The ModFOLD server for the quality assessment of protein structural models

The reliable assessment of the quality of protein structural models is fundamental to the progress of structural bioinformatics. The ModFOLD server provides access to two accurate techniques for the global and local prediction of the quality of 3D models of proteins. Firstly ModFOLD, which is a fast Model Quality Assessment Program (MQAP) used for the global assessment of either single or multiple models. Secondly ModFOLDclust, which is a more intensive method that carries out clustering of multiple models and provides per-residue local quality assessment.

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.

Hygiene assessment system (HAS) scores: an analysis of the available data from English slaughterhouses

As control systems have developed and the implications of poor hygienic practices have become better known, the evaluation of the hygienic status of premises has become more critical. The assessment of the overall status of premises hygiene call provide useful management data indicating whether the premises are improving or whether, whilst still meeting legal requirements, they might be failing to maintain previously high standards. Since the creation, for the United Kingdom, of the meat hygiene service (MHS), one of the aims of the service was to monitor hygiene on different premises to provide a means of comparing standards and to identify and encourage improvements. This desire led to the implementation of a scoring system known as the hygiene assessment system (HAS). This paper analyses English slaughterhouses HAS scores between 1998 and 2005 outlining the main incidents throughout this period, Although rising initially, the later results displayed a clear decrease in the general hygiene scores. These revealing results coincide with the start of a new meat inspection system where, after several years of discussion, risk based inspection is finally coming to a reality within Europe. The paper considers the implications of these changes in the way hygiene standards will be monitored in the future.

Seeing 'things' differently : recognition, ethics, praxis

This essay focuses on the recent introduction by the Australian Federal Government of standardised literacy testing in all states across Australia (that is, the National Assessment Program – Literacy and Numeracy, or NAPLAN), and explores the way this reform is mediating the work of English literacy educators in primary and secondary schools. We draw on data collected as part of a research project funded by the Australian Research Council, involving interviews with teachers about their experiences of implementing standardised testing. These interviews indicate that the introduction of standardised testing does not merely constitute an additional part of teachers” workloads, but that it is having a significant impact on their identity as language educators, their understanding of curriculum and pedagogy, and the relationships they seek to maintain with their students. By introducing the NAPLAN tests, the Australian Federal Government is going down the path of other neo-liberal governments around the world. No doubt the story we tell will be familiar to readers in other countries. Our aim, however, is more than simply to give yet another account of the tensions experienced by committed language and literacy teachers as they implement neoliberal policy mandates. Key questions for us include: Why is the Australian government persisting with such policies, even when they have had such dubious consequences (teaching to the test, dumbing down, and so on.) in other national settings? How might educators resist these reforms? What intellectual resources might enable us to articulate an alternative vision of language education to that imposed by neoliberal reforms?
We present an account of conversations with a group of teachers in a primary school in the northern suburbs of Melbourne, not in order to make large claims about how the profession in Australia as a whole judges standards based reforms, but because their talk prompts reflection about the possibility of resisting such policy initiatives. Our impulse is largely a philosophical one – we are raising questions about how neoliberal reforms construct teachers and their students, what they presuppose about the nature of life and its potential, and how educators might dissent from the world view that is being imposed. And rather than simply investigating how teachers are grappling with standards-based reforms, as though it is yet again a matter of putting teachers under the spotlight, we also raise questions about the responsibility of academics and teacher educators to maintain a critical standpoint within the policy environment created by such changes.

Closing the emergency facility: Moving schools from literacy triage to better literacy outcomes

This article focuses on the tensions between national and international testing, educational policy and professionalism for middle school English teachers. I argue that state and federal government(s) are responding to the impact of Australia's falling results on the international testing in PISA (Programme for International Student Assessment) through the usage of their own testing program, the National Assessment Program for Literacy and Numeracy (NAPLAN). The publication of NAPLAN results on the MySchool website in a searchable and comparable form has been detrimental to many schools and has pushed these schools into "emergency mode", as they struggle to improve their scores. At the same time, the results from recent PISA examinations reveal extensive inequities in educational outcomes across Australia, as well as some consistent general trends in the Australian data. I use the metaphor of the hospital emergency department to explore this situation. Drawing on Sahlberg's (2011) notion of the Global Educational Reform Movement (GERM), I explore this metaphor becoming a pandemic. I draw on Gillborn and Youdell's (2000) usage of educational triage and cast different and multiple educational professionals playing the role of the triage nurse-the alternate federal and state government education ministers responding to international and state test results in triage; and principals of poor performing schools operating their school as though it is an emergency department; poor literacy results triaged Code Red receiving immediate focus and attention, but "treated" in terms of immediate survival and a focus on basic skills. I argue that the international testing provides better markers for how we are doing as a nation, and what might be done to improve our international standing with respect to our literacy scores. I argue that true gains in literacy and the development of more complex literacy skills are not made through triaging literacy through an emergency department, but through a long-term focus on school redesign.

The corrections Victoria program change manual

This manual has been written to guide the assessment of change in each of the programs currently offered by the Offending Behaviour Programs Branch, Corrections Victoria. The aim is to identify a set of outcome measures that can be used to both evaluate the overall effectiveness of a program as well as inform judgements about the changes that individual offenders have made over the course of their program participation. Accordingly, the focus is on the assessment of short-term change and not on other areas of assessment, such as assessing changes in risk of reoffending, identifying intervention needs, or establishing an offender’s suitability or eligibility to take part in a program.

Defining a fish bio-assessment tool to monitoring the biological condition of a cascade reservoirs system in tropical area

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Water-quality assessment of the Lower Susquehanna River Basin, Pennsylvania and Maryland : sources, characteristics, anaylsis, and limitations of nutrient and suspended-seditment data, 1975-90 /

"National Water-Quality Assessment Program"

Project plan 1977-1979 : national coal utilization assessment.

Prepared for the ERDA Integrated Assessment Program.

Mathematics assessment report, Spring 1977 /

WI docs. no.: Ed.3/2:9320

Guide to the 1992 Illinois state assessment.

"September 1992."--P. [4] of cover.

Models planned for use in the NAPAP integrated assessment.

Mode of access: Internet.

Assessment plan update.

Mode of access: Internet.