Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it

BACKGROUND: The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources. RESULTS: This paper proposes a model-driven approach for the partial generation of user interfaces for searching and browsing bioinformatics data repositories. Inspired by the Model Driven Architecture (MDA) of the Object Management Group (OMG), we have developed a system that generates interfaces designed for use with bioinformatics resources. This approach helps laboratory domain experts decrease the amount of time they have to spend dealing with the repetitive aspects of user interface development. As a result, the amount of time they can spend on gathering requirements and helping develop specialised features increases. The resulting system is known as Pierre, and has been validated through its application to use cases in the life sciences, including the PEDRoDB proteomics database and the e-Fungi data warehouse. CONCLUSION: MDAs focus on generating software from models that describe aspects of service capabilities, and can be applied to support rapid development of repository interfaces in bioinformatics. The Pierre MDA is capable of supporting common database access requirements with a variety of auto-generated interfaces and across a variety of repositories. With Pierre, four kinds of interfaces are generated: web, stand-alone application, text-menu, and command line. The kinds of repositories with which Pierre interfaces have been used are relational, XML and object databases

When a 520 million-year-old Chengjiang fossil meets a modern micro-CT - a case study

The 520 million-year-old Chengjiang biota of China (UNESCO World Heritage) presents the earliest known evidence of the so-called Cambrian Explosion. Studies, however, have mainly been limited to the information exposed on the surface of the slabs. Thus far, structures preserved inside the slabs were accessed by careful removal of the matrix, in many cases with the unfortunate sacrifice of some "less important" structures, which destroys elements of exceptionally preserved specimens. Here, we show for the first time that microtomography (micro-CT) can reveal structures situated inside a Chengjiang fossil slab without causing any damage. In the present study a trilobitomorph arthropod (Xandarella spectaculum) can be reliably identified only with the application of micro-CT. We propose that this technique is an important tool for studying three-dimensionally preserved Chengjiang fossils and, most likely, also those from other biota with a comparable type of preservation, specifically similar iron concentrations

Development and implementation of clinical practice guidelines: An update and synthesis of the literature with a focus in application to spinal conditions

Study Design:Review.Objectives:The objectives of this review are to (a) summarize the role of clinical practice guidelines (CPGs), (b) outline the methodology involved in formulating CPGs, (c) provide an illustration of these principles using a CPG developed for degenerative cervical myelopathy, and (d) highlight the importance of knowledge translation.Methods:A review of the literature was conducted to summarize current standards in CPG development and implementation.Results:CPGs are systematically developed statements intended to affect decisions made by health care providers, policy makers, and patients. The main objectives of CPGs are to synthesize and translate evidence into recommendations, optimize patient outcomes, standardize care, and facilitate shared decision making among physicians, patients, and their caregivers. The main steps involved in the development of CPGs include defining the clinical problem, assembling a multidisciplinary guideline development group and systematic review team, conducting a systematic review of the literature, translating the evidence to recommendations, critically appraising the CPG and updating the document when new studies arise. The final step in developing a CPG is to implement it into clinical practice; this step requires an assessment of the barriers to implementation and the formulation of effective dissemination strategies.Conclusion:CPGs are an important component in the teaching and practice of medicine and are available for a wide spectrum of diseases. CPGs, however, can only be used to influence clinical practice if the recommendations are informed by a systematic review of the literature and developed using rigorous methodology. The opportunity to transform clinical management of spinal conditions is an attractive outcome of the application of high-quality CPGs

Customer-engineer relationship management for converged ICT service companies

Thanks to the advent of converged communications services (often referred to as ‘triple play’), the next generation Service Engineer will need radically different skills, processes and tools from today’s counterpart. Why? in order to meet the challenges of installing and maintaining services based on multi-vendor software and hardware components in an IP-based network environment. The converged services environment is likely to be ‘smart’ and support flexible and dynamic interoperability between appliances and computing devices. These radical changes in the working environment will inevitably force managers to rethink the role of Service Engineers in relation to customer relationship management. This paper aims to identify requirements for an information system to support converged communications service engineers with regard to customer-engineer relationship management. Furthermore, an architecture for such a system is proposed and how it meets these requirements is discussed

Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments

YesRecently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challenged on the basis of a lack of signal of cytosine deamination relative to three other data sets generated from young samples of herbarium and museum specimens, and a 7,000 year old human skeleton preserved in a cave environment (2). The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 palaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (alpha,beta,gamma,epsilon) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA would be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5 prime region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5 prime cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3 prime end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level

Tolerant to air σ-alkane complexes by surface modification of single crystalline solid-state molecular organometallics using vapour-phase cationic polymerisation : SMOM@polymer

Vapour-phase surface-initiated cationic polymerisation of ethylvinylether occurs at single-crystals of the σ-alkane complex [Rh(Cy2PCH2CH2PCy2)(NBA)][BArF4]. This new surface interface makes these normally very air sensitive materials tolerant to air, while also allowing for onward single-crystal to single-crystal reactivity at metal sites within the lattice

The origin of abundance gradients in the Milky Way: the predictions of different models

We aim at studying the abundance gradients along the Galactic disk and their dependence upon several parameters: a threshold in the surface gas density regulating star formation, the star formation efficiency, the timescale for the formation of the thin disk and the total surface mass density of the stellar halo. We test a model which considers a cosmological infall law. This law does not predict an inside-out disk formation, but it allows to well fit the properties of the solar vicinity. We study several cases. We find that to reproduce at the same time the abundance, star formation rate and surface gas density gradients along the Galactic disk it is necessary to assume an inside-out formation for the disk. The threshold in the gas density is not necessary and the same effect could be reached by assuming a variable star formation efficiency. A cosmologically derived infall law with an inside-out process for the disk formation and a variable star formation efficiency can indeed well reproduce all the properties of the disk. However, the cosmological model presented here does not have sufficient resolution to capture the requested inside-out formation for the disk.Comment: 13 pages, 17 figures and 2 tables. Accepted for publication in Astronomy & Astrophysic

Application of Optimal Control to CPMG Refocusing Pulse Design

We apply optimal control theory (OCT) to the design of refocusing pulses suitable for the CPMG sequence that are robust over a wide range of B0 and B1 offsets. We also introduce a model, based on recent progress in the analysis of unitary dynamics in the field of quantum information processing (QIP), that describes the multiple refocusing dynamics of the CPMG sequence as a dephasing Pauli channel. This model provides a compact characterization of the consequences and severity of residual pulse errors. We illustrate the methods by considering a specific example of designing and analyzing broadband OCT refocusing pulses of length 10 t180 that are constrained by the maximum instantaneous pulse power. We show that with this refocusing pulse, the CPMG sequence can refocus over 98% of magnetization for resonance offsets up to 3.2 times the maximum RF amplitude, even in the presence of +/- 10% RF inhomogeneity.Comment: 23 pages, 10 figures; Revised and reformatted version with new title and significant changes to Introduction and Conclusions section

Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago

YesThe Mesolithic-to-Neolithic transition marked the time when a hunter-gatherer economy gave way to agriculture, coinciding with rising sea levels. Bouldnor Cliff, is a submarine archaeological site off the Isle of Wight in the United Kingdom that has a well-preserved Mesolithic paleosol dated to 8000 years before the present. We analyzed a core obtained from sealed sediments, combining evidence from microgeomorphology and microfossils with sedimentary ancient DNA (sedaDNA) analyses to reconstruct floral and faunal changes during the occupation of this site, before it was submerged. In agreement with palynological analyses, the sedaDNA sequences suggest a mixed habitat of oak forest and herbaceous plants. However, they also provide evidence of wheat 2000 years earlier than mainland Britain and 400 years earlier than proximate European sites. These results suggest that sophisticated social networks linked the Neolithic front in southern Europe to the Mesolithic peoples of northern Europe

Remarkable preservation of brain tissues in an Early Cretaceous iguanodontian dinosaur

It has become accepted in recent years that the fossil record can preserve labile tissues. We report here the highly detailed mineralization of soft tissues associated with a naturally occurring brain endocast of an iguanodontian dinosaur found in c. 133 Ma fluvial sediments of the Wealden at Bexhill, Sussex, UK. Moulding of the braincase wall and the mineral replacement of the adjacent brain tissues by phosphates and carbonates allowed the direct examination of petrified brain tissues. Scanning electron microscopy (SEM) imaging and computed tomography (CT) scanning revealed preservation of the tough membranes (meninges) that enveloped and supported the brain proper. Collagen strands of the meningeal layers were preserved in collophane. The blood vessels, also preserved in collophane, were either lined by, or infilled with, microcrystalline siderite. The meninges were preserved in the hindbrain region and exhibit structural similarities with those of living archosaurs. Greater definition of the forebrain (cerebrum) than the hindbrain (cerebellar and medullary regions) is consistent with the anatomical and implied behavioural complexity previously described in iguanodontian-grade ornithopods. However, we caution that the observed proximity of probable cortical layers to the braincase walls probably resulted from the settling of brain tissues against the roof of the braincase after inversion of the skull during decay and burial