous meeting process is observed between two ants and meeting spot of two ants is localized in the experimental field.

Considering the normative, systemic and procedural dimensions in indicator-based sustainability assessments in agriculture

This paper develops a framework for evaluating sustainability assessment methods by separately analyzing their normative, systemic and procedural dimensions as suggested by Wiek and Binder [Wiek, A, Binder, C. Solution spaces for decision-making – a sustainability assessment tool for city-regions. Environ Impact Asses Rev 2005, 25: 589-608.]. The framework is then used to characterize indicator-based sustainability assessment methods in agriculture. For a long time, sustainability assessment in agriculture has focused mostly on environmental and technical issues, thus neglecting the economic and, above all, the social aspects of sustainability, the multifunctionality of agriculture and the applicability of the results. In response to these shortcomings, several integrative sustainability assessment methods have been developed for the agricultural sector. This paper reviews seven of these that represent the diversity of tools developed in this area. The reviewed assessment methods can be categorized into three types: (i) top-down farm assessment methods; (ii) top-down regional assessment methods with some stakeholder participation; (iii) bottom-up, integrated participatory or transdisciplinary methods with stakeholder participation throughout the process. The results readily show the trade-offs encountered when selecting an assessment method. A clear, standardized, top-down procedure allows for potentially benchmarking and comparing results across regions and sites. However, this comes at the cost of system specificity. As the top-down methods often have low stakeholder involvement, the application and implementation of the results might be difficult. Our analysis suggests that to include the aspects mentioned above in agricultural sustainability assessment, the bottomup, integrated participatory or transdisciplinary methods are the most suitable ones.

Normative, systemic and procedural aspects: a review of indicator‐based sustainability assessments in agriculture

Several methods for assessing the sustainability of agricultural systems have been developed. These methods do not fully: (i) take into account the multi‐functionality of agriculture; (ii) include multidimensionality; (iii) utilize and implement the assessment knowledge; and (iv) identify conflicting goals and trade‐offs. This paper reviews seven recently developed multidisciplinary indicator‐based assessment methods with respect to their contribution to these shortcomings. All approaches include (1) normative aspects such as goal setting, (2) systemic aspects such as a specification of scale of analysis, (3) a reproducible structure of the approach. The approaches can be categorized into three typologies. The top‐down farm assessments focus on field or farm assessment. They have a clear procedure for measuring the indicators and assessing the sustainability of the system, which allows for benchmarking across farms. The degree of participation is low, potentially affecting the implementation of the results negatively. The top‐down regional assessment assesses the on‐farm and the regional effects. They include some participation to increase acceptance of the results. However, they miss the analysis of potential trade‐offs. The bottom‐up, integrated participatory or transdisciplinary approaches focus on a regional scale. Stakeholders are included throughout the whole process assuring the acceptance of the results and increasing the probability of implementation of developed measures. As they include the interaction between the indicators in their system representation, they allow for performing a trade‐off analysis. The bottom‐up, integrated participatory or transdisciplinary approaches seem to better overcome the four shortcomings mentioned above.

ASSET: moving forward through feedback

Providing high quality and timely feedback to students is often a challenge for many staff in higher education as it can be both time-consuming and frustratingly repetitive. From the student perspective, feedback may sometimes be considered unhelpful, confusing and inconsistent and may not always be provided within a timeframe that is considered to be ‘useful’. The ASSET project, based at the University of Reading, addresses many of these inherent challenges by encouraging the provision of feedback that supports learning, i.e. feedback that contains elements of ‘feed-forward’, is of a high quality and is delivered in a timely manner. In particular, the project exploits the pedagogic benefits of video/audio media within a Web 2.0 context to provide a new, interactive resource, ‘ASSET’, to enhance the feedback experience for both students and staff. A preliminary analysis of both our quantitative and qualitative pedagogic data demonstrate that the ASSET project has instigated change in the ways in which both staff and students think about, deliver, and engage with feedback. For example, data from our online questionnaires and focus groups with staff and students indicate a positive response to the use of video as a medium for delivering feedback to students. In particular, the academic staff engaged in piloting the ASSET resource indicated that i) using video has made them think more, and in some cases differently, about the ways in which they deliver feedback to students and ii) they now see video as an effective means of making feedback more useful and engaging for students. Moreover, the majority of academic staff involved in the project have said they will continue to use video feedback. From the student perspective, 60% of those students whose lecturers used ASSET to provide video feedback said that “receiving video feedback encouraged me to take more notice of the feedback compared with normal methods” and 80% would like their lecturer to continue to use video as a method for providing feedback. An important aim of the project was for it to complement existing University-wide initiatives on feedback and for ASSET to become a ‘model’ resource for staff and students wishing to explore video as a medium for feedback provision. An institutional approach was therefore adopted and key members of Senior Management, academics, T&L support staff, IT support and Student Representatives were embedded within the project from the start. As with all initiatives of this kind, a major issue is the future sustainability of the ASSET resource and to have had both ‘top-down’ and ‘bottom-up’ support for the project has been extremely beneficial. In association with the project team the University is currently exploring the creation of an open-source, two-tiered video supply solution and a ‘framework’ (that other HEIs can adopt and/or adapt) to support staff in using video for feedback provision. In this way students and staff will have new opportunities to explore video and to exploit the benefits of this medium for supporting learning.

Normative, systemic and procedural aspects: a review of indicator-based sustainability assessments in agriculture

Methods for assessing the sustainability of agricultural systems do often not fully (i) take into account the multifunctionality of agriculture, (ii) include multidimensionality, (iii) utilize and implement the assessment knowledge and (iv) identify conflicting goals and trade-offs. This chapter reviews seven recently developed multidisciplinary indicator-based assessment methods with respect to their contribution to these shortcomings. All approaches include (1) normative aspects such as goal setting, (2) systemic aspects such as a specification of scale of analysis and (3) a reproducible structure of the approach. The approaches can be categorized into three typologies: first, top-down farm assessments, which focus on field or farm assessment; second, top-down regional assessments, which assess the on-farm and the regional effects; and third, bottom-up, integrated participatory or transdisciplinary approaches, which focus on a regional scale. Our analysis shows that the bottom-up, integrated participatory or transdisciplinary approaches seem to better overcome the four shortcomings mentioned above.

Do phytoplankton communities evolve through a self-regulatory abundance-diversity relationship?

A small group of phytoplankton species that produce toxic or allelopathic chemicals has a significant effect on plankton dynamics in marine ecosystems. The species of non-toxic phytoplankton, which are large in number, are affected by the toxin-allelopathy of those species. By analysis of the abundance data of marine phytoplankton collected from the North-West coast of the Bay of Bengal, an empirical relationship between the abundance of the potential toxin-producing species and the species diversity of the non-toxic phytoplankton is formulated. A change-point analysis demonstrates that the diversity of non-toxic phytoplankton increases with the increase of toxic species up to a certain level. However, for a massive increase of the toxin-producing species the diversity of phytoplankton at species level reduces gradually. Following the results, a deterministic relationship between the abundance of toxic phytoplankton and the diversity of non-toxic phytoplankton is developed. The abundance–diversity relationship develops a unimodal pathway through which the abundance of toxic species regulates the diversity of phytoplankton. These results contribute to the current understanding of the coexistence and biodiversity of phytoplankton, the top-down vs. bottom-up debate, and to that of abundance–diversity relationship in marine ecosystems.