Towards a matrix mechanics framework for dynamic protein network

Protein–protein interaction networks are currently visualized by software generated interaction webs based upon static experimental data. Current state is limited to static, mostly non-compartmental network and non time resolved protein interactions. A satisfactory mathematical foundation for particle interactions within a viscous liquid state (situation within the cytoplasm) does not exist nor do current computer programs enable building dynamic interaction networks for time resolved interactions. Building mathematical foundation for intracellular protein interactions can be achieved in two increments (a) trigger and capture the dynamic molecular changes for a select subset of proteins using several model systems and high throughput time resolved proteomics and, (b) use this information to build the mathematical foundation and computational algorithm for a compartmentalized and dynamic protein interaction network. Such a foundation is expected to provide benefit in at least two spheres: (a) understanding physiology enabling explanation of phenomenon such as incomplete penetrance in genetic disorders and (b) enabling several fold increase in biopharmaceutical production using impure starting materials.     

Towards a whole-system framework for wildfire monitoring using Earth observations

Fire seasons have become increasingly variable and extreme due to changing climatological, ecological, and social conditions. Earth observation data are critical for monitoring fires and their impacts. Herein, we present a whole-system framework for identifying and synthesizing fire monitoring objectives and data needs throughout the life cycle of a fire event. The four stages of fire monitoring using Earth observation data include the following: (1) pre-fire vegetation inventories, (2) active-fire monitoring, (3) post-fire assessment, and (4) multi-scale synthesis. We identify the challenges and opportunities associated with current approaches to fire monitoring, highlighting four case studies from North American boreal, montane, and grassland ecosystems. While the case studies are localized to these ecosystems and regional contexts, they provide insights for others experiencing similar monitoring challenges worldwide. The field of remote sensing is experiencing a rapid proliferation of new data sources, providing observations that can inform all aspects of our fire monitoring framework; however, significant challenges for meeting fire monitoring objectives remain. We identify future opportunities for data sharing and rapid co-development of information products using cloud computing that benefits from open-access Earth observation and other geospatial data layers.     

Towards a lightweight generic computational grid framework for biological research

Background  

An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology.     

Towards a general framework for including noise impacts in LCA

Purpose  

Several damages have been associated with the exposure of human beings to noise. These include auditory effects, i.e., hearing impairment, but also non-auditory physiological ones such as hypertension and ischemic heart disease, or psychological ones such as annoyance, depression, sleep disturbance, limited performance of cognitive tasks or inadequate cognitive development. Noise can also interfere with intended activities, both in daytime and nighttime. ISO 14'040 also indicated the necessity of introducing noise, together with other less developed impact categories, in a complete LCA study, possibly changing the results of many LCA studies already available. The attempts available in the literature focused on the integration of transportation noise in LCA. Although being considered the most frequent source of intrusive impact, transportation noise is not the only type of noise that can have a malign impact on public health. Several other sources of noise such as industrial or occupational need to be taken into account to have a complete consideration of noise into LCA. Major life cycle inventories (LCI) typically do not contain data on noise emissions yet and characterisation factors are not yet clearly defined. The aim of the present paper is to briefly review what is already available in the field and propose a new framework for the consideration of human health impacts of any type of noise that could be of interest in the LCA practice, providing indications for the introduction of noise in LCI and analysing what data is already available and, in the form of a research agenda, what other resources would be needed to reach a complete coverage of the problem.     

Neural correlates of behavioral preference for culturally familiar drinks

Coca-Cola (Coke) and Pepsi are nearly identical in chemical composition, yet humans routinely display strong subjective preferences for one or the other. This simple observation raises the important question of how cultural messages combine with content to shape our perceptions; even to the point of modifying behavioral preferences for a primary reward like a sugared drink. We delivered Coke and Pepsi to human subjects in behavioral taste tests and also in passive experiments carried out during functional magnetic resonance imaging (fMRI). Two conditions were examined: (1) anonymous delivery of Coke and Pepsi and (2) brand-cued delivery of Coke and Pepsi. For the anonymous task, we report a consistent neural response in the ventromedial prefrontal cortex that correlated with subjects' behavioral preferences for these beverages. In the brand-cued experiment, brand knowledge for one of the drinks had a dramatic influence on expressed behavioral preferences and on the measured brain responses.     

Object retrieval by Norway rats as a framework for preference and choice

Object retrieval by Norway rats consists of locomotion to an object, object seizure, carriage to a refuge and release. These studies examined choices in this sequence and object preferences (relative numbers retrieved) for objects varying in sweetness. In Experiment 1, rats could retrieve two types of object on each trial, drawn from a set of three, each placed in quantity in one arm of a Y-maze connected to the home cage. After a period of learning, a stable preference hierarchy was demonstrated that depended on choices in different parts of the retrieval sequence i.e. decision making was broadly distributed. For the middle object in the hierarchy, response probabilities varied with object pairing, suggesting that rats responded in terms of object-sets. Preferences also involved rapid updating at the beginning of each trial (working memory) manifested in shifts in responding in all segments that supported consistent choices. Experiments 2–3, with an empty arm as an extra alternative, indicated that visits to an arm with less-preferred objects represented exploration interspersed with retrieval. Preference and choice are fundamental to object retrieval in this species and choice consistency in a dynamic environment is based on learning and memory.     

Towards a common framework for defining ancillary material quality across the development spectrum

Ancillary materials (AMs) play a critical role in the manufacture of cell and gene therapies, and best practices for their quality management are the subject of ongoing discussion. Given that the final product cannot be sterilized, AM quality becomes increasingly critical to the clinical advancement of cell and gene therapies. Despite a lack of direct legislative direction regarding AM quality, internationally harmonized guidance is available from several industry-standard bodies that describe the principles and application of a risk-based approach to AM qualification and related supply-chain risk management. According to a best-practice risk-based approach, AMs must be adequately qualified to a degree that reflects the level of risk the material presents to patient safety and the drug product's specification. This general approach can be implemented in different ways, and balancing quality with cost of goods is critical to the cost-effective manufacture of advanced therapy medicinal products. In some cases, it may be preferable or necessary to use AMs that are produced in compliance with current Good Manufacturing Practice. However, developers may be able to suppress manufacturing costs without undermining safety or regulatory compliance in the case that a material presents a lower risk profile. Despite a great deal of attention and interest in the quality of AMs in the cell and gene therapy space, there is still a need for greater harmonization to create a shared understanding of what constitutes a risk-based approach to AM production and sourcing. In this article, we propose a staged approach to AM quality that achieves a balance between the competing demands of risk mitigation and cost of goods containment at the various stages of AM quality development. Our novel, heuristic framework for communication among AM suppliers, users and regulators aims to bring down development and manufacturing costs and lessen the workload around regulatory compliance.     

Isolating neural correlates of the pacemaker for food anticipation

Mice fed a single daily meal at intervals within the circadian range exhibit food anticipatory activity. Previous investigations strongly suggest that this behaviour is regulated by a circadian pacemaker entrained to the timing of fasting/refeeding. The neural correlate(s) of this pacemaker, the food entrainable oscillator (FEO), whether found in a neural network or a single locus, remain unknown. This study used a canonical property of circadian pacemakers, the ability to continue oscillating after removal of the entraining stimulus, to isolate activation within the neural correlates of food entrainable oscillator from all other mechanisms driving food anticipatory activity. It was hypothesized that continued anticipatory activation of central nuclei, after restricted feeding and a return to ad libitum feeding, would elucidate a neural representation of the signaling circuits responsible for the timekeeping component of the food entrainable oscillator. Animals were entrained to a temporally constrained meal then placed back on ad libitum feeding for several days until food anticipatory activity was abolished. Activation of nuclei throughout the brain was quantified using stereological analysis of c-FOS expressing cells and compared against both ad libitum fed and food entrained controls. Several hypothalamic and brainstem nuclei remained activated at the previous time of food anticipation, implicating them in the timekeeping mechanism necessary to track previous meal presentation. This study also provides a proof of concept for an experimental paradigm useful to further investigate the anatomical and molecular substrates of the FEO.     

Towards a framework for monitoring cloud application platforms as sensor networks

With the continued growth in software environments on cloud application platforms, self-management at the Platform-as-a-Service (PaaS) level has become a pressing concern, and the run-time monitoring, analysis and detection of critical situations are all fundamental requirements if we are to achieve autonomic behaviour in complex PaaS environments. In this paper we focus on cloud application platforms offering their customers a range of generic built-in re-usable services. By identifying key characteristics of these complex dynamic systems, we compare cloud application platforms to distributed sensor networks, and investigate the viability of exploiting these similarities with a case study. We treat cloud data storage services as “virtual” sensors constantly emitting monitoring data, such as numbers of connections and storage space availability, which are then analysed by the central component of a monitoring framework so as to detect and react to SLA violations. We discuss the potential benefits, as well as some shortcomings, of adopting this approach.     

Towards a harmonised framework methodology for the environmental assessment of food and drink products

Introduction

??Food and drink?? products are the basis of life. However, it is recognised that their supply also contributes to the environmental impacts associated with production and consumption. Recently, an increasing number of food chain partners and public authorities have introduced a widening range of initiatives to provide information about the environmental performance of food and drink products. These initiatives show a high degree of diversity in terms of their chosen scope, assessment methodologies and means of communication, which has the potential to confuse or even mislead consumers and other stakeholders. In this context, the European Food Sustainable Consumption and Production (SCP) Round Table was launched by food supply chain partners and the European Commission with the vision of promoting a science-based, coherent approach to sustainable consumption and production in the European food sector.

Objectives

This article presents this European initiative by introducing its Guiding Principles and summarizing the proceedings of the scientific workshop held in Ispra on 14?C15 June 2010. The aim of the workshop was to identify scientific inputs for developing the harmonised framework methodology for assessing the environmental issues of food and drink products. In this context, the main purpose was to provide a common understanding of what is involved in reliable and robust environmental assessments of the food chain, current limitations, and how to go from detailed assessments to more focused criteria, guidance and tools.

Conclusion

The current experiences presented in the workshop demonstrate that much advancement has already been made towards the measurement and management of the environmental performance of food and drink products. Detailed methodologies and tools are already being used by various players. According to the workshop speakers, the definition of methodological choices concerning the functional unit, system boundaries, cut-off criteria, allocation rules and environmental impact categories are some of the key issues to be fixed in the harmonised framework methodology. The Round Table process has the potential to make a substantial contribution to the sustainable consumption and production of food and drink products. This model might be proposed and reiterated for other sectors as well.     

Context effects on the neural correlates of recognition memory: an electrophysiological study

Event-related potentials (ERPs) were recorded during a recognition memory test for previously studied visual objects. Some studied objects were paired with the same context (landscape scenes) as at study, some were superimposed on a different studied context, and some were paired with new contexts. Unstudied objects were paired with either a studied or a new context. Three ERP memory effects were observed: an early effect elicited by all stimuli containing at least one studied component; a second effect elicited only by stimuli in which both object and context had been studied; and a third effect elicited by stimuli containing a studied object. Thus, test stimuli engaged three distinct kinds of memory-related neural activity which differed in their specificity for task-relevant features.     

Visual ecology: exploring the relationships between ecological quality and aesthetic preference

High ecological quality and an attractive environment are usually two primary goals of landscape design. Understanding the relationships between ecological quality and visual aesthetic preference is needed to reach the two goals simultaneously. However, previous work has not provided definite answers regards these relationships. The current study took place in the riparian zone of Xuzhou, China, to check ecological quality using the qualitat del bosc de ribera (or riparian forest quality) index, and visual aesthetic preference using pictures as surrogates, which were assessed by undergraduate students. Regression analysis revealed a U-shaped distribution of ecological quality in relation to visual aesthetic preference, which indicated that, with higher ecological quality, the visual aesthetic preference could be higher or lower, and a lower ecological quality implied a medium visual aesthetic preference. In addition, enhancing the cover quality (introducing more native plants and reducing man-made elements) of riparian vegetation was an efficient way to align the ecological goal with a visually pleasing landscape.