SNIFFER WFD119: Enhancement of the River Invertebrate Classification Tool (RICT)

EXECUTIVE SUMMARY Project funders/partners: Environment Agency (EA), Northern Ireland Environment Agency (NIEA), Scotland & Northern Ireland Forum for Environmental Research (SNIFFER), Scottish Environment Protection Agency (SEPA) Background to research The Regulatory Agencies in the UK (the Environment Agency; Scottish Environment Protection Agency; and the Northern Ireland Environment Agency) now use the River Invertebrate Classification Tool (RICT) to classify the ecological quality of rivers for Water Framework Directive compliance monitoring. RICT incorporates RIVPACS IV predictive models and is a highly capable tool written in a modern software programming language. While RICT classifies waters for general degradation and organic pollution stress, producing assessments of status class and uncertainty, WFD compliance monitoring also requires the UK Agencies to assess the impacts of a wide range of pressures including hydromorphological and acidification stresses. Some of these pressures alter the predictor variables that current RIVPACS models use to derive predicted biotic indices. This project has sought to broaden the scope of RICT by developing one or more RIVPACS model(s) that do not use predictor variables that are affected by these stressors, but instead use alternative GIS based variables that are wholly independent of these pressures. This project has also included a review of the wide range of biotic indices now available in RICT, identifying published sources, examining index performance, and where necessary making recommendations on further needs for index testing and development. Objectives of research •To remove and derive alternative predictive variables that are not affected by stressors, with particular emphasis on hydrological/acidification metric predictors. •To construct one or more new RIVPACS model(s) using stressor independent variables. •Review WFD reporting indices notably AWIC(species), LIFE (species), PSI & WHPT. Key findings and recommendations : Predictor variables and intellectual property rights : An extensive suite of new variables have been derived by GIS for the RIVPACS reference sites that have been shown to act as stressor-independent predictor variables. These include measures of stream order, solid and drift geology, and a range of upstream catchment characteristics (e.g. catchment area, mean altitude of upstream catchment, and catchment aspect). It is recommended that decisions are reached on which of the newly derived model(s) are implemented in RICT so that IPR issues for the relevant datasets can be quickly resolved and the datasets licensed. It is also recommended that licensing is sought for a point and click system (where the dataset cannot be reverse engineered) that is capable of calculating any of the time-invariant RIVPACS environmental predictor variables used by any of the newly derived (and existing) RIVPACS models, and for any potential users. New stressor-independent RIVPACS models : Using the existing predictor variables, together with new ones derived for their properties of stressor-independence, initial step-wise forward selection discriminant models suggested a range of 36 possible models that merited further testing. Following further testing, the following models are recommended for assessing watercourses affected by flow/hydromorphological and/or acidity stress: • For flow/hydromorphological stressors that may have modified width, depth and/or substrate in GB, it is suggested that a new ‘RIVPACS IV – Hydromorphology Independent’ model (Model 24) is used (this does not use the predictor variables width, depth and substratum, but includes a suite of new stressor-independent variables). • For acidity related stressors in GB, it is suggested that a new ‘RIVPACS IV – Alkalinity Independent’ model (Model 35) is used (this does not use the predictor variable alkalinity, but includes new stressor-independent variables). • For flow/hydromorphological stressors and acidity related stressors in GB, it is suggested that a new ‘RIVPACS IV – Hydromorphology & Alkalinity Independent’ model (Model 13) is used (this does not use the predictor variables width, depth, substratum and alkalinity, but includes a suite of new stressor-independent variables). • Reduced availability of appropriate GIS tools at this time has meant that no new models have been developed for Northern Ireland. Discriminant functions and end group means have now been calculated to enable any of these models to be easily implemented in the RICT software. Biotic indices : The RIVPACS models in RICT can now produce expected values for a wide range of biotic indices addressing a variety of stressors. These indices will support the use of RICT as a primary tool for WFD classification and reporting of the quality of UK streams and rivers. There are however a number of outstanding issues with indices that need to be addressed: • There is a need to develop a biotic index for assessing metal pollution. • WFD EQR banding schemes are required for many of the indices to report what is considered an acceptable degree of stress (High-Good) and what is not (Moderate, Poor or Bad). • A comprehensive objective testing process needs to be undertaken on the indices in RICT using UK-wide, large-scale, independent test datasets to quantify their index-stressor relationships and their associated uncertainty, for example following the approach to acidity index testing in Murphy et al., (in review) or organic/general degradation indices in Banks & McFarland (2010). • Following objective testing, the UK Agencies should make efforts to address any index under-performance issues that have been identified, and where necessary new work should be commissioned to modify existing indices, or develop new ones where required so that indices for all stress types meet certain minimum performance criteria. • Testing needs to be done to examine index-stressor relationships with both observed index scores and RIVPACS observed/expected ratios. Work should also be done to compare the existing RIVPACS IV and the new stressor-independent models (developed in this project) as alternative sources of the expected index values for these tests. • Consideration should be given to assessing the extent to which chemical and biological monitoring points co-occur. Site-matched (rather than reach-matched) chemical and biological monitoring points would i) generate the substantial training datasets needed to refine or develop new indices and ii) generate the independent datasets for testing

Necessary and sufficient condition on global optimality without convexity and second order differentiability

The main goal of this paper is to give a necessary and sufficient condition of global optimality for unconstrained optimization problems, when the objective function is not necessarily convex. We use Gâteaux differentiability of the objective function and its bidual (the latter is known from convex analysis)

Physiological characteristics of recent Canada western red spring wheat cultivars: nitrogen uptake and remobilization

Non-Peer ReviewedGenetic yield gains have been difficult to achieve within the CWRS wheat class because of stringent quality requirements, and a growing-season environment of low precipitation and high temperatures. Understanding the physiological basis of yield gains may provide breeders with better insight as to the selection of parents, or provide screening tools to identify desirable genotypes. The objective of the present study was to compare four new CWRS wheat cultivars, which averaged higher yields than Neepawa in three years of multi-location testing within registration trials, both as a group and individually while maintaining or even increasing protein content, with two older cultivars, Neepawa and Marquis, in terms of N uptake and N remobilization. Results indicated that new cultivars had higher N uptake and/or higher N remobilization than old cultivars. Low tissue N concentration at maturity could be a criterion for selecting high-yielding and high-protein cultivars.Grain protein concentration (GPC) is an important trait of major interest in breeding of bread wheat (T. aestivum L.), because it determines both baking and nutritional properties. Breeding for both high yield and high GPC is very difficult as a negative relationship between yield and GPC was found by many studies (Simmonds 1995; McNeal, et al., 1972; Whitehouse, 1973; Bhatia, 1975; Costa and Kronstad, 1994). Simmonds (1996), therefore, concluded that high yield and high GPC were unattainable simultaneously. However, Kibite and Evans (1984) indicated that the negative relationship between yield and GPC was not primarily driven by genetic factors, but mainly by environmental factors. Cox et al. (1985) found that negative correlations between yield and GPC for some wheat lines were low, although significant, which indicated that simultaneous increase in yield and GPC could be achieved by selection. This is supported by some studies (Davis et al., 1961; Terman et al. 1969; Johnson, 1978; McKendry et al. 1995). Jenner et al. (1991) indicated there is no fundamental conflict on physiological grounds in selecting cultivars for high carbohydrate yield at acceptable, even high, levels of GPC. GPC is determined by plant total nitrogen (N) uptake and N remobilization to the grain. Many studies found genetic differences in N uptake (Löffler, et al. 1985; Van Sanford and MacKown, 1986; Le et al. 2000; Desai and Bhatia, 1978; McKendry, et al. 1995), while Oscarson et al. (1995) did not find any major differences in NO3 uptake capacity among wheat grown hydroponically. A positive correlation between N uptake and GPC was found by Beninati and Busch (1992) and McKendry et al. (1995), but not by others (McNeal et al. 1966; Johnson et al. 1967; Desai and Bhatia 1978). Cultivar difference in N remobilization was also found by some authors (Seth et al. 1960; Johnson et al. 1968; Van Sanford and MacKown, 1987). However, the relationship between plant N metabolism and GPC was not clear. Some reported that N partitioning was associated with GPC (Johnson et al. 1968; Cox et al. 1986; McKendry et al. 1995), but others (McNeal et al. 1972; Woodruff 1972; Van Sanford and MacKown 1987; May et al. 1991) did not support this. Nitrogen harvest index was (grain N at maturity/maximum N uptake, %) used as a selection criterion by some authors (Desai and Bhatia 1978; Cregan and Berkum 1984; Löffler et al. 1985; Jenner et al. 1991; McKendry et al. 1995). Borghi et al. (1987) suggested that both higher biomass yield and efficiency of N remobilization are important traits to overcome the negative relationship between grain yield and GPC. Some studies suggested to use tissue N (Rostami and Giriaei 1998; Rostami and O'Brien 1996; Sylvester-Bradley 1990) or tissue protein concentrations (Noaman and Taylor 1990; Noaman et al. 1990) as selection criteria for increasing GPC because they were positively correlated with GPC. However, Jenner et al. (1991) indicated that from a physiological point of view, there is little logic in using grain protein percentage as a selection criterion. Delzer et al. (1995) also pointed that selection for grain protein only is questionable because the higher GPC is often associated with lower grain yield. Although there are not short of studies on N mechanisms, there are lack of consistencies in the results. Clarke et al. (1990) indicated that unless greater variation in N utilization parameters among cultivars can be demonstrated, there seems to be little justification for selection for parameters other than grain yield and protein concentration. Some recently developed bread wheat cultivars in western Canada have significantly increased yields, while maintaining or increasing percent protein content, relative to earlier cultivars (Wang et al. 2002). These cultivars can be used to study the physiological basis for these genetic improvements in N utilization. A better understanding of these improvements may allow breeders to design more efficient screening methods to develop future high yield and high GPC cultivars. This information may also assist agronomists and producers design soil and crop management practices that will permit full expression of these improved traits. The objective of this study was to estimate the characteristics of these new cultivars in N utilization in comparison with older cultivars and to identify potential criteria for selection of high yield and high GPC cultivars in the western Canadian semiarid prairie

What makes medical students better listeners?

Diagnosing heart conditions by auscultation is an important clinical skill commonly learnt by medical students. Clinical proficiency for this skill is in decline [1], and new teaching methods are needed. Successful discrimination of heartbeat sounds is believed to benefit mainly from acoustical training [2]. From recent studies of auditory training [3,4] we hypothesized that semantic representations outside the auditory cortex contribute to diagnostic accuracy in cardiac auscultation. To test this hypothesis, we analysed auditory evoked potentials (AEPs) which were recorded from medical students while they diagnosed quadruplets of heartbeat cycles. The comparison of trials with correct (Hits) versus incorrect diagnosis (Misses) revealed a significant difference in brain activity at 280-310 ms after the onset of the second cycle within the left middle frontal gyrus (MFG) and the right prefrontal cortex. This timing and locus suggest that semantic rather than acoustic representations contribute critically to auscultation skills. Thus, teaching auscultation should emphasize the link between the heartbeat sound and its meaning. Beyond cardiac auscultation, this issue is of interest for all fields where subtle but complex perceptual differences identify items in a well-known semantic context

Representation of Sound Objects within Early-Stage Auditory Areas: A Repetition Effect Study Using 7T fMRI.

Environmental sounds are highly complex stimuli whose recognition depends on the interaction of top-down and bottom-up processes in the brain. Their semantic representations were shown to yield repetition suppression effects, i. e. a decrease in activity during exposure to a sound that is perceived as belonging to the same source as a preceding sound. Making use of the high spatial resolution of 7T fMRI we have investigated the representations of sound objects within early-stage auditory areas on the supratemporal plane. The primary auditory cortex was identified by means of tonotopic mapping and the non-primary areas by comparison with previous histological studies. Repeated presentations of different exemplars of the same sound source, as compared to the presentation of different sound sources, yielded significant repetition suppression effects within a subset of early-stage areas. This effect was found within the right hemisphere in primary areas A1 and R as well as two non-primary areas on the antero-medial part of the planum temporale, and within the left hemisphere in A1 and a non-primary area on the medial part of Heschl's gyrus. Thus, several, but not all early-stage auditory areas encode the meaning of environmental sounds

Steady non-ideal detonations in cylindrical sticks of expolsives

Numerical simulations of detonations in cylindrical rate-sticks of highly non-ideal explosives are performed, using a simple model with a weakly pressure dependent rate law and a pseudo-polytropic equation of state. Some numerical issues with such simulations are investigated, and it is shown that very high resolution (hundreds of points in the reaction zone) are required for highly accurate (converged) solutions. High resolution simulations are then used to investigate the qualitative dependences of the detonation driving zone structure on the diameter and degree of confinement of the explosive charge. The simulation results are used to show that, given the radius of curvature of the shock at the charge axis, the steady detonation speed and the axial solution are accurately predicted by a quasi-one-dimensional theory, even for cases where the detonation propagates at speeds significantly below the Chapman-Jouguet speed. Given reaction rate and equation of state models, this quasi-one-dimensional theory offers a significant improvement to Wood-Kirkwood theories currently used in industry

Emotional pre-eminence of human vocalizations.

Human vocalizations (HV), as well as environmental sounds, convey a wide range of information, including emotional expressions. The latter have been relatively rarely investigated, and, in particular, it is unclear if duration-controlled non-linguistic HV sequences can reliably convey both positive and negative emotional information. The aims of the present psychophysical study were: (i) to generate a battery of duration-controlled and acoustically controlled extreme valence stimuli, and (ii) to compare the emotional impact of HV with that of other environmental sounds. A set of 144 HV and other environmental sounds was selected to cover emotionally positive, negative, and neutral values. Sequences of 2 s duration were rated on Likert scales by 16 listeners along three emotional dimensions (arousal, intensity, and valence) and two non-emotional dimensions (confidence in identifying the sound source and perceived loudness). The 2 s stimuli were reliably perceived as emotionally positive, negative or neutral. We observed a linear relationship between intensity and arousal ratings and a "boomerang-shaped" intensity-valence distribution, as previously reported for longer, duration-variable stimuli. In addition, the emotional intensity ratings for HV were higher than for other environmental sounds, suggesting that HV constitute a characteristic class of emotional auditory stimuli. In addition, emotionally positive HV were more readily identified than other sounds, and emotionally negative stimuli, irrespective of their source, were perceived as louder than their positive and neutral counterparts. In conclusion, HV are a distinct emotional category of environmental sounds and they retain this emotional pre-eminence even when presented for brief periods

River Invertebrate Classification Tool

Background to research The Regulatory Agencies in the UK (the Environment Agency; Scottish Environment Protection Agency; and the Environment & Heritage Service) currently use RIVPACS III+ software to classify the ecological quality of rivers. However, because RIVPACS III+ pre-dates the WFD, there has been a requirement to ensure that the RIVPACS reference sites are fully WFD compliant, to add new biotic indices to the RIVPACS models, and to improve the robustness of the RIVPACS software to fully meet the needs of the Agencies in their delivery of WFD monitoring. These issues have been addressed in this project and have led to the development of new RIVPACS IV predictive models that will be programmed into a new River Invertebrate Classification Tool being built by SEPA. This new system will be based on a modern software programming language, be compatible with the agencies’ computer systems and include the ability to predict new biological indices, produce biological status assessments based on these new indices and be able to estimate the errors involved in using these new indices. Because access to the new system will be essential for the UK Agencies to be able to implementation the WFD, the new tool will be readily and freely available to anyone who might seek to use it. Objectives of research • The overall objective of the project was to produce a new set of RIVPACS predictive models for use within a new River Invertebrate Classification Tool that will be used to classify the ecological status of rivers for Water Framework Directive compliance monitoring • The new RIVPACS models constructed with this project required considerably enhanced functionality compared to RIVPACS III+ to properly address the monitoring requirements of the UK Agencies in their implementation of the Water Framework Directive. Key findings and recommendations This project has produced new RIVPACS IV models with considerably enhanced functionality compared to RIVPACS III+. These models incorporate: • A full revision of the taxonomic framework of RIVPACS to bring the taxonomy up-to-date and enable compatiability across the revised Miatland, Furse code and National Biodiversity Network taxon coding systems used across the UK Agencies and beyond • Predictions that fully satisfy the WFD definition of ‘reference condition’ by adjusting predictions for certain stream types and by removal of sites that were not in reference condition when sampled • Allocation of actual abundance values to family level records in the RIVPACS reference data set. Lack of actual abundance data, especially at family level, has affected all versions of RIVPACS and has constrained the types of biotic indices that RIVPACS can predict • Extension to the suite of biotic indices so that the new system can predict a wider range of reference state “expected” index values. This enables full WFD quality reporting capabilities as well as providing the system with the general functionality to predict a much wider range of indices e.g. intercalibration indices (e.g. ICMi), stress-specific indices, and ecological and functional trait indices • Extension of the uncertainty/errors module to estimate and assess uncertainty in (i) assignment to status class and (ii) comparison of samples for temporal change in quality and status. This needs to be done for a wider range of biotic indices (including those incorporating abundance data) These new RIVPACS IV models can be used by the UK Agencies across Great Britain and Northern Ireland in their WFD compliance monitoring. All of the algorithms, variables and data necessary to build these models have been provided to SEPA for programming into a new River Invertebrate Classification Tool that will be disseminated made free of charge to all interested user

The DIP-approach:Student-staff partnerships as a vital tool for learning developers and educators to develop academic [and digital] literacies

Student-staff partnerships can be used to support the development of contextualised digital learning and teaching practices. This can be done by shifting the focus from IT skills to addressing a priority in learning and teaching using a digital approach that is appropriate for that discipline. The development of a formal ‘Digital Innovation Partnership’ (DIP) scheme at the University of Leicester brings students’ digital confidence, perspectives and motivation to enhance learning and teaching. It also recognises the valuable contribution and expertise of student and staff participants. This draws on the academic literacies work of Lea and Street (1998; 2006) and digital literacies work of Sharpe and Beetham (2010) to appreciate that staff and students are developing social practices that are situated within a discipline and intertwined with social, cultural and political factors, power and identity. The reasons for the success of the scheme are explored here, with recommendations for how the model can be applied more generally to educational design to support students’ academic literacies development