Demonstration of hyper-programming in Java

We demonstrate the use of a hyper-programming system to build persistent Java applications in PJama, an orthogonally persistent version of Java. This allows program representations to contain type-safe links to persistent objects embedded directly within the source code. The potential benefits include greater potential for static program checking, improved efficiency, and reduced programming effort.Postprin

Evolving database systems : a persistent view

Submitted to POS7 This work was supported in St Andrews by EPSRC Grant GR/J67611 "Delivering the Benefits of Persistence"Orthogonal persistence ensures that information will exist for as long as it is useful, for which it must have the ability to evolve with the growing needs of the application systems that use it. This may involve evolution of the data, meta-data, programs and applications, as well as the users' perception of what the information models. The need for evolution has been well recognised in the traditional (data processing) database community and the cost of failing to evolve can be gauged by the resources being invested in interfacing with legacy systems. Zdonik has identified new classes of application, such as scientific, financial and hypermedia, that require new approaches to evolution. These applications are characterised by their need to store large amounts of data whose structure must evolve as it is discovered by the applications that use it. This requires that the data be mapped dynamically to an evolving schema. Here, we discuss the problems of evolution in these new classes of application within an orthogonally persistent environment and outline some approaches to these problems.Postprin

Linguistic Reflection in Java

Reflective systems allow their own structures to be altered from within. Here we are concerned with a style of reflection, called linguistic reflection, which is the ability of a running program to generate new program fragments and to integrate these into its own execution. In particular we describe how this kind of reflection may be provided in the compiler-based, strongly typed object-oriented programming language Java. The advantages of the programming technique include attaining high levels of genericity and accommodating system evolution. These advantages are illustrated by an example taken from persistent programming which shows how linguistic reflection allows functionality (program code) to be generated on demand (Just-In-Time) from a generic specification and integrated into the evolving running program. The technique is evaluated against alternative implementation approaches with respect to efficiency, safety and ease of use.Comment: 25 pages. Source code for examples at http://www-ppg.dcs.st-and.ac.uk/Java/ReflectionExample/ Dynamic compilation package at http://www-ppg.dcs.st-and.ac.uk/Java/DynamicCompilation

Occupational asthma: a review.

Occupational asthma is the most common form of occupational lung disease in the developed world at the present time. In this review, the epidemiology, pathogenesis/mechanisms, clinical presentations, management, and prevention of occupational asthma are discussed. The population attributable risk of asthma due to occupational exposures is considerable. Current understanding of the mechanisms by which many agents cause occupational asthma is limited, especially for low-molecular-weight sensitizers and irritants. The diagnosis of occupational asthma is generally established on the basis of a suggestive history of a temporal association between exposure and the onset of symptoms and objective evidence that these symptoms are related to airflow limitation. Early diagnosis, elimination of exposure to the responsible agent, and early use of inhaled steroids may play important roles in the prevention of long-term persistence of asthma. Persistent occupational asthma is often associated with substantial disability and consequent impacts on income and quality of life. Prevention of new cases is the best approach to reducing the burden of asthma attributable to occupational exposures. Future research needs are identified

Symptoms of ADHD are related to education and work experience among incarcerated adults

Several reports document increased prevalence of attention deficit and hyperactivity (ADHD) and similar symptoms in incarcerated members of the community, but little is known about how the symptoms are related to education and work experience. An ongoing study among Norwegian inmates reveals that 60 % report signs of ADHD. In the present study a sample of 600 inmates incarcerated in Norway filled out a questionnaire including the WURS-k (Wender Utah Rating Scale, short form) and questions to survey completed education level and work experience. A clear relationship was found between the WURS-k score and earlier job-experience, with increased probability of ADHD with work experience from low socio-economic status jobs. The scale was also found to share variance with the inmates’ reported education history, as higher education reduces the probability of ADHD among the incarcerated adults. Thus, the WURS-k could be a useful screening instrument in education assessment among inmates. The link between the present findings and development of anti-social behaviour is discussed

Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner.

BackgroundRewriting of the epigenome has risen as a promising alternative to gene editing for precision medicine. In nature, epigenetic silencing can result in complete attenuation of target gene expression over multiple mitotic divisions. However, persistent repression has been difficult to achieve in a predictable manner using targeted systems.ResultsHere, we report that persistent epigenetic memory required both a DNA methyltransferase (DNMT3A-dCas9) and a histone methyltransferase (Ezh2-dCas9 or KRAB-dCas9). We demonstrate that the histone methyltransferase requirement can be locus specific. Co-targeting Ezh2-dCas9, but not KRAB-dCas9, with DNMT3A-dCas9 and DNMT3L induced long-term HER2 repression over at least 50 days (approximately 57 cell divisions) and triggered an epigenetic switch to a heterochromatic environment. An increase in H3K27 trimethylation and DNA methylation was stably maintained and accompanied by a sustained loss of H3K27 acetylation. Interestingly, substitution of Ezh2-dCas9 with KRAB-dCas9 enabled long-term repression at some target genes (e.g., SNURF) but not at HER2, at which H3K9me3 and DNA methylation were transiently acquired and subsequently lost. Off-target DNA hypermethylation occurred at many individual CpG sites but rarely at multiple CpGs in a single promoter, consistent with no detectable effect on transcription at the off-target loci tested. Conversely, robust hypermethylation was observed at HER2. We further demonstrated that Ezh2-dCas9 required full-length DNMT3L for maximal activity and that co-targeting DNMT3L was sufficient for persistent repression by Ezh2-dCas9 or KRAB-dCas9.ConclusionsThese data demonstrate that targeting different combinations of histone and DNA methyltransferases is required to achieve maximal repression at different loci. Fine-tuning of targeting tools is a necessity to engineer epigenetic memory at any given locus in any given cell type

Seven Dimensions of Portability for Language Documentation and Description

The process of documenting and describing the world's languages is undergoing radical transformation with the rapid uptake of new digital technologies for capture, storage, annotation and dissemination. However, uncritical adoption of new tools and technologies is leading to resources that are difficult to reuse and which are less portable than the conventional printed resources they replace. We begin by reviewing current uses of software tools and digital technologies for language documentation and description. This sheds light on how digital language documentation and description are created and managed, leading to an analysis of seven portability problems under the following headings: content, format, discovery, access, citation, preservation and rights. After characterizing each problem we provide a series of value statements, and this provides the framework for a broad range of best practice recommendations.Comment: 8 page

Twelve Theses on Reactive Rules for the Web

Reactivity, the ability to detect and react to events, is an essential functionality in many information systems. In particular, Web systems such as online marketplaces, adaptive (e.g., recommender) systems, and Web services, react to events such as Web page updates or data posted to a server. This article investigates issues of relevance in designing high-level programming languages dedicated to reactivity on the Web. It presents twelve theses on features desirable for a language of reactive rules tuned to programming Web and Semantic Web applications

Report on the XBase Project

This project addressed the conceptual fundamentals of data storage, investigating techniques for provision of highly generic storage facilities that can be tailored to produce various individually customised storage infrastructures, compliant to the needs of particular applications. This requires the separation of mechanism and policy wherever possible. Aspirations include: actors, whether users or individual processes, should be able to bind to, update and manipulate data and programs transparently with respect to their respective locations; programs should be expressed independently of the storage and network technology involved in their execution; storage facilities should be structure-neutral so that actors can impose multiple interpretations over information, simultaneously and safely; information should not be discarded so that arbitrary historical views are supported; raw stored information should be open to all; where security restrictions on its use are required this should be achieved using cryptographic techniques. The key advances of the research were: 1) the identification of a candidate set of minimal storage system building blocks, which are sufficiently simple to avoid encapsulating policy where it cannot be customised by applications, and composable to build highly flexible storage architectures 2) insight into the nature of append-only storage components, and the issues arising from their application to common storage use-cases