Benchmarking secondary structure prediction for fold recognition

If secondary structure predictions are to be incorporated into fold recognition methods, an assessment of the effect of specific types of errors in predicted secondary structures on the sensitivity of fold recognition should be carried out. Here, we present a systematic comparison of different secondary structure prediction methods by measuring frequencies of specific types of error. We carry out an evaluation of the effect of specific types of error on secondary structure element alignment (SSEA), a baseline fold recognition method. The results of this evaluation indicate that missing out whole helix or strand elements, or predicting the wrong type of element, is more detrimental than predicting the wrong lengths of elements or overpredicting helix or strand. We also suggest that SSEA scoring is an effective method for assessing accuracy of secondary structure prediction and perhaps may also provide a more appropriate assessment of the “usefulness” and quality of predicted secondary structure, if secondary structure alignments are to be used in fold recognition.

Benchmarking energy use in licensed restaurants and pubs

Commercial kitchens often leave a large carbon footprint. A new dataset of energy performance metrics from a leading industrial partner is presented. Categorising these types of buildings is challenging. Electricity use has been analysed using data from automated meter readings (AMR) for the purpose of benchmarking and discussed in terms of factors such as size and food output. From the analysed results, consumption is found to be almost double previous sector estimates of 6480 million kWh per year. Recommendations are made to further improve the current benchmarks in order to attain robust, reliable and transparent figures, such as the introduction of normalised performance indicators to include kitchen size (m2) and kWh per thousand-pound turnover.

Energy benchmarking in commercial kitchens

Commercial kitchens are one of the most profligate users of gas, water and electricity in the UK and can leave a large carbon footprint. It is estimated that the total energy consumption of Britain’s catering industry is in excess of 21,600 million kWh per year. In order to facilitate appropriate energy reduction within licensed restaurants, energy use must be translated into a form that can be compared between kitchens to enable operators to assess how they are improving and to allow rapid identification of facilities which require action. A review of relevant literature is presented and current benchmarking methods are discussed in order to assist in the development and categorisation of benchmarking energy reduction in commercial kitchens. Energy use within UK industry leading brands is discussed for the purpose of benchmarking in terms of factors such as size and output.

A comprehensive benchmarking system for evaluating global vegetation models.

We present a benchmark system for global vegetation models. This system provides a quantitative evaluation of multiple simulated vegetation properties, including primary production; seasonal net ecosystem production; vegetation cover, composition and 5 height; fire regime; and runoff. The benchmarks are derived from remotely sensed gridded datasets and site-based observations. The datasets allow comparisons of annual average conditions and seasonal and inter-annual variability, and they allow the impact of spatial and temporal biases in means and variability to be assessed separately. Specifically designed metrics quantify model performance for each process, 10 and are compared to scores based on the temporal or spatial mean value of the observations and a “random” model produced by bootstrap resampling of the observations. The benchmark system is applied to three models: a simple light-use efficiency and water-balance model (the Simple Diagnostic Biosphere Model: SDBM), and the Lund-Potsdam-Jena (LPJ) and Land Processes and eXchanges (LPX) dynamic global 15 vegetation models (DGVMs). SDBM reproduces observed CO2 seasonal cycles, but its simulation of independent measurements of net primary production (NPP) is too high. The two DGVMs show little difference for most benchmarks (including the interannual variability in the growth rate and seasonal cycle of atmospheric CO2), but LPX represents burnt fraction demonstrably more accurately. Benchmarking also identified 20 several weaknesses common to both DGVMs. The benchmarking system provides a quantitative approach for evaluating how adequately processes are represented in a model, identifying errors and biases, tracking improvements in performance through model development, and discriminating among models. Adoption of such a system would do much to improve confidence in terrestrial model predictions of climate change 25 impacts and feedbacks.

eRPUK 2003: eCommerce and Retail Property in the UK: third annual benchmarking survey

This new survey, which has just been completed and includes brand new data, has been funded by the RICS Education Trust and the European Shopping Centre Trust. It follows up our 2000 survey of UK retailers, investors and developers. The report presents results from our new 2001 survey. This continuing benchmark series of studies includes an extensive review of developments in ecommerce and retail in Europe and the USA. The survey reveals a cooling in attitude towards ecommerce in the UK, but there is rapid growth in some sectors and polarisation and marginalisation of secondary centres are likely to increase. In Europe the growth of a three tier system of ecommerce 'pioneers', 'followers' and 'laggards' is becoming established, and the research also reveals results from a recent joint survey on US and UK retailers conducted with Colorado State University. There is a danger of complacency as UK online sales (in percentage terms) now outstrip USA.

Climate model benchmarking with glacial and mid-Holocene climates

Past climates provide a test of models’ ability to predict climate change. We present a comprehensive evaluation of state-of-the-art models against Last Glacial Maximum and mid-Holocene climates, using reconstructions of land and ocean climates and simulations from the Palaeoclimate Modelling and Coupled Modelling Intercomparison Projects. Newer models do not perform better than earlier versions despite higher resolution and complexity. Differences in climate sensitivity only weakly account for differences in model performance. In the glacial, models consistently underestimate land cooling (especially in winter) and overestimate ocean surface cooling (especially in the tropics). In the mid-Holocene, models generally underestimate the precipitation increase in the northern monsoon regions, and overestimate summer warming in central Eurasia. Models generally capture large-scale gradients of climate change but have more limited ability to reproduce spatial patterns. Despite these common biases, some models perform better than others.

A comprehensive benchmarking system for evaluating global vegetation models

We present a benchmark system for global vegetation models. This system provides a quantitative evaluation of multiple simulated vegetation properties, including primary production; seasonal net ecosystem production; vegetation cover; composition and height; fire regime; and runoff. The benchmarks are derived from remotely sensed gridded datasets and site-based observations. The datasets allow comparisons of annual average conditions and seasonal and inter-annual variability, and they allow the impact of spatial and temporal biases in means and variability to be assessed separately. Specifically designed metrics quantify model performance for each process, and are compared to scores based on the temporal or spatial mean value of the observations and a "random" model produced by bootstrap resampling of the observations. The benchmark system is applied to three models: a simple light-use efficiency and water-balance model (the Simple Diagnostic Biosphere Model: SDBM), the Lund-Potsdam-Jena (LPJ) and Land Processes and eXchanges (LPX) dynamic global vegetation models (DGVMs). In general, the SDBM performs better than either of the DGVMs. It reproduces independent measurements of net primary production (NPP) but underestimates the amplitude of the observed CO2 seasonal cycle. The two DGVMs show little difference for most benchmarks (including the inter-annual variability in the growth rate and seasonal cycle of atmospheric CO2), but LPX represents burnt fraction demonstrably more accurately. Benchmarking also identified several weaknesses common to both DGVMs. The benchmarking system provides a quantitative approach for evaluating how adequately processes are represented in a model, identifying errors and biases, tracking improvements in performance through model development, and discriminating among models. Adoption of such a system would do much to improve confidence in terrestrial model predictions of climate change impacts and feedbacks.

The development of a data-driven application benchmarking approach to performance modelling

Performance modelling is a useful tool in the lifeycle of high performance scientific software, such as weather and climate models, especially as a means of ensuring efficient use of available computing resources. In particular, sufficiently accurate performance prediction could reduce the effort and experimental computer time required when porting and optimising a climate model to a new machine. In this paper, traditional techniques are used to predict the computation time of a simple shallow water model which is illustrative of the computation (and communication) involved in climate models. These models are compared with real execution data gathered on AMD Opteron-based systems, including several phases of the U.K. academic community HPC resource, HECToR. Some success is had in relating source code to achieved performance for the K10 series of Opterons, but the method is found to be inadequate for the next-generation Interlagos processor. The experience leads to the investigation of a data-driven application benchmarking approach to performance modelling. Results for an early version of the approach are presented using the shallow model as an example.

BnP1, a novel P-I metalloproteinase from Bothrops neuwiedi venom: Biological effects benchmarking relatively to jararhagin, a P-IIISVMP

Snake venom metalloproteinases (SVMPs) have been extensively studied and their effects associated with the local bleeding observed in human accidents by viper snakes. Representatives of P-I and P-III classes of SVMPs similarly hydrolyze extracellular matrix proteins or coagulation factors while only P-III SVMPs induce significant hemorrhage in experimental models. In this work, the effects of P-I and P-III SVMPs on plasma proteins and cultures of muscle and endothelial cells were compared in order to enlighten the mechanisms involved in venom-induced hemorrhage. To reach this comparison, BnP1 was isolated from B. neuwiedi venom and used as a weakly hemorrhagic P-I SVMPs and jararhagin was used as a model of potently hemorrhagic P-III SVMP. BnP1 was isolated by size exclusion and anion-exchange chromatographies, showing apparent molecular mass of approximately 24kDa and sequence similarity with other members of SVMPs, which allowed its classification as a group P-I SVMP. The comparison of local effects induced by SVMPs showed that BnP1 was devoid of significant myotoxic and hemorrhagic activities and jararhagin presented only hemorrhagic activity. BnP1 and jararhagin were able to hydrolyze fibrinogen and fibrin, although the latter displayed higher activity in both systems. Using HUVEC primary cultures, we observed that BnP1 induced cell detachment and a decrease in the number of viable endothelial cells in levels comparable to those observed by treatment with jararhagin. Moreover, both BnP1 and jararhagin induced apoptosis in HUVECs while only a small increase in LDH supernatant levels was observed after treatment with jararhagin, suggesting that the major mechanism involved in endothelial cell death is apoptosis. Jararhagin and BnP1 induced little effects on C2C12 muscle cell cultures, characterized by a partial detachment 24h after treatment and a mild necrotic effect as evidenced by a small increase in the supernatants LDH levels. Taken together, our data show that P-I and P-III SVMPs presented comparable effects except for the hemorrhagic activity, suggesting that hydrolysis of coagulation factors or damage to endothelial cells are not sufficient for induction of local bleeding. (C) 2007 Elsevier Ltd. All rights reserved.

Outsourcing and benchmarking in a rural public hospital : does economic theory provide the complete answer?

INTRODUCTION: The ideology and pronouncements of the Australian Government in introducing 'competitive neutrality' to the public sector has improved efficiency and resource usage. In the health sector, the Human Services Department directed that non-clinical and clinical areas be market tested through benchmarking services against the private sector, with the possibility of outsourcing. These services included car parking, computing, laundry, engineering, cleaning, catering, medical imaging (radiology), pathology, pharmacy, allied health and general practice. Managers, when they choose between outsourcing, and internal servicing and production, would thus ideally base their decision on economic principles. Williamson's transaction cost theory studies the governance mechanisms that can be used to achieve economic efficiency and proposes that the optimal organisation structure is that which minimises transaction costs or the costs of exchange. Williamson proposes that four variables will affect such costs, namely: (i) frequency of exchange; (ii) asset specificity; (iii) environmental uncertainty; and (iv) threat of opportunism. This paper provides evidence from a rural public hospital and examines whether Williamson's transaction cost theory is applicable. d into an analysis that relies solely on transaction

Rationale and design of the national benchmarking and evidence-based national clinical guidelines for chronic heart failure management programs study

OBJECTIVES: The National Benchmarks and Evidence-Based National Clinical Guidelines for Heart Failure Management Programs Study is a national, multicenter study designed to determine the nature, range, and effect of interventions applied by chronic heart failure management programs (CHF-MPs) throughout Australia on patient outcomes. Its primary objective is to use these data to develop national benchmarks and evidence-based clinical guidelines and optimize their cost-effective application by reducing quality and outcome variability. DATA SOURCES/STUDY SETTING: Primary data will be collected from CHF-MP coordinators and CHF patients enrolled in these programs on a national basis. Secondary outcome data will be collected from a national morbidity record and from patients' medical records. STUDY DESIGN: Stage I of the study involves a prospective clinical audit of all CHF-MPs throughout Australia (n = 45) to determine the extent of variability in programs currently. Stage II is a prospective cross-sectional survey design enrolling 1,500 patients (average of 40 patients per program) to firstly determine the typical profile of patients being managed via a CHF-MP in Australia and, secondly, the subsequent morbidity and mortality during the 6-month follow-up. Outcome data will be subject to multivariate analysis to determine the key components of care in this regard. All study data will be then examined in the final stage of the study (III) to develop national benchmarks for the application and auditing of CHF-MPs in Australia. CONCLUSION: Variability in patient outcomes is a product of heterogeneity among CHF-MPs. The development of national benchmarks will minimize such heterogeneity and will provide a greater level of evidence for their cost-effective application.

Environmental benchmarking of Hong Kong buildings

A method for assessing the environmental performance of Hong Kong’s buildings has been developed, known as the Hong Kong Building Environmental Assessment Method or HK-BEAM. The assessment is a type of expert-based survey, either of the design, in the case of proposed buildings, or an evaluation of building performance for newly built or existing buildings. The assessment essentially provides a benchmark of environmental performance against a series of qualitative and quantitative measures that earn “credits”. Buildings can be rated as “excellent”, “very good”, “good” or “fair”. The assessment covers global, local and indoor issues. The original assessment has been in use since 1996 and allowed appraisal of new and existing air-conditioned offices. A new version has been recently produced for residential buildings. The latest version has addressed some of the criticisms of the earlier versions and covers a wider range of issues, taking a life-cycle approach. Reviews the latest new residential version, making comparisons with the earlier new offices scheme.

Benchmarking e-business security : a model and framework

The dynamic nature of threats and vulnerabilities within the E-business environment can impede online functionality, compromise organisational or customer information, contravene security implementations and thereby undermine online customer confidence. To negate these problems, E-business security has to become proactive, by reviewing and continuously improving security to strengthen E-business security measures and policies. This can be achieved through benchmarking the security measures and policies utilised within the Ebusiness, against recognised information technology (IT) and information security (IS) security standards.

The role of benchmarking and service level agreement (SLA) practices in IT outsourcing success

Despite claims in the trade literature that a number of recommended practices have been proved to lead to IT outsourcing success, few of these practices have been subject to disconfirmatory research. Even fewer have been tested statistically to determine whether they generalize to wider populations, or to determine the magnitude of their effect. In this paper, several recommended outsourcing practices associated with service level agreements (SLAs) and benchmarking are investigated. These practices are recommended extensively on the basis of case study research, yet they do have downsides, and they add substantially to the transaction costs of outsourcing. Based on a large survey of organizations engaged in IT outsourcing, this paper established that developing detailed SLAs did improve cost and service outcome, and that clients who met with vendors more frequently to renegotiate service levels reported greater outsourcing success. The research also established that benchmarking both before outsourcing commences, and once the outsourcing contract is in place, led to improvements in cost and service outcomes. Benchmarking during the outsourcing contract had the greatest effect, accounting for 10% of the variance in a success vector that included strategic, technical, cost-related and service outcomes plus an overall evaluation of satisfaction and value.