Technologies for biological containment of GM and Non-GM crops

International Perspective The development of GM technology continues to expand into increasing numbers of crops and conferred traits. Inevitably, the focus remains on the major field crops of soybean, maize, cotton, oilseed rape and potato with introduced genes conferring herbicide tolerance and/or pest resistance. Although there are comparatively few GM crops that have been commercialised to date, GM versions of 172 plant species have been grown in field trials in 31 countries. European Crops with Containment Issues Of the 20 main crops in the EU there are four for which GM varieties are commercially available (cotton, maize for animal feed and forage, and oilseed rape). Fourteen have GM varieties in field trials (bread wheat, barley, durum wheat, sunflower, oats, potatoes, sugar beet, grapes, alfalfa, olives, field peas, clover, apples, rice) and two have GM varieties still in development (rye, triticale). Many of these crops have hybridisation potential with wild and weedy relatives in the European flora (bread wheat, barley, oilseed rape, durum wheat, oats, sugar beet and grapes), with escapes (sunflower); and all have potential to cross-pollinate fields non-GM crops. Several fodder crops, forestry trees, grasses and ornamentals have varieties in field trials and these too may hybridise with wild relatives in the European flora (alfalfa, clover, lupin, silver birch, sweet chestnut, Norway spruce, Scots pine, poplar, elm, Agrostis canina, A. stolonifera, Festuca arundinacea, Lolium perenne, L. multiflorum, statice and rose). All these crops will require containment strategies to be in place if it is deemed necessary to prevent transgene movement to wild relatives and non-GM crops. Current Containment Strategies A wide variety of GM containment strategies are currently under development, with a particular focus on crops expressing pharmaceutical products. Physical containment in greenhouses and growth rooms is suitable for some crops (tomatoes, lettuce) and for research purposes. Aquatic bioreactors of some non-crop species (algae, moss, and duckweed) expressing pharmaceutical products have been adopted by some biotechnology companies. There are obvious limitations of the scale of physical containment strategies, addressed in part by the development of large underground facilities in the US and Canada. The additional resources required to grow plants underground incurs high costs that in the long term may negate any advantage of GM for commercial productioNatural genetic containment has been adopted by some companies through the selection of either non-food/feed crops (algae, moss, duckweed) as bio-pharming platforms or organisms with no wild relatives present in the local flora (safflower in the Americas). The expression of pharmaceutical products in leafy crops (tobacco, alfalfa, lettuce, spinach) enables growth and harvesting prior to and in the absence of flowering. Transgenically controlled containment strategies range in their approach and degree of development. Plastid transformation is relatively well developed but is not suited to all traits or crops and does not offer complete containment. Male sterility is well developed across a range of plants but has limitations in its application for fruit/seed bearing crops. It has been adopted in some commercial lines of oilseed rape despite not preventing escape via seed. Conditional lethality can be used to prevent flowering or seed development following the application of a chemical inducer, but requires 100% induction of the trait and sufficient application of the inducer to all plants. Equally, inducible expression of the GM trait requires equally stringent application conditions. Such a method will contain the trait but will allow the escape of a non-functioning transgene. Seed lethality (‘terminator’ technology) is the only strategy at present that prevents transgene movement via seed, but due to public opinion against the concept it has never been trialled in the field and is no longer under commercial development. Methods to control flowering and fruit development such as apomixis and cleistogamy will prevent crop-to-wild and wild-to-crop pollination, but in nature both of these strategies are complex and leaky. None of the genes controlling these traits have as yet been identified or characterised and therefore have not been transgenically introduced into crop species. Neither of these strategies will prevent transgene escape via seed and any feral apomicts that form are arguably more likely to become invasives. Transgene mitigation reduces the fitness of initial hybrids and so prevents stable introgression of transgenes into wild populations. However, it does not prevent initial formation of hybrids or spread to non-GM crops. Such strategies could be detrimental to wild populations and have not yet been demonstrated in the field. Similarly, auxotrophy prevents persistence of escapes and hybrids containing the transgene in an uncontrolled environment, but does not prevent transgene movement from the crop. Recoverable block of function, intein trans-splicing and transgene excision all use recombinases to modify the transgene in planta either to induce expression or to prevent it. All require optimal conditions and 100% accuracy to function and none have been tested under field conditions as yet. All will contain the GM trait but all will allow some non-native DNA to escape to wild populations or to non-GM crops. There are particular issues with GM trees and grasses as both are largely undomesticated, wind pollinated and perennial, thus providing many opportunities for hybridisation. Some species of both trees and grass are also capable of vegetative propagation without sexual reproduction. There are additional concerns regarding the weedy nature of many grass species and the long-term stability of GM traits across the life span of trees. Transgene stability and conferred sterility are difficult to trial in trees as most field trials are only conducted during the juvenile phase of tree growth. Bio-pharming of pharmaceutical and industrial compounds in plants Bio-pharming of pharmaceutical and industrial compounds in plants offers an attractive alternative to mammalian-based pharmaceutical and vaccine production. Several plantbased products are already on the market (Prodigene’s avidin, β-glucuronidase, trypsin generated in GM maize; Ventria’s lactoferrin generated in GM rice). Numerous products are in clinical trials (collagen, antibodies against tooth decay and non-Hodgkin’s lymphoma from tobacco; human gastric lipase, therapeutic enzymes, dietary supplements from maize; Hepatitis B and Norwalk virus vaccines from potato; rabies vaccines from spinach; dietary supplements from Arabidopsis). The initial production platforms for plant-based pharmaceuticals were selected from conventional crops, largely because an established knowledge base already existed. Tobacco and other leafy crops such as alfalfa, lettuce and spinach are widely used as leaves can be harvested and no flowering is required. Many of these crops can be grown in contained greenhouses. Potato is also widely used and can also be grown in contained conditions. The introduction of morphological markers may aid in the recognition and traceability of crops expressing pharmaceutical products. Plant cells or plant parts may be transformed and maintained in culture to produce recombinant products in a contained environment. Plant cells in suspension or in vitro, roots, root cells and guttation fluid from leaves may be engineered to secrete proteins that may be harvested in a continuous, non-destructive manner. Most strategies in this category remain developmental and have not been commercially adopted at present. Transient expression produces GM compounds from non-GM plants via the utilisation of bacterial or viral vectors. These vectors introduce the trait into specific tissues of whole plants or plant parts, but do not insert them into the heritable genome. There are some limitations of scale and the field release of such crops will require the regulation of the vector. However, several companies have several transiently expressed products in clinical and pre-clinical trials from crops raised in physical containment.

Testing for non-linearity in daily sterling exchange rates

A number of tests for non-linear dependence in time series are presented and implemented on a set of 10 daily sterling exchange rates covering the entire post Bretton-Woods era until the present day. Irrefutable evidence of non-linearity is shown in many of the series, but most of this dependence can apparently be explained by reference to the GARCH family of models. It is suggested that the literature in this area has reached an impasse, with the presence of ARCH effects clearly demonstrated in a large number of papers, but with the tests for non-linearity which are currently available being unable to classify any additional non-linear structure.

Observation impact in data assimilation: the effect of non-Gaussian observation error.

Data assimilation methods which avoid the assumption of Gaussian error statistics are being developed for geoscience applications. We investigate how the relaxation of the Gaussian assumption affects the impact observations have within the assimilation process. The effect of non-Gaussian observation error (described by the likelihood) is compared to previously published work studying the effect of a non-Gaussian prior. The observation impact is measured in three ways: the sensitivity of the analysis to the observations, the mutual information, and the relative entropy. These three measures have all been studied in the case of Gaussian data assimilation and, in this case, have a known analytical form. It is shown that the analysis sensitivity can also be derived analytically when at least one of the prior or likelihood is Gaussian. This derivation shows an interesting asymmetry in the relationship between analysis sensitivity and analysis error covariance when the two different sources of non-Gaussian structure are considered (likelihood vs. prior). This is illustrated for a simple scalar case and used to infer the effect of the non-Gaussian structure on mutual information and relative entropy, which are more natural choices of metric in non-Gaussian data assimilation. It is concluded that approximating non-Gaussian error distributions as Gaussian can give significantly erroneous estimates of observation impact. The degree of the error depends not only on the nature of the non-Gaussian structure, but also on the metric used to measure the observation impact and the source of the non-Gaussian structure.

How the magnetopause transition parameter works

The transition parameter is based on the electron characteristics close to the Earth's dayside magnetopause, but reveals systematic ordering of other, independent, data such as the ion flow, density and temperature and the rientation and strength of the magnetic field. Potentially, therefore, it is a very useful tool for resolving ambiguities in a sequence of satellite data caused by the effects of structure and motion of the boundary; however, its application has been limited because there has been no clear understanding of how it works. We present an analysis of data from the AMPTE-UKS satellite which shows that the transition parameter orders magnetopause data because magnetic reconnection generates newly-opened field lines which coat the boundary: a direct relationship is found with the time elapsed since the boundary-layer field line was opened. A simple model is used to reproduce this behaviour.

Study of optimization for cooperative motion between two humans in mutual tracking

Verbal communication is essential for human society and human civilization. Non-verbal communication, on the other hand, is more widely used not only by human but also other kind of animals, and the content of information is estimated even larger than the verbal communication. Among the non-verbal communication mutual motion is the simplest and easiest to study experimentally and analytically. We measured the power spectrum of the hand velocity in various conditions and clarified the following points on the feed-back and feed- forward mechanism as basic knowledge to understand the condition of good communication.

The perception of support received from breast care nurses by depressed patients following a diagnosis of breast cancer

INTRODUCTION Due to their specialist training, breast care nurses (BCNs) should be able to detect emotional distress and offer support to breast cancer patients. However, patients who are most distressed after diagnosis generally experience least support from care staff. To test whether BCNs overcome this potential barrier, we compared the support experienced by depressed and non-depressed patients from their BCNs and the other main professionals involved in their care: surgeons and ward nurses. PATIENTS AND METHODS Women with primary breast cancer (n = 355) 2–4 days after mastectomy or wide local excision, self-reported perceived professional support and current depression. Analysis of variance compared support ratings of depressed and non-depressed patients across staff types. RESULTS There was evidence of depression in 31 (9%) patients. Depressed patients recorded less surgeon and ward nurse support than those who were not depressed but the support received by patients from the BCN was high, whether or not patients were depressed. CONCLUSIONS BCNs were able to provide as much support to depressed patients as to non-depressed patients, whereas depressed patients felt less supported by surgeons and ward nurses than did non-depressed patients. Future research should examine the basis of BCNs' ability to overcome barriers to support in depressed patients. Our findings confirm the importance of maintaining the special role of the BCN.

CGIAR research program on grain legumes

EXECUTIVE SUMMARY Background and context The Grain Legumes CRP was established to bring all research and development work on grain legumes within the CGIAR system under one umbrella. It was set up to provide public goods outcomes to serve the needs of the sustainable production and consumption of grain legumes in the developing world, capitalising upon their properties that enhance the natural resource base upon which production so unequivocally depends. The choice of species and research foci were finalised following extensive consultation with all stakeholders (though perhaps fewer end users), and cover all disciplines that contribute to long-lasting solutions to the issues of developing country production and consumption. ICRISAT leads Grain Legumes and is partnered by the CGIAR centers ICARDA, IITA and CIAT and a number of other important partners, both public and private, and of course farmers in the developed and developing world. Originally in mid-2012 Grain Legumes was structured around eight Product Lines (PL) (i.e. technological innovations) intersecting five Strategic Components (SC) (i.e. arranged as components along the value chain). However, in 2015, it was restructured along a more R4D output model leading to Intermediate Development Outcomes (IDOs). Thus five Flagship Projects (FP) more closely reflecting a systematic pipeline of progression from fundamental science, implementation of interventions and the development of capacity and partnerships to promote and adopt impactful outcomes: FP1) Managing Productivity through crop interactions with biotic and abiotic constraints; FP2) Determination of traits that address production constraints and opportunities; FP3) Trait Deployment of those traits through breeding; FP4) Seed Systems, post-harvest processing and nutrition; FP5) Capacity-Building and Partnerships. Another three cross-cutting FPs analyse the broader environment surrounding the adoption of outputs, the capitalising of investments in genomics research, and a focus on the Management and Governance of Grain Legumes: FP6) Knowledge, impacts, priorities and gender organisation; FP7) Tools and platforms for high throughput genotyping and bioinformatics; and FP8) Management and Governance. Five FPs focus on R4D; FPs 5 and 6 are considered cross-cutting; FP 7 has a technical focus and FP 8 has an overarching objective. Over the three year period since its inception in July 1012, Grain Legumes has had a total budget of $140 million, with $62M originally to come from W1/W2 and the remaining $78M to come from W3/bilateral. In actuality only $45M came from W1/W2 but $106M from W3/bilateral corresponding to 106% of expectation. Purpose, scope and objectives of the external evaluation Principally, the evaluation of Grain Legumes is to ensure that the program is progressing in an effective manner towards addressing the system-level outcomes of the CGIAR as they relate to grain legumes. In essence, the evaluation aims to provide essential evaluative information for decision-making by Program Management and its funders on issues such as extension, expansion and structuring of the program and adjustments in relevant parts of the program. Subsequent to the formal signing of the agreed terms of reference, the evaluation team was also invited to comment upon the mooted options for merging and/or disaggregating of Grain Legumes. The audiences are therefore manifold, from the CGIAR Fund Council and Consortium, the Boards of Trustees of the four component CGIAR centres, the Grain Legumes Steering, Management and Independent Advisory Committees, to the researchers and others involved in the delivery of R4D outcomes and their partner organisations. The evaluation was not only summative in measuring results from Grain Legumes at arm’s length; it was also formative in promoting learning and improvements, and developmental in nurturing adaption to transformational change with time. The evaluation report was written in a manner that allows for engagement of key partners and funders in a dialogue as to how to increase ownership and a common understanding of how the goals are to be achieved. We reviewed research undertaken before the CRPs but leading to impacts during Grain Legumes, and research commenced over the past 2.5 years. For related activities pre- and post-commencement of Grain Legumes, we reviewed the relevance of activities and their relation to CGIAR and the Grain Legumes goals, whether they were likely to lead to the outcomes and impacts as documented in the Grain Legumes proposal, and the quality of the science underpinning the likelihood to deliver outcomes. Throughout, we were cognisant of the extent of the reach of CGIAR centres’ activities, and those of stakeholders upon which the impact of CGIAR R4D depends. Within our remit we evaluated the original and modified management and governance structures, and all the processes/responsibilities managed within those structures. Besides the evaluation of the technical and managerial issues of Grain Legumes, we addressed cross-cutting issues of gender sensitivity, capacity building and the creation and nurturing of partnerships. The evaluation also has the objective to provide information relating to the development of full proposals for the new CRP funding cycle. The evaluation addressed six overarching questions developed from the TOR questions (listed in the Inception Report, 2015 [http://1drv.ms/1POQSZh] and others including cross-cutting issues, phrasing them within the context of traditional evaluation criteria: 1. Relevance: Global development, urbanisation and technological innovation are progressing rapidly, are the aims and focus of Grain Legumes coherent, robust, fit for purpose and relevant to the global community? 2. Efficiency: Is the structure and effectiveness of leadership across Grain Legumes developing efficient partnership management and project management across PLs? 3. Quality of science: Is Grain Legumes utilising a wide range of technologies in a way that will increase our fundamental understanding of the biology that underpins several PLs; and are collected data used in the most effective way? 4. Effectiveness: Are Product Lines strategic contributors to the overarching aims and vision for Grain Legumes? 5. Impact: Are the impact pathways that underlie each PL well defined, measureable and achievable; and are they sufficiently defined in terms of beneficiaries? Does progress towards achieving outputs and outcomes from the major research areas indicate a lasting benefit for CGIAR and the communities it serves? 6. Sustainability: Is Grain Legumes managing the increasing level of restricted funding in terms of program quality and effectiveness, including attracting and retaining quality staff? Questions for the evaluation of governance and management focused on accountability, transparency, the effectiveness and success of program execution, change management processes and communication methods, taking account of the effects of CGIAR reform. The three crosscutting issues were considered as follows: i) gender balance in program delivery, e.g. whether each PL is able to contribute to the increased income, food security, nutrition, environmental and resource conservation for resource-poor women and men existing in rural livelihoods; ii) are internal and external capacity gaps identified/met, is capacity effectively developed within each product line, and are staff at all levels engaged in contributing ideas towards capacity building; and iii) is there effective involvement of partners in research and activity programming, what are the criteria for developing partnerships, how they are formalised and how is communication between partners and within Grain Legumes managed? It was not in remit to search for output, outcomes or impact, however as highlighted later, much of our time was spent on searching for information to support claims of impact, since Grain Legumes had no effective dedicated M&E in place at the time of undertaking the review. Approach and methodology The evaluation was conducted when Grain Legumes had been operational for approximately 3 years. The approach and methodology followed that outlined in the Inception Report [http://1drv.ms/1POQSZh]. The CCEE Team based its findings, conclusions and recommendations on data collection from several sources:  review of program documents, communications with the CO, minutes and presentations from all management and governance committee meetings  review of previous assessments and evaluations  sampling of Grain Legume projects in 7 countries1  more than 66 face to face interviews, a further 133 persons in groups and 4 phone/Skype conversations: ICRISAT, ICARDA, CIAT and IITA staff, partners and stakeholders. Meetings with one Independent Science and Partnership Council (ISPC) member.  meetings with over 100 people in 16 external groups, such as farmers’ groups  online survey completed by 126 (33.4%) scientists who contribute to Grain Legumes and a number of non-CGIAR partners and Management representatives  bibliometric review of 10 publications within each PL to qualitatively assess the design, conduct, analysis and presentation of results  quantitative and qualitative self-assessment of the contributions of each of the PLs to the six criteria and 3 cross-cutting issues of evaluation mentioned above completed by PLCs (see below). We reviewed the Logical Framework that underpins the desired Goals, or Impacts of Grain Legumes, and the links between the outputs and inputs as they related to the organisational units of Grain Legumes. The logical framework approach to planning and management of Grain Legumes activities implies a linear process, leading from activities, outputs, outcomes, to impacts, but within such an approach there may be room for a more systems dynamics approach allowing for feedback at every step and within every step, in order to refine and improve upon the respective activities as new results, ideas, and directions come to light. We then developed a matrix that summarised quantitatively and qualitatively the contributions of each of the PLs to the six criteria and 3 cross-cutting issues of evaluation mentioned above. Main findings and conclusions Grain legume production and consumption remain of great importance to the food security of not inconsiderable populations in the developing world, and merit sustained research investment. We conclude that Grain Legumes continues to contribute significant returns to research investments by the CGIAR, and such investment should continue. The global research community looks to the CGIAR for leadership in Grain legumes, but needs to be assured of value adding when bringing CGIAR centres under the expected umbrella of synergy. However, there is considerable scope for improving the efficiency with which outcomes are achieved. We note that an absence of an effective M&E has hampered the assessment of the effectiveness of proposed impact pathways. Likewise progress has been hampered by the limited numbers of research partnerships with Advanced Institutes and by budgetary constraints (lamented for their stifling effects on continuation of ongoing exciting research). The unworkable management structure constrains the CRP Director’s leadership role; responsibility without authority will never lead to effective outcomes. Good fortune is responsible for many of the successes of Grain Legumes, underpinned by a devoted work force across the participating CGIAR centres and partners. The quality of the science is not uniformly high, and we believe that mentoring of scientists should be given priority where quality is poor. Simplified yet informative reporting is an imperative to this. World class science underpins the identification of, and molecular basis for, traits important for yield improvement and this expertise should be extended to all grain legume species, capitalising upon the germplasm collections. The linking of Grain Legumes with regional research and development consortia has been very successful, with outcomes aligning with those of Grain Legumes. We see that with declining funding consolidation of research effort based on likely successes will be necessary, and welcome the move afoot to incorporate grain legumes into an agri-food system focused on successful value chains that deliver sustainable outcomes. Relevance and Strategy Grain Legumes has geographic and disciplinary relevance, addressing the major supply chain issues of variety development seed system and agronomy, with some attention to quality and postharvest marketing systems. The CRP has provided the opportunity to cut ongoing and to initiate new research. Research funded by the Gates Foundation (Anon, 2014) suggests that the need for improvement is greatest in Africa and advocates reducing the number of crop by country combinations when resources are sparse. The lesser research investment in Latin America, however, is not in line with the regions’ dependency on legumes. In spite of the fact that there is no evidence of strong inter-partner CGIAR centre or internal synergy, the program is still moving ahead on most fronts in line with the overall project logframe. This is in spite of continual pushing and pulling by in particular donors and the CO. However, to quantify real impact, we believe Grain Legumes must have access to reliable baseline data on production and consumption, and this is missing. Similarly, there is little evidence of the proposed ‘Inclusive Market Oriented Development’ (IMOD) framework being used to assist with priority setting. The product lines, eight of which cover most of the historical programmes in place in the partner CGIAR centres at the commencement of the Grain Legumes, do not cover all the constraints for formal constraints analysis was not undertaken at the inception of the Grain Legumes, and some of this additionally identified research is undertaken under the umbrella of the FPs; this needs to be rationalised. We found the PLs to be isolated in activity, even with minimally-integrated activities within each PL, with little evidence of synergy between PLs. Even though the SCs should ensure a systems approach, as with the new FPs, we did not get a feel that this is so. The underplaying of agronomy, and production practices may be one reason for this. We believe that treating legume crops as if they were horticultural crops will increase farmer returns from investment. The choice of Flagship Projects makes sense, with the flow of activity firstly around crop management and agronomy followed by the logical sequence of trait discovery, incorporation into improved varieties, dissemination of those varieties through appropriate seed chains leading to market impacts, and the capacity building required at all steps. One obvious omission, however, is the lack of a central and strategic policy on the role of transgenics in Grain Legumes. We found four notable comparative advantages for Grain Legumes: the access to germplasm of component species, the use of the phenotyping facility at ICRISAT, the approach for village level industry for IPM, and the emphasis on hybrid pigeonpea. Efficiency Each centre has strong control of, and emphasis on, their ‘species’ domains, and ownership of the same detracts from possible synergy. Without synergy or value add, the Grain Legumes brings with it no comparative advantage over each centre continuing their own pre-CRP research agendas. We found little evidence of integration of programmes between centres and almost no cross-centre authorship of publications, such as could have occurred with the integrated cross-centre approaches to stress tolerance including crop modelling: the one publication (Gaur et al., 2015) on heat tolerance by ICRISAT, CIAT and ICARDA does not provide any keys to inter-centre collaboration. The integration of each centre with NARS and university research programmes is good, but the cross-centre links with NARS are poor. A better coordinated integration with Grain Legumes, , rather than through the individual centres, may reduce transactions costs for NARS, Monitoring and evaluation is, as noted throughout our report, one area of Grain Legumes research management that has not been given the attention it should have received. If it had have received proper attention, some of the issues of poor efficiency might have been nipped in the bud. A strong monitoring and evaluation system would have provided the baseline data and set the milestones that would have allowed both efficiency and effectiveness to be better appraised. We found no attempt to define comparative advantages of the CGIAR centres and their R4D activities, although practice showed the better grasp of CIAT in developing innovative seed distribution systems. During field visits and interviews, the CCEE Team observed shortcomings in the communication processes within Grain Legumes and with the broader scientific community and the public. For example, the public face of the program on the internet is out of date. Survey findings, however, suggest that information is shared freely and routinely within the PL within which scientists work. Some external issues, such as those with funding, low W1/W2 and poor sustainability of funding (especially if funding is top heavy with a few agencies), undermine research investment and confidence of partners in the system (e.g. as voiced by researchers working on crops and countries not included in TL III and the cessation of ongoing competitively-funded projects especially in India), but other issues attributable to the governance and management of the Grain Legumes, such as opaque integration of W3/bilaterals with W1/W2 funding require attention. Offsetting this, the existence of the Grain Legumes did mobilise additional funding [that it would not have if Grain Legumes did not exist]. We were concerned that Grain Legumes is simply not recognised outside of the CRP, with a limited www presence and centres promote themselves, rather than Grain Legumes (with exception in IITA). This is not a good move if one wishes to increase investment in the Grain Legumes. Although funding agencies require cost:benefit ratios, for example for each PL we faced difficulty in determining comparative value for money between investment in different types of research, and in being able to clearly attribute research and development outcomes to financial investment. There was also a time CCEE frame issue too. There is poor interaction with the private sector, notably in areas where they have a comparative financial advantage. We questioned in particular the apparent lack of interaction with the major agro-chemical companies, with respect to the development of herbicide tolerant (HT) grain legumes and the lack of evidence that the regulatory and trade aspects related to herbicide tolerant crops had been considered. Quality of science The quality of the science is highly variable across Grain Legumes, with pockets of real excellence that are linked to good levels of productivity, whereas other PLs are struggling to deliver quality publications, and outputs and outcomes that are based on these. There is much evidence of gradualism in terms of research output and outcomes, i.e. essentially the same activities that were ongoing at the time of the launch of Grain Legumes are still in place. However, there are examples of game changers including those from valuable investments in genomics, phenotyping, and bio-control. We were pleased to see large proportions of collaboration on publications with non-CGIAR centres, reflecting cooperation with partners in developed and developing countries. The value of collaboration when ensuring quality of science cannot be stressed highly enough both within the CRP, and with other global and national partners. PLs should be given incentives to collaborate with other CRPs and external institutions. There is little cohesion between PLs and with other CRPs as evidenced by publications, although there are some exceptions. We suspect the reasons for this are driven by funding. Productivity from the different PLs is also highly variable and it is not clear what other activities staff are engaged in since, in some PLs, they do not appear to lead to quality publications. Effectiveness Grain Legumes has been very effective in addressing component issues of research, but not the continuum from variety development to legumes on someone’s dinner plate. Our overall assessment of the effectiveness of Grain Legumes in stimulating synergy, innovation and impact indicate that gradualism is more prevalent than innovation. It also shows, as do publications, that there is little integration of disciplines or a focus on ‘systems’. The absence of socio-economists from research teams is evident in the general lack of an end user focus. However, research on genomics, plant breeding and seed systems have made great strides forward, on the brink of delivering impact. Agronomy has been a poor sister, but some of the competitive grants within Grain Legumes have unearthed some potential game changers, such as objective use of transplanting as an agronomic practice. As mentioned earlier, the lack of effective M&E (however, this was part of some major projects such as TL II/TL III), and therefore the ability to monitor impact pathways and achievement of impact, implies no systematic management of data. This creates difficulty when attempting to evaluate the achievement of the Grain Legumes objectives. One might have expected at least one attempt to try to develop publications between centres arguing for similar biologies/research approaches, bringing species together under one umbrella, but we did not find any evidence for this. It is most unfortunate that, due to budgetary cuts, the new ‘schemes’, e.g. competitive grants and scholarships, were cut off before gaining a foothold. With 8 species addressed by Grain Legumes, it is not unexpected that there will be little evidence of shared protocols across centres/species. One rare example was that hosted by the United States Department of Agriculture (USDA) on shared methods for phenotyping of legume germplasm. Researchers from CIAT, IITA, ICRISAT and three USDA stations attended, focusing in simple canopy temperature and root morphology measurements. It is our belief that as a set of research centres, the CGIAR centres should be focusing on the research for which they have a comparative advantage. While imposing the restructure to FPs, which is fine for development objectives and outcomes (funded through W3/bilateral), it is less so for a research institute, and the structure should not detract from the more basic work expected of an international CGIAR centre (or set of centres as in a CRP). Impact It is well known that research does not always lead to scientific breakthroughs. Also, activities such as plant breeding are long term; making impacts difficult to assess. We believe that sufficient progress with genomics and associated research has been made to warrant impact, but we are unable to quantify the levels of impact, or the timeframe for the same. Work in Grain Legumes has enormous potential for real impact in scientific research, commercial, farming, smallholder and household communities, much of which is being realised. However, the PLs need to become more adept at providing convincing cases that are strongly evidenced for these impacts, as this is likely to be a key factor in leveraging future funding. Claimed gains must be referenced against baseline data, and these are not always readily available. The CCEE Team realises that such impact evaluation represents a significant drain on resources, and Grain Legumes should determine whether the balance of costs to benefits favours such investment. Interviews conducted by the CCEE during site visits showed that PLs are quantifying the area of adoption of varieties, but in most cases they are not measuring the impact on environment, health/nutrition. Since the health and nutritional benefits and the environmental gains from growing legumes are major arguments for supporting grain legume research, the community is currently missing substantial opportunities to strengthen its own case for continued support. Whilst there are some impressive examples of considering the whole value chain, e.g. white beans from production through to export; in the main, the pipeline to end user is somewhat piece-meal, with no clear definition of the end user nor differential responsibility of Grain Legumes and of partners. The lack of robust time-defined impact pathways is highlighted in Section 7.4, and even though developed for PL5, timeframes are essential for measuring progress against prediction. Sustainability In summary, there is general acknowledgement that future funding is likely to become more limited, specifically in W1&2 and there is understandable concern over the support for the staff and basic infrastructure that underpin the Grain Legumes programme. For example, it is reported that staffing in parts of CIAT has been dependent on W1&2 and that this is too unstable to re-establish a critical mass. The present system whereby W3 and bilateral projects do not pay a realistic level of overheads means that such projects are being effectively subsidised by W1&2. This position is not sustainable in the long term as there will be a progressive but definite loss of basic skills and resources in the core centres. The only obvious options to prevent this outcome include a severe reduction in the fixed costs of the centres and/or a refusal to accept W3 and bilateral funding with an inadequate overhead component. In the latter case, there is an obvious danger that funders will move their resources away from the CGIAR system towards other, perhaps less expensive, suppliers of research, and possibly more relevant development expertise. This issue must be addressed. As the Grain Legumes moves into the future, and if sustainable funding cannot be assured, decisions must be made concerning a reduction in activities, keeping some caretaker breeding maintenance, and focus (as has TL III) on fewer species and a reduced geographic focus. Cross cutting issues: Gender, capacity building and partnerships Gender is not mainstreamed, but there is some evidence that this is improving, especially with dedicated gender specialists and the slow integration of gender across CRPs. There is a need to approach gender through the vision of agriculture as a social practice, with recognition of what changes will be acceptable culturally and what not, and capitalising upon the perceived and actual features of production and processing that grain legumes are primarily women-based crops. Gender awareness may be high among Scientists, but it appears to be a predominantly passive attribute with few proactively seeking opportunities for gender equity. It is, however, a sound sensitivity base on which to build. Nevertheless, examples of notable gender initiatives were identified during field visits. For example, in Benin, the development of biocontrol technologies has enthusiastically integrated diversity, engaging with women farmers’ and youths while maintaining cultural norms. Women are gathering and processing, youths are taking the product to market. The implication is that several groups benefit, rather than domination by the majority group. In Malawi, innovative approaches have been developed to improving nutrition for children, such as incorporating nutrient enriched bean flour products into snacks. In India, scientists collaborating with gender scientists and socio-economists are identifying the impact of mechanical harvesting on agricultural labour and the potential displacement of female labourers. In Kenya, a novel initiative is improving the accessibility of certified seed for new varieties. Seed suppliers have introduced small packs of grain legume seed at low unit cost, which are being purchased by young people and women. Capacity building efforts for external partners are not clearly aligned with the research mandate and delivery of Grain Legumes. However, there are a number of training activities that are being undertaken by Grain Legumes, largely through the W3/bilateral project. Gender balance never reaches parity, but it appears that efforts are made to include female participants. Within the evaluation timeframe it was not possible to conduct external surveys to further validate or review external capacity building efforts in Grain Legumes. Training of scientists is significant, with >40 benefiting. Postgraduate training is varied across PLs, and there is some opportunity to increase the numbers being supervised. We consider that support for postgraduates at ICRISAT could be better coordinated, satisfying more of the students’ needs. It is important, however, to follow up investments in capacity building by monitoring effectiveness, career progressions and so on. Training activities appear to be rather centre-specific, not following a coordinated programme managed by, nor at the level of, the Grain Legumes. Numbers of persons trained and their gender are important, but a measure of the effectiveness of the training is more important. Although optimism is expressed by the great majority of Research Managers that partnerships were working well to leverage knowledge and research capacities, scientists have a less favourable view, particularly in terms of their incentives to participate. It seems likely that the activities taking place within Grain Legumes were, in the most part, continuations of previous collaborations. This is not surprising in light of the reduction in the emphasis on partnerships as Grain Legumes evolved to a funded project, and the consequent lack of opportunity and ambition for establishing novel partnerships. Where they exist, partnerships are good on the whole, especially with US. They could be expanded where comparative advantages exist (for example with Canada and Australia for machine harvestable legumes), but some earlier identified partnerships, e.g. with Turkey, have not been capitalised upon. Others experience problems of variety access (the embargo on exports of some sources of materials from India), yet others do have relevance e.g. imported Brazilian varieties in pre-release in Ethiopia (even though two of the three are from CIAT materials). Governance and Management The standard format of committee structure and responsibilities is common to other CRPs, as are the attendant problems. One of the major problems is that the Grain Legumes Director has responsibility but no authority; hence, even with the support of the RMC, the Director is unable to ‘direct’ in the literal sense of the work the activities of Grain Legumes. We also see the same sense of helplessness with the role of the PLCs. They have responsibility but no authority in managing the affairs of their PL, and they have no access to funds with which to promote intellectual collaboration and cooperation. Minutes from governance and management meetings do not reflect the compromised weak position of the Director and the associated difficulties in the management of Grain Legumes. Nor do the minutes reflect concerns about the amount of time spent by scientists in meetings for planning, integration, evaluation and reporting. Many scientists reported significant opportunity costs in participating in the ongoing imposed [by the CO] evolution of Grain Legumes and CRPs in general. The changes brought in by the CO have not helped promote any greater authority and capacity of the Grain Legumes Director to direct. Likewise, they do not address any of the issues with the conflict of interest in having the Lead Centre chair the Steering Committee. Indeed, we believe that the combining of the Steering Committee with the Independent Advisory Committee, besides becoming unwieldy in number, annuls any sense of independence in advice offered to the Grain Legumes management. We have concerns with the declining proportion of W1/W2 funds (as expressed in the section on Sustainability), and believe that when basic financial planning takes place, integration of W1/W2 and W3/bilateral sources must occur, and be linked to anticipated outcomes and impacts. This will ensure a close alignment of collaborators’ and partners’ objectives and contributions to that of the Grain Legumes. We also queried the process for, and the formality, or lack of, surrounding, the approval of annual budgets, and the level of priority setting when budgets are cut. Recommendations for Grain Legumes The CCEE Team makes the following recommendations, critical issues are highlighted in bold, and those that require action by an entity other than the Grain Legumes Research Management Committee or Project Management united are identified in a footnote. Relevance and Strategy Recommendation 1: A period of consistency is necessary to raise confidence, morale and trust across scientists, managers and partners to foster the assembly of enduring Grain Legumes outcomes2.  There needs to be a concerted effort to undertake baseline studies and to implement a robust M&E activity during this period. Without these data the foundation for integrated research in grain legumes is jeopardised.  There is a strong need to link more closely with the private sector, especially where there are financial and other comparative advantages to do so. Recommendation 2: The agronomic and physiological trait targets of Grain Legumes (tolerance to changing climate patterns, to the pests and diseases of today and of the future, incorporation of quality traits and adaptations to intensive production systems [machine-harvestability and herbicide tolerance], and short season high yielding characters) are all worthy of continued investment when selecting for improved varieties.  There needs to be a common strategy, implemented across centres and species, as to how to address these trait targets through conventional and modern breeding approaches, but only if adequate funding is assured and secured and if a consistency and unity of purpose can be achieved across a large-scale. This should take the form of cross-species coordinated research programmes to address these breeding targets that cooperate across centres and make efficient use of facilities and other resources.  The CRP should undertake a detailed strategic review of the role of transgenics across the range of targets in the mandate crops. Efficiency Recommendation 3: The lack of an effective M&E process is a significant omission, not least in terms of more efficient use of resources and the lack of baseline data with which to measure impact, and must be rectified.  Reinforcing Recommendation 1, an effective M&E system initially directed towards baseline studies must be implemented.  Transaction costs may be reduced through bilateral projects, which are seen as more cost effective than W1/W2 where transaction costs are disproportionately higher. Recommendation 4: To improve communication and coordination within the CRP, and with a broader audience:  There is a priority need for a central database containing, names of staff associated with Grain Legumes and their time commitments, their responsibilities, and involvement in CRP activities, their progress and achievements, their publications, plans of training, travel, and other opportunities for interaction.  Regular global meetings of staff involved in managing PLs, the entire CRP management staff and the IAC are essential for effective coordination of all activity within Grain Legumes.  The website must be given a complete overhaul and improvement and then regular maintenance must be provided to keep it current. Quality of Science Recommendation 5: It is essential to continue investment in good science and to institute a change from gradualism in research output and outcomes to an expectation of innovative and concrete achievements that can be attributed clearly to people, centres and core facilities.  A cost:benefit analysis and subsequent strategic planning must be undertaken to justify further investment in the genomics and phenotyping facilities at ICRISAT especially as such technologies advance rapidly. Strategic planning and coordination must also be implemented for capitalising on the investment in crop simulation modelling. (The phenotyping facility of ICRISAT needs to focus on delivering some outcomes, not only outputs.)  PLs should be given incentives to collaborate with other CRPs and external institutions. The CCEE recommends special recognition of high quality collaborative papers, thereby encouraging increased quality of the research programmes and widening the penetration of research impacts.  More importance should be placed on the quality of publication, rather than quantity of outputs and there should be recognition of other types of outputs from Grain Legumes. The CRP Director must be party to this.  If staff are engaged in activities that relate more to impact than publication then this needs to be monitored and recorded and a clearer understanding developed of what constitutes a pathway to impact and how success of such activities can be evaluated. A system must be devised and incorporated into the M&E to enable recognition of other types of outputs (non- publication based) from Grain Legumes, e.g. varieties for breeders. Effectiveness Recommendation 6: To develop greater synergy, Grain Legumes should review management processes and the direction of research activities. In particular, far more extensive integration of research and knowledge exchange should take place across both African and Asian continents so that the best aspects of both can be shared. A multidisciplinary approach is recommended that considers processing solutions, as well as breeding solutions, to capitalise upon the nutritional benefits of the grain legume crops. We recommend:  A better collaboration with social scientists at the design stage of experiments in order to improve the utility of the work carried out and to understand its reach.  Supporting3 the adoption of best practice electronic data collection, central storage and open access, particularly of genomic data, for public use.  Given the focus on the link between phenotyping and genotyping, we note that there is a lack of congruence between the populations that are being phenotyped and those being genotyped, and therefore these could be better aligned within each species.  Concentrating investment external to Grain Legumes on scaling up production of varieties with the most promising trait profiles to meet the basic seed requirement.  Developing a more holistic approach that coordinates an understanding of the disease pathology and epidemiology, and of new chemicals before they become commercially available, together with agronomic practice such that recommendations can be made for growers. Continuing work to establish whether agronomic factors hold true in different environments and to assess GxE effects within breeding programmes. Such rigorous trial practices should be used to inform the evaluation of breeding lines and to provide phenotype data to associate with markers for traits such as heat, drought and herbicide tolerance.  Considering grain legumes as if they were vegetable crops in terms of the strategy for intensification of production, both from the management perspective and for seed systems, will be a useful development objective into the future. This will bring about more rapid intensification and is likely to increase farmer returns from investment. Recommendation 7: The CGIAR centres should focus in on the research for which they have a comparative advantage. While imposing the restructure to FPs, which is fine for development objectives and outcomes (funded through W3/bilateral) it is less so for a research institute, and should not detract from the more basic work expected of an international CGIAR centre (or set of centres in a CRP).  Collaborative approaches should be explored within Grain Legumes, e.g. similar biologies/research approaches, bringing species together under one umbrella. Similarly better alignment is needed to address the lack of congruence between the populations that are being phenotyped and those being genotyped.  Despite positive impacts from research in genomics, plant breeding and seed systems, the lack of an effective M&E, already mentioned elsewhere, has reduced the ability to monitor impact pathways. This must be addressed.  The absence of socio-economists from research teams is evident in the general lack of an end user focus. Responsibilities of the different actors in the whole value chain must be considered and identified when developing impact targets, and the pathway leading to them, for individual projects. People with socio-economist skills must be part of the team from project inception so that appropriate frameworks are incorporated for measuring and influencing sociological and economic changes brought about by Grain Legumes research. Impact Recommendation 8: PLs need to become more adept at providing convincing cases in which impact is strongly evidenced, as this is likely to be a key factor in leveraging future funding.  Claimed gains must be referenced against baseline data, and these are not always readily available. The CCEE Team realises that such impact evaluation represents a significant drain on resources, and Grain Legumes should determine whether the balance of costs to benefits favours such investment.  It is essential that Grain Legumes provides training to staff on what constitutes impact and how it can be recorded.  Specific, rather than generalised, potential impacts arising from activity within Grain Legumes should be defined at the time of justifying the programme of work and a pathway to impact should form part of the documentation prepared ahead of a piece of research commencing. . In other words, centres should submit work plans to Grain Legumes before they are undertaken using W1/W2 funds Recommendation 9: The reporting activity must be streamlined to a single (brief) format that can be used to report to Grain Legumes, Centres and to donors for special project activities4. Sustainability Recommendation 10: As Grain Legumes moves into the future, and if sustainable funding cannot be assured, decisions must be made concerning a reduction in activities, keeping some caretaker breeding maintenance, and focus (as has TL III) on fewer species and a reduced geographic focus. Zeigler (Director General of IRRI) states “…time and effort would be better spent … making tough decisions about which programs deserve the precious support.”  The present system whereby W3 and bilateral projects do not pay a realistic level of overheads means that such projects are being effectively subsidised by W1&2 and there will be a progressive but definite loss of basic skills and resources in the core centres. To prevent this outcome it is necessary to significantly reduce the fixed costs of the centres and/or refuse to accept W3 and bilateral funding without an adequate overhead component.  In the absence of long term certainty, the scale of the budget allocated to each of the new CRPs should be very conservative, a feature that can only be achieved by restricting/reducing the scope, probably quite significantly. Cross cutting issues: Gender, capacity building and partnerships Recommendation 11: The challenge for Grain Legumes is to achieve pro-active gender mainstreaming, which facilitates opportunities for gender diversity within all activities, from employment processes through research to end users.  Strategic measurable gender indicators need to be embedded in research design, for instance, through specific IDOs for each of the flagships projects. Accurate baseline data are also required to facilitate M&E reviews of progress.  Implementation of the Gender Strategy is the responsibility of everyone, not solely the Gender Team. Thus, ownership could be encouraged by setting personal development for key personnel objectives with specific outcomes, e.g. employment practices or research outcomes.  Recognising the positive gender initiatives in progress or planned, feedback must be communicated and integrated into broader research planning to share opportunities, methods and outcomes.  In addition to promoting gender equity in research, Grain Legumes also needs to ensure that working environments are gender sensitive and that recruitment processes, including promotion opportunities are equitable. Gender imbalance in management should be actively examined to identify further opportunities for developing female leadership. Recommendation 12: It is recommended that a training plan be devised to ensure that capacity building efforts are more clearly aligned with the research mandate, delivery and timeframe of Grain Legumes. Moreover, we recommend that ICRISAT develop a strategy to treat their new cohort of researchers more equitably in the future. Recommendation 13: To develop a more coherent strategic programme designed to eliminate overlap and promote synergy between programmes with common aims, Grain Legumes should hold a meeting with a range of partners. Governance Recommendation 14: Governance processes should be re-assessed and the structure altered to ensure that the Grain Legumes Director has the authority and budget control to drive the execution of strategy.  The ISC should be truly independent and given the power to influence strategic decisions before they become final. We also recommend that PLCs are provided with the authority to manage the direction and finances of their PL; and that ring-fenced funds are provided for the promotion of collaboration, coordination and staff training5. The way ahead In our view, having seen the ineffectiveness of much of the attempts [or lack of attempts] to harness synergies between multiple centres, and of the strength in few or sole centre partnerships, we believe that there is little to justify a full retention of the 8 legume species and 4 CGIAR centres in a CRP. TL I and II and PABRA have shown to be reasonably good cross-centre and single centre integrated programmes, but even they suffer from incomplete value chain approaches to increasing rural incomes while increasing food and nutritional security; they both need multi-faceted solutions which are not immediately forthcoming from Grain Legumes. It is important to embed Grain Legumes research within the agri-food systems these crops serve. Figure ES1 broadly shows the perceived current and potential degrees of synergy between centres, PLs and species, and is discussed more in the text. It is clear that the value chains for individual species from trait determination to nutritional impact have more cohesion than do the individual activities (e.g. trait deployment) across species. For this reason we believe that the future for research in Grain Legumes is best addressed by focusing on each of the species separately, and within an ecosystem framework; any synergy for research across species can be effected through communication and not necessarily through obligatory cooperative research. The ecosystem framework will allow for strengthening of agronomy type systems research, the arguments for benefits of inclusion of grain legumes in cropping systems, which is notable by its absence in much of what Grain Legumes currently undertakes. Figure ES1. Current and potential degrees of synergy between centres, PLs and crop species We therefore agree with the innovation in agri-food systems approach of the CG, and believe that Grain Legumes rightly belongs in the Dryland Cereals and Legumes Agri-food Systems. We believe that the option of combining the crops of dryland cereals and legumes in the cereal-legume-livestock systems of subsistence farming communities for whole-farm productivity is closest to the best way forward. Indeed the inclusion of grain legumes may not warrant even a CRP alone, rather the legume components should fit in with the major crops that determine the production systems. Legumes will always be subservient to the major cereals, as necessary adjuncts to the whole production system, providing both nutritional diversity and environmental services, neither achievable from cereals alone. Figure ES2. Most suitable option for integration of Grain Legumes and Dryland Cereals into an Agri-Food Systems CRP Most suitable option for integration of Grain Legumes and Dryland Cereals into an Agri-Food Systems CRP, which  Incorporates ex-Dryland Systems, Dryland Cereals, Grain Legumes, some HumidTropics, some ex-Livestock &Fisheries into a new CRP  Will cover full agri-food system VC for all 8 legumes in all ecologies, but must interact (dock) with the relevant AFS-CRPs for the dominant cereal in the relevant ecology  Hence, will need to negotiate with other Agrifood Systems-CRPs on who does what for legumes  In addition, responsible for sorghum and millet in the mixed dryland crop-livestock agro-ecologies For major game changers to be effected, we believe that the game has to change, and there is little evidence of this. The direction of CRPs is the correct route, but the journey has not yet come to its destination. A major change of game [such as the adoption of a Flagship Project approach as exemplified by the Australian CSIRO – where flagships contract services from centres of research excellence] would be painful to implant. The CGIAR system is going down the right pathway but it has not gone far enough.

An Integrated Traffic and Pedestrian Model_based Vision System

The paper describes a novel integrated vision system in which two autonomous visual modules are combined to interpret a dynamic scene. The first module employs a 3D model-based scheme to track rigid objects such as vehicles. The second module uses a 2D deformable model to track non-rigid objects such as people. The principal contribution is a novel method for handling occlusion between objects within the context of this hybrid tracking system. The practical aim of the work is to derive a scene description that is sufficiently rich to be used in a range of surveillance tasks. The paper describes each of the modules in outline before detailing the method of integration and the handling of occlusion in particular. Experimental results are presented to illustrate the performance of the system in a dynamic outdoor scene involving cars and people.

Detection of flood extent in urban areas using high resolution TerraSAR-X data

Flooding is a major hazard in both rural and urban areas worldwide, but it is in urban areas that the impacts are most severe. An investigation of the ability of high resolution TerraSAR-X data to detect flooded regions in urban areas is described. An important application for this would be the calibration and validation of the flood extent predicted by an urban flood inundation model. To date, research on such models has been hampered by lack of suitable distributed validation data. The study uses a 3m resolution TerraSAR-X image of a 1-in-150 year flood near Tewkesbury, UK, in 2007, for which contemporaneous aerial photography exists for validation. The DLR SETES SAR simulator was used in conjunction with airborne LiDAR data to estimate regions of the TerraSAR-X image in which water would not be visible due to radar shadow or layover caused by buildings and taller vegetation, and these regions were masked out in the flood detection process. A semi-automatic algorithm for the detection of floodwater was developed, based on a hybrid approach. Flooding in rural areas adjacent to the urban areas was detected using an active contour model (snake) region-growing algorithm seeded using the un-flooded river channel network, which was applied to the TerraSAR-X image fused with the LiDAR DTM to ensure the smooth variation of heights along the reach. A simpler region-growing approach was used in the urban areas, which was initialized using knowledge of the flood waterline in the rural areas. Seed pixels having low backscatter were identified in the urban areas using supervised classification based on training areas for water taken from the rural flood, and non-water taken from the higher urban areas. Seed pixels were required to have heights less than a spatially-varying height threshold determined from nearby rural waterline heights. Seed pixels were clustered into urban flood regions based on their close proximity, rather than requiring that all pixels in the region should have low backscatter. This approach was taken because it appeared that urban water backscatter values were corrupted in some pixels, perhaps due to contributions from side-lobes of strong reflectors nearby. The TerraSAR-X urban flood extent was validated using the flood extent visible in the aerial photos. It turned out that 76% of the urban water pixels visible to TerraSAR-X were correctly detected, with an associated false positive rate of 25%. If all urban water pixels were considered, including those in shadow and layover regions, these figures fell to 58% and 19% respectively. These findings indicate that TerraSAR-X is capable of providing useful data for the calibration and validation of urban flood inundation models.

Proceedings of the Ninth Annual Conference of the British Association for Biological Anthropology and Osteoarchaeology, Department of Archaeology, University of Reading

The Proceedings of the Ninth Annual Conference of the British Association for Biological Anthropology and Osteoarchaeology (BABAO) held at the University of Reading in 2007. Contents: 1) A life course perspective of growing up in medieval London: evidence of sub-adult health from St Mary Spital (London) (Rebecca Redfern and Don Walker); 2) Preservation of non-adult long bones from an almshouse cemetery in the United States dating to the late nineteenth to the early twentieth centuries (Colleen Milligan, Jessica Zotcavage and Norman Sullivan); 3) Childhood oral health: dental palaeopathology of Kellis 2, Dakhleh, Egypt. A preliminary investigation (Stephanie Shukrum and JE Molto); 4) Skeletal manifestation of non-adult scurvy from early medieval Northumbria: the Black Gate cemetery, Newcastle-upon-Tyne (Diana Mahoney-Swales and Pia Nystrom); 5) Infantile cortical hyperostosis: cases, causes and contradictions (Mary Lewis and Rebecca Gowland); 6) Biological Anthropology Tuberculosis of the hip in the Victorian Britain (Benjamin Clarke and Piers Mitchell); 7) The re-analysis of Iron Age human skeletal material from Winnall Down (Justine Tracey); 8) Can we estimate post-mortem interval from an individual body part? A field study using sus scrofa (Branka Franicevec and Robert Pastor); 9) The expression of asymmetry in hand bones from the medieval cemetery at Écija, Spain (Lisa Cashmore and Sonia Zakrezewski); 10) Returning remains: a curator’s view (Quinton Carroll); 11) Authority and decision making over British human remains: issues and challenges (Piotr Bienkowski and Malcolm Chapman); 12) Ethical dimensions of reburial, retention and repatriation of archaeological human remains: a British perspective (Simon Mays and Martin Smith); 13) The problem of provenace: inaccuracies, changes and misconceptions (Margaret Clegg); 14) Native American human remains in UK collections: implications of NAGPRA to consultation, repatriation, and policy development (Myra J Giesen); 15) Repatriation – a view from the receiving end: New Zealand (Nancy Tayles).

Radiative forcing due to changes in ozone and methane caused by the transport sector

The year 2000 radiative forcing (RF) due to changes in O3 and CH4 (and the CH4-induced stratospheric water vapour) as a result of emissions of short-lived gases (oxides of nitrogen (NOx), carbon monoxide and non-methane hydrocarbons) from three transport sectors (ROAD, maritime SHIPping and AIRcraft) are calculated using results from five global atmospheric chemistry models. Using results from these models plus other published data, we quantify the uncertainties. The RF due to short-term O3 changes (i.e. as an immediate response to the emissions without allowing for the long-term CH4 changes) is positive and highest for ROAD transport (31mWm-2) compared to SHIP (24 mWm-2) and AIR (17 mWm-2) sectors in four of the models. All five models calculate negative RF from the CH4 perturbations, with a larger impact from the SHIP sector than for ROAD and AIR. The net RF of O3 and CH4 combined (i.e. including the impact of CH4 on ozone and stratospheric water vapour) is positive for ROAD (+16(±13)(one standard deviation) mWm-2) and AIR (+6(±5) mWm-2) traffic sectors and is negative for SHIP (-18(±10) mWm-2) sector in all five models. Global Warming Potentials (GWP) and Global Temperature change Potentials (GTP) are presented for AIR NOx emissions; there is a wide spread in the results from the 5 chemistry models, and it is shown that differences in the methane response relative to the O3 response drive much of the spread.

Benchmarking consensus model quality assessment for protein fold recognition

Background: Selecting the highest quality 3D model of a protein structure from a number of alternatives remains an important challenge in the field of structural bioinformatics. Many Model Quality Assessment Programs (MQAPs) have been developed which adopt various strategies in order to tackle this problem, ranging from the so called "true" MQAPs capable of producing a single energy score based on a single model, to methods which rely on structural comparisons of multiple models or additional information from meta-servers. However, it is clear that no current method can separate the highest accuracy models from the lowest consistently. In this paper, a number of the top performing MQAP methods are benchmarked in the context of the potential value that they add to protein fold recognition. Two novel methods are also described: ModSSEA, which based on the alignment of predicted secondary structure elements and ModFOLD which combines several true MQAP methods using an artificial neural network. Results: The ModSSEA method is found to be an effective model quality assessment program for ranking multiple models from many servers, however further accuracy can be gained by using the consensus approach of ModFOLD. The ModFOLD method is shown to significantly outperform the true MQAPs tested and is competitive with methods which make use of clustering or additional information from multiple servers. Several of the true MQAPs are also shown to add value to most individual fold recognition servers by improving model selection, when applied as a post filter in order to re-rank models. Conclusion: MQAPs should be benchmarked appropriately for the practical context in which they are intended to be used. Clustering based methods are the top performing MQAPs where many models are available from many servers; however, they often do not add value to individual fold recognition servers when limited models are available. Conversely, the true MQAP methods tested can often be used as effective post filters for re-ranking few models from individual fold recognition servers and further improvements can be achieved using a consensus of these methods.

Tracer concentration profiles measured in central London as part of the REPARTEE campaign

There have been relatively few tracer experiments carried out that have looked at vertical plume spread in urban areas. In this paper we present results from two tracer (cyclic perfluorocarbon) experiments carried out in 2006 and 2007 in central London centred on the BT Tower as part of the REPARTEE (Regent’s Park and Tower Environmental Experiment) campaign. The height of the tower gives a unique opportunity to study vertical dispersion profiles and transport times in central London. Vertical gradients are contrasted with the relevant Pasquill stability classes. Estimation of lateral advection and vertical mixing times are made and compared with previous measurements. Data are then compared with a simple operational dispersion model and contrasted with data taken in central London as part of the DAPPLE campaign. This correlates dosage with non-dimensionalised distance from source. Such analyses illustrate the feasibility of the use of these empirical correlations over these prescribed distances in central London.

Mid-term evaluation of African Technology Policy Studies Network Phase VI Strategic Plan: for the period January 1, 2009 to December 31, 2010

The African Technology Policy Studies Network (ATPS) is a multidisciplinary network of researchers, private sector actors, policymakers and civil society. ATPS has the vision to become the leading international centre of excellence and reference in science, technology and innovation (STI) systems research, training and capacity building, communication and sensitization, knowledge brokerage, policy advocacy and outreach in Africa. It has a Regional Secretariat in Nairobi Kenya, and operates through national chapters in 29 countries (including 27 in Africa and two Chapters in the United Kingdom and USA for Africans in the Diaspora) with an expansion plan to cover the entire continent by 2015. The ATPS Phase VI Strategic Plan aims to improve the understanding and functioning of STI processes and systems to strengthen the learning capacity, social responses, and governance of STI for addressing Africa's development challenges, with a specific focus on the Millennium Development Goals (MDGs). A team of external evaluators carried out a midterm review to assess the effectiveness and efficiency of the implementation of the Strategic Plan for the period January 1, 2009 to December 31, 2010. The evaluation methodology involved multiple quantitative and qualitative methods to assess the qualitative and quantitative inputs (human resources, financial resources, time, etc.) into ATPS activities (both thematic and facilitative) and their tangible and intangible outputs, outcomes and impacts. Methods included a questionnaire survey of ATPS members and stakeholders, key informant interviews, and focus group discussions (FGDs) with members in six countries. Effectiveness of Programmes Under all six strategic goals, very good progress has been made towards planned outputs and outcomes. This is evidenced by key performance indicators (KPIs) generated from desk review, ratings from the survey respondents, and the themes that run through the FGDs. Institutional and Programme Cost Effectiveness Institutional Effectiveness: assessment of institutional effectiveness suggests that adequate management frameworks are in place and are being used effectively and transparently. Also technical and financial accounting mechanisms are being followed in accordance with grant agreements and with global good practice. This is evidenced by KPIs generated from desk review. Programme Cost Effectiveness: assessment of cost-effectiveness of execution of programmes shows that organisational structure is efficient, delivering high quality, relevant research at relatively low cost by international standards. The evidence includes KPIs from desk review: administrative costs to programme cost ratio has fallen steadily, to around 10%; average size of research grants is modest, without compromising quality. There is high level of pro bono input by ATPS members. ATPS Programmes Strategic Evaluation ATPS research and STI related activities are indeed unique and well aligned with STI issues and needs facing Africa and globally. The multi-disciplinary and trans-boundary nature of the research activities are creating a unique group of research scientists. The ATPS approach to research and STI issues is paving the way for the so called Third Generation University (3GU). Understanding this unique positioning, an increasing number of international multilateral agencies are seeking partnership with ATPS. ATPS is seeing an increasing level of funding commitments by Donor Partners. Recommendations for ATPS Continued Growth and Effectiveness On-going reform of ATPS administrative structure to continue The on-going reforms that have taken place within the Board, Regional Secretariat, and at the National Chapter coordination levels are welcomed. Such reform should continue until fully functional corporate governance policy and practices are fully established and implemented across the ATPS governance structures. This will further strengthen ATPS to achieve the vision of being the leading STI policy brokerage organization in Africa. Although training in corporate governance has been carried out for all sectors of ATPS leadership structure in recent time, there is some evidence that these systems have not yet been fully implemented effectively within all the governance structures of the organization, especially at the Board and National chapter levels. Future training should emphasize practical application with exercises relevant to ATPS leadership structure from the Board to the National Chapter levels. Training on Transformational Leadership - Leading a Change Though a subject of intense debate amongst economists and social scientists, it is generally agreed that cultural mindsets and attitudes could enhance and/or hinder organizational progress. ATPS’s vision demands transformational leadership skills amongst its leaders from the Board members to the National Chapter Coordinators. To lead such a change, ATPS leaders must understand and avoid personal and cultural mindsets and value systems that hinder change, while embracing those that enhance it. It requires deliberate assessment of cultural, behavioural patterns that could hinder progress and the willingness to be recast into cultural and personal habits that make for progress. Improvement of relationship amongst the Board, Secretariat, and National Chapters A large number of ATPS members and stakeholders feel they do not have effective communications and/or access to Board, National Chapter Coordinators and Regional Secretariat activities. Effort should be made to improve the implementation of ATPS communication strategy to improve on information flows amongst the ATPS management and the members. The results of the survey and the FGDs suggest that progress has been made during the past two years in this direction, but more could be done to ensure effective flow of pertinent information to members following ATPS communications channels. Strategies for Increased Funding for National Chapters There is a big gap between the fundraising skills of the Regional Secretariat and those of the National Coordinators. In some cases, funds successfully raised by the Secretariat and disbursed to national chapters were not followed up with timely progress and financial reports by some national chapters. Adequate training in relevant skills required for effective interactions with STI key policy players should be conducted regularly for National Chapter coordinators and ATPS members. The ongoing training in grant writing should continue and be made continent-wide if funding permits. Funding of National Chapters should be strategic such that capacity in a specific area of research is built which, with time, will not only lead to a strong research capacity in that area, but also strengthen academic programmes. For example, a strong climate change programme is emerging at University of Nigeria Nsukka (UNN), with strong collaborations with Universities from neighbouring States. Strategies to Increase National Government buy-in and support for STI Translating STI research outcomes into policies requires a great deal of emotional intelligence, skills which are often lacking in the first and second generation universities. In the epoch of the science-based or 2GUs, governments were content with universities carrying out scientific research and providing scientific education. Now they desire to see universities as incubators of new science- or technology-based commercial activities, whether by existing firms or start-ups. Hence, governments demand that universities take an active and leading role in the exploitation of their knowledge and they are willing to make funds available to support such activities. Thus, for universities to gain the attention of national leadership they must become centres of excellence and explicit instruments of economic development in the knowledge-based economy. The universities must do this while working collaboratively with government departments, parastatals, and institutions and dedicated research establishments. ATPS should anticipate these shifting changes and devise programmes to assist both government and universities to relate effectively. New administrative structures in member organizations to sustain and manage the emerging STI multidisciplinary teams Second Generation universities (2GUs) tend to focus on pure science and often do not regard the application of their know-how as their task. In contrast, Third Generation Universities (3GUs) objectively stimulate techno-starters – students or academics – to pursue the exploitation or commercialisation of the knowledge they generate. They view this as being equal in importance to the objectives of scientific research and education. Administratively, research in the 2GU era was mainly monodisciplinary and departments were structured along disciplines. The emerging interdisciplinary scientific teams with focus on specific research areas functionally work against the current mono-disciplinary faculty-based, administrative structure of 2GUs. For interdisciplinary teams, the current faculty system is an obstacle. There is a need for new organisational forms for university management that can create responsibilities for the task of know-how exploitation. ATPS must anticipate this and begin to strategize solutions for their member institutions to transition to 3Gus administrative structure, otherwise ATPS growth will plateau, and progress achieved so far may be stunted.