What are the baselines for protein fold recognition?

What constitutes a baseline level of success for protein fold recognition methods? As fold recognition benchmarks are often presented without any thought to the results that might be expected from a purely random set of predictions, an analysis of fold recognition baselines is long overdue. Given varying amounts of basic information about a protein—ranging from the length of the sequence to a knowledge of its secondary structure—to what extent can the fold be determined by intelligent guesswork? Can simple methods that make use of secondary structure information assign folds more accurately than purely random methods and could these methods be used to construct viable hierarchical classifications?

Integrating methods for developing sustainability indicators that can facilitate learning and action

Bossel's (2001) systems-based approach for deriving comprehensive indicator sets provides one of the most holistic frameworks for developing sustainability indicators. It ensures that indicators cover all important aspects of system viability, performance, and sustainability, and recognizes that a system cannot be assessed in isolation from the systems upon which it depends and which in turn depend upon it. In this reply, we show how Bossel's approach is part of a wider convergence toward integrating participatory and reductionist approaches to measure progress toward sustainable development. However, we also show that further integration of these approaches may be able to improve the accuracy and reliability of indicators to better stimulate community learning and action. Only through active community involvement can indicators facilitate progress toward sustainable development goals. To engage communities effectively in the application of indicators, these communities must be actively involved in developing, and even in proposing, indicators. The accuracy, reliability, and sensitivity of the indicators derived from local communities can be ensured through an iterative process of empirical and community evaluation. Communities are unlikely to invest in measuring sustainability indicators unless monitoring provides immediate and clear benefits. However, in the context of goals, targets, and/or baselines, sustainability indicators can more effectively contribute to a process of development that matches local priorities and engages the interests of local people.

Verb retrieval in fluent aphasia: a clinical study

Background: Problems with lexical retrieval are common across all types of aphasia but certain word classes are thought to be more vulnerable in some aphasia types. Traditionally, verb retrieval problems have been considered characteristic of non-fluent aphasias but there is growing evidence that verb retrieval problems are also found in fluent aphasia. As verbs are retrieved from the mental lexicon with syntactic as well as phonological and semantic information, it is speculated that an improvement in verb retrieval should enhance communicative abilities in this population as in others. We report on an investigation into the effectiveness of verb treatment for three individuals with fluent aphasia. Methods & Procedures: Multiple pre-treatment baselines were established over 3 months in order to monitor language change before treatment. The three participants then received twice-weekly verb treatment over approximately 4 months. All pre-treatment assessments were administered immediately after treatment and 3 months post-treatment. Outcome & Results: Scores fluctuated in the pre-treatment period. Following treatment, there was a significant improvement in verb retrieval for two of the three participants on the treated items. The increase in scores for the third participant was statistically nonsignificant but post-treatment scores moved from below the normal range to within the normal range. All participants were significantly quicker in the verb retrieval task following treatment. There was an increase in well-formed sentences in the sentence construction test and in some samples of connected speech. Conclusions: Repeated systematic treatment can produce a significant improvement in verb retrieval of practised items and generalise to unpractised items for some participants. An increase in well-formed sentences is seen for some speakers. The theoretical and clinical implications of the results are discussed.

Blood-clotting response tests for resistance to diphacinone and chlorophacinone in the Norway rat (Rattus norvegicus Berk.)

Resistance baselines were obtained for the first generation anticoagulant rodenticides chlorophacinone and diphacinone using laboratory, caesarian-derived Norway rats (Rattus norvegicus) as the susceptible strain and the blood clotting response test method. The ED99 estimates for a quantal response were: chlorophacinone, males 0.86 mg kg−1, females 1.03 mg kg−1; diphacinone, males 1.26 mg kg−1, females 1.60 mg kg−1. The dose-response data also showed that chlorophacinone was significantly (p<0.0001) more potent than diphacinone for both male and female rats, and that male rats were more susceptible than females to both compounds (p<0.002). The ED99 doses were then given to groups of five male and five female rats of the Welsh and Hampshire warfarin-resistant strains. Twenty-four hours later, prothrombin times were slightly elevated in both strains but all the animals were classified as resistant to the two compounds, indicating cross-resistance from warfarin to diphacinone and chlorophacinone. When rats of the two resistant strains were fed for six consecutive days on baits containing either diphacinone or chlorophacinone, many animals survived, indicating that their resistance might enable them to survive treatments with these compounds in the field.

Warfarin susceptibility in the lesser bandicoot rat (Bandicota bengalensis)

Warfarin is a first generation anticoagulant that relies on multiple feeding events to achieve lethality in susceptible rodents. For the Bandicoot rat, warfarin susceptibility baselines were established using the lethal feeding period (LFP) test methodology. Against a 0.003% warfarin formulation, LFP50 values of 2 and 4 days, and LFP99 values of 16 and 10 days were obtained for males and females respectively. However, consumption of rodenticide was significantly reduced after the 4th and 5th days of test, at a time when animals would be expected to experience symptoms of warfarin toxicity. This would seriously compromise the Probit analysis, particularly for estimates of higher percentiles. Possible modifications to the methodology are discussed to overcome this problem. Although the majority of animals were highly susceptible to warfarin, one female animal that survived a high dose of active ingredient (79.1 mg kg-1) may bode for future resistance

Resistance to the first and second generation anticoagulant rodenticides: a new perspective

Warfarin resistance was first discovered among Norway rat (Rattus norvegicus) populations in Scotland in 1958 and further reports of resistance, both in this species and in others, soon followed from other parts of Europe and the United States. Researchers quickly defined the practical impact of these resistance phenomena and developed robust methods by which to monitor their spread. These tasks were relatively simple because of the high degree of immunity to warfarin conferred by the resistance genes. Later, the second generation anticoagulants were introduced to control rodents resistant to the warfarin-like compounds, but resistance to difenacoum, bromadiolone and brodifacoum is now reported in certain localities in Europe and elsewhere. However, the adoption of test methods designed initially for use with the first generation compounds to identify resistance to compounds of the second generation has led to some practical difficulties in conducting tests and in establishing meaningful resistance baselines. In particular, the results of certain test methodologies are difficult to interpret in terms of the likely impact on practical control treatments of the resistance phenomena they seek to identify. This paper defines rodenticide resistance in the context of both first and second generation anticoagulants. It examines the advantages and disadvantages of existing laboratory and field methods used in the detection of rodent populations resistant to anticoagulants and proposes some improvements in the application of these techniques and in the interpretation of their results.

Impact of the modal aerosol scheme GLOMAP-mode on aerosol forcing in the Hadley Centre Global Environmental Model

The Hadley Centre Global Environmental Model (HadGEM) includes two aerosol schemes: the Coupled Large-scale Aerosol Simulator for Studies in Climate (CLASSIC), and the new Global Model of Aerosol Processes (GLOMAP-mode). GLOMAP-mode is a modal aerosol microphysics scheme that simulates not only aerosol mass but also aerosol number, represents internally-mixed particles, and includes aerosol microphysical processes such as nucleation. In this study, both schemes provide hindcast simulations of natural and anthropogenic aerosol species for the period 2000–2006. HadGEM simulations of the aerosol optical depth using GLOMAP-mode compare better than CLASSIC against a data-assimilated aerosol re-analysis and aerosol ground-based observations. Because of differences in wet deposition rates, GLOMAP-mode sulphate aerosol residence time is two days longer than CLASSIC sulphate aerosols, whereas black carbon residence time is much shorter. As a result, CLASSIC underestimates aerosol optical depths in continental regions of the Northern Hemisphere and likely overestimates absorption in remote regions. Aerosol direct and first indirect radiative forcings are computed from simulations of aerosols with emissions for the year 1850 and 2000. In 1850, GLOMAP-mode predicts lower aerosol optical depths and higher cloud droplet number concentrations than CLASSIC. Consequently, simulated clouds are much less susceptible to natural and anthropogenic aerosol changes when the microphysical scheme is used. In particular, the response of cloud condensation nuclei to an increase in dimethyl sulphide emissions becomes a factor of four smaller. The combined effect of different 1850 baselines, residence times, and abilities to affect cloud droplet number, leads to substantial differences in the aerosol forcings simulated by the two schemes. GLOMAP-mode finds a presentday direct aerosol forcing of −0.49Wm−2 on a global average, 72% stronger than the corresponding forcing from CLASSIC. This difference is compensated by changes in first indirect aerosol forcing: the forcing of −1.17Wm−2 obtained with GLOMAP-mode is 20% weaker than with CLASSIC. Results suggest that mass-based schemes such as CLASSIC lack the necessary sophistication to provide realistic input to aerosol-cloud interaction schemes. Furthermore, the importance of the 1850 baseline highlights how model skill in predicting present-day aerosol does not guarantee reliable forcing estimates. Those findings suggest that the more complex representation of aerosol processes in microphysical schemes improves the fidelity of simulated aerosol forcings.

Assessing and monitoring impacts of genetically modified plants on agro-ecosystems: the approach of AMIGA project

The environmental impacts of genetically modified crops is still a controversial issue in Europe. The overall risk assessment framework has recently been reinforced by the European Food Safety Authority(EFSA) and its implementation requires harmonized and efficient methodologies. The EU-funded research project AMIGA − Assessing and monitoring Impacts of Genetically modified plants on Agro-ecosystems − aims to address this issue, by providing a framework that establishes protection goals and baselines for European agro-ecosystems, improves knowledge on the potential long term environmental effects of genetically modified (GM) plants, tests the efficacy of the EFSA Guidance Document for the Environmental Risk Assessment, explores new strategies for post market monitoring, and provides a systematic analysis of economic aspects of Genetically Modified crops cultivation in the EU. Research focuses on ecological studies in different EU regions, the sustainability of GM crops is estimated by analysing the functional components of the agro-ecosystems and specific experimental protocols are being developed for this scope.

Formal linguistic approaches to heritage language acquisition: bridges for pedagogically oriented research

The goal of this chapter is to lay out the central themes of heritage language acquisition research adopting a formal/theoretical linguistic perspective.  Specifically, we aim to provide a detailed discussion of the nature of heritage language grammars. In doing so, we will address the debates on how to explain heritage speaker competence differences from monolingual baselines and more. This chapter will not be limited to discussions of Spanish as a heritage language, but rather will highlight the important role that Spanish has played and will continue to play in the development of heritage language acquisition studies. Finally, we will offer some comments/insights on how the information covered regarding the formal linguistic properties of heritage speaker knowledge should be considered for and implemented in heritage language pedagogies and thus dealing with heritage speakers in the classroom setting.