Issues in knowledge representation to support maintainability: A case study in scientific data preparation

Scientific data preparation is the process of extracting usable scientific data from raw instrument data. This task involves noise detection (and subsequent noise classification and flagging or removal), extracting data from compressed forms, and construction of derivative or aggregate data (e.g. spectral densities or running averages). A software system called PIPE provides intelligent assistance to users developing scientific data preparation plans using a programming language called Master Plumber. PIPE provides this assistance capability by using a process description to create a dependency model of the scientific data preparation plan. This dependency model can then be used to verify syntactic and semantic constraints on processing steps to perform limited plan validation. PIPE also provides capabilities for using this model to assist in debugging faulty data preparation plans. In this case, the process model is used to focus the developer's attention upon those processing steps and data elements that were used in computing the faulty output values. Finally, the dependency model of a plan can be used to perform plan optimization and runtime estimation. These capabilities allow scientists to spend less time developing data preparation procedures and more time on scientific analysis tasks. Because the scientific data processing modules (called fittings) evolve to match scientists' needs, issues regarding maintainability are of prime importance in PIPE. This paper describes the PIPE system and describes how issues in maintainability affected the knowledge representation used in PIPE to capture knowledge about the behavior of fittings

Whole-body sensorimotor skill learning in football players: No evidence for motor transfer effects

Besides simple movement sequences, precise whole-body motor sequences are fundamental for top athletic performance. It has long been questioned whether athletes have an advantage when learning new whole-body motor sequences. In a previous study, we did not find any superior learning or transfer effects of strength and endurance athletes in a complex whole-body serial reaction time task (CWB-SRTT). In the present study, we aimed to extend this research by increasing the overlap of task requirements between CWB-SRTT and a specific sports discipline. For this purpose, we assessed differences between football players and non-athletes during motor sequence learning using CWB-SRTT. 15 non-athletes (CG) and 16 football players (FG) performed the CWB-SRTT over 2 days separated by one week. Median reaction times and movement times were analyzed as well as differences in sequence-specific CWB-SRTT learning rates and retention. Our findings did not reveal any differences in sequence-specific or non-sequence-specific improvement, nor retention rates between CG and FG. We speculate that this might relate to a predominately cognitive-induced learning effect during CWB-SRTT which negates the assumed motor advantage of the football players

Intelligent assistance in scientific data preparation

Scientific data preparation is the process of extracting usable scientific data from raw instrument data. This task involves noise detection (and subsequent noise classification and flagging or removal), extracting data from compressed forms, and construction of derivative or aggregate data (e.g. spectral densities or running averages). A software system called PIPE provides intelligent assistance to users developing scientific data preparation plans using a programming language called Master Plumber. PIPE provides this assistance capability by using a process description to create a dependency model of the scientific data preparation plan. This dependency model can then be used to verify syntactic and semantic constraints on processing steps to perform limited plan validation. PIPE also provides capabilities for using this model to assist in debugging faulty data preparation plans. In this case, the process model is used to focus the developer's attention upon those processing steps and data elements that were used in computing the faulty output values. Finally, the dependency model of a plan can be used to perform plan optimization and run time estimation. These capabilities allow scientists to spend less time developing data preparation procedures and more time on scientific analysis tasks

Improving Requirements-Test Alignment by Prescribing Practices that Mitigate Communication Gaps

The communication of requirements within software development is vital for project success. Requirements engineering and testing are two processes that when aligned can enable the discovery of issues and misunderstandings earlier, rather than later, and avoid costly and time-consuming rework and delays. There are a number of practices that support requirements-test alignment. However, each organisation and project is different and there is no one-fits-all set of practices. The software process improvement method called Gap Finder is designed to increase requirements-test alignment. The method contains two parts: an assessment part and a prescriptive part. It detects potential communication gaps between people and between artefacts (the assessment part), and identifies practices for mitigating these gaps (the prescriptive part). This paper presents the design and formative evaluation of the prescriptive part; an evaluation of the assessment part was published previously. The Gap Finder method was constructed using a design science research approach and is built on the Theory of Distances for Software Engineering, which in turn is grounded in empirical evidence from five case companies. The formative evaluation was performed through a case study in which Gap Finder was applied to an on-going development project. A qualitative and mixed-method approach was taken in the evaluation, including ethnographically-informed observations. The results show that Gap Finder can detect relevant communication gaps and seven of the nine prescribed practices were deemed practically relevant for mitigating these gaps. The project team found the method to be useful and supported joint reflection and improvement of their requirements communication. Our findings demonstrate that an empirically-based theory can be used to improve software development practices and provide a foundation for further research on factors that affect requirements communicatio

Broad Overview of Energy Efficiency and Renewable Energy Opportunities for Department of Defense Installations

The Strategic Environmental Research and Developmental Program (SERDP)/Environmental Security Technology Certification Program (ESTCP) is the Department of Defense?s (DOD) environmental science and technology program focusing on issues related to environment and energy for the military services. The SERDP/ESTCP Office requested that the National Renewable Energy Laboratory (NREL) provide technical assistance with strategic planning by evaluating the potential for several types of renewable energy technologies at DOD installations. NREL was tasked to provide technical expertise and strategic advice for the feasibility of geothermal resources, waste-to-energy technology, photovoltaics (PV), wind, microgrids, and building system technologies on military installations. This technical report is the deliverable for these tasks

ActEarly: a City Collaboratory approach to early promotion of good health and wellbeing

Economic, physical, built, cultural, learning, social and service environments have a profound effect on lifelong health. However, policy thinking about health research is dominated by the ‘biomedical model’ which promotes medicalisation and an emphasis on diagnosis and treatment at the expense of prevention. Prevention research has tended to focus on ‘downstream’ interventions that rely on individual behaviour change, frequently increasing inequalities. Preventive strategies often focus on isolated leverage points and are scattered across different settings. This paper describes a major new prevention research programme that aims to create City Collaboratory testbeds to support the identification, implementation and evaluation of upstream interventions within a whole system city setting. Prevention of physical and mental ill-health will come from the cumulative effect of multiple system-wide interventions. Rather than scatter these interventions across many settings and evaluate single outcomes, we will test their collective impact across multiple outcomes with the goal of achieving a tipping point for better health. Our focus is on early life (ActEarly) in recognition of childhood and adolescence being such critical periods for influencing lifelong health and wellbeing

The spatial pattern of premature mortality in Hong Kong: how does it relate to public housing?

Research into understanding the relationship between access to housing, health and wellbeing in cities has yielded mixed evidence to date and has been limited to case studies from Western countries. Many studies appear to highlight the negative effects of public housing in influencing the health of its residents. Current trends in the urban housing markets in cities of advanced Asian economies and debates surrounding the role of government in providing housing underscore the need for more focused research into housing and health. In this paper, we investigate Hong Kong as an example of a thriving Asian city by exploring and comparing the intra-urban geographies of premature mortality and public housing provision in the city. Using a fully Bayesian spatial structural model, we estimate associations between public housing provision and different types of premature mortality. We find significant geographic variations in premature mortality within Hong Kong during the five-year period 2005–2009, with positive associations between the residents of public housing and premature mortality risk. But the associations attenuate or are even reversed for premature mortality of injuries and non-communicable diseases after controlling for local deprivation, housing instability, access to local amenities and other neighbourhood characteristics. The results indicate that public housing may have a protective effect on community health, which contradicts the findings of similar studies carried out in Western cities. We suggest reasons why the association between public housing and health differs in Hong Kong and discuss the implications for housing policy in Hong Kong and other Asian cities

INHERITED DELETION AT DUCHENNE DYSTROPHY LOCUS IN NORMAL MALE

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/28022/1/0000458.pd

Molecular dynamics simulations reveal that AEDANS is an inert fluorescent probe for the study of membrane proteins

Computer simulations were carried out of a number of AEDANS-labeled single cysteine mutants of a small reference membrane protein, M13 major coat protein, covering 60% of its primary sequence. M13 major coat protein is a single membrane-spanning, α-helical membrane protein with a relatively large water-exposed region in the N-terminus. In 10-ns molecular dynamics simulations, we analyze the behavior of the AEDANS label and the native tryptophan, which were used as acceptor and donor in previous FRET experiments. The results indicate that AEDANS is a relatively inert environmental probe that can move unhindered through the lipid membrane when attached to a membrane protein

Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques

Extensive experimental information supports the formation of ligand-specific conformations of G protein-coupled receptors (GPCRs) as a possible molecular basis for their functional selectivity for signaling pathways. Taking advantage of the recently published inactive and active crystal structures of GPCRs, we have implemented an all-atom computational strategy that combines different adaptive biasing techniques to identify ligand-specific conformations along pre-determined activation pathways. Using the prototypic GPCR β2-adrenergic receptor as a suitable test case for validation, we show that ligands with different efficacies (either inverse agonists, neutral antagonists, or agonists) modulate the free-energy landscape of the receptor by shifting the conformational equilibrium towards active or inactive conformations depending on their elicited physiological response. Notably, we provide for the first time a quantitative description of the thermodynamics of the receptor in an explicit atomistic environment, which accounts for the receptor basal activity and the stabilization of different active-like states by differently potent agonists. Structural inspection of these metastable states reveals unique conformations of the receptor that may have been difficult to retrieve experimentally