Spherical coding algorithm for wavelet image compression

PubMed ID: 19342336In recent literature, there exist many high-performance wavelet coders that use different spatially adaptive coding techniques in order to exploit the spatial energy compaction property of the wavelet transform. Two crucial issues in adaptive methods are the level of flexibility and the coding efficiency achieved while modeling different image regions and allocating bitrate within the wavelet subbands. In this paper, we introduce the "spherical coder," which provides a new adaptive framework for handling these issues in a simple and effective manner. The coder uses local energy as a direct measure to differentiate between parts of the wavelet subband and to decide how to allocate the available bitrate. As local energy becomes available at finer resolutions, i.e., in smaller size windows, the coder automatically updates its decisions about how to spend the bitrate. We use a hierarchical set of variables to specify and code the local energy up to the highest resolution, i.e., the energy of individual wavelet coefficients. The overall scheme is nonredundant, meaning that the subband information is conveyed using this equivalent set of variables without the need for any side parameters. Despite its simplicity, the algorithm produces PSNR results that are competitive with the state-of-art coders in literature.Publisher's VersionAuthor Post Prin

PET Imaging a MPTP-Induced Mouse Model of Parkinson’s Disease Using the Fluoropropyl-Dihydrotetrabenazine Analog [18F]-DTBZ (AV-133)

Parkinson’s disease (PD) is characterized by the loss of dopamine-producing neurons in the nigrostriatal system. Numerous researchers in the past have attempted to track the progression of dopaminergic depletion in PD. We applied a quantitative non-invasive PET imaging technique to follow this degeneration process in an MPTP-induced mouse model of PD. The VMAT2 ligand 18F-DTBZ (AV-133) was used as a radioactive tracer in our imaging experiments to monitor the changes of the dopaminergic system. Intraperitoneal administrations of MPTP (a neurotoxin) were delivered to mice at regular intervals to induce lesions consistent with PD. Our results indicate a significant decline in the levels of striatal dopamine and its metabolites (DOPAC and HVA) following MPTP treatment as determined by HPLC method. Images obtained by positron emission tomography revealed uptake of 18F-DTBZ analog in the mouse striatum. However, reduction in radioligand binding was evident in the striatum of MPTP lesioned animals as compared with the control group. Immunohistochemical analysis further confirmed PET imaging results and indicated the progressive loss of dopaminergic neurons in treated animals compared with the control counterparts. In conclusion, our findings suggest that MPTP induced PD in mouse model is appropriate to follow the degeneration of dopaminergic system and that 18F-DTBZ analog is a potentially sensitive radiotracer that can used to diagnose changes associated with PD by PET imaging modality

Improving response rates using a monetary incentive for patient completion of questionnaires: an observational study

Background: Poor response rates to postal questionnaires can introduce bias and reduce the statistical power of a study. To improve response rates in our trial in primary care we tested the effect of introducing an unconditional direct payment of 5 pound for the completion of postal questionnaires. Methods: We recruited patients in general practice with knee problems from sites across the United Kingdom. An evidence-based strategy was used to follow-up patients at twelve months with postal questionnaires. This included an unconditional direct payment of 5 pound to patients for the completion and return of questionnaires. The first 105 patients did not receive the 5 pound incentive, but the subsequent 442 patients did. We used logistic regression to analyse the effect of introducing a monetary incentive to increase the response to postal questionnaires. Results: The response rate following reminders for the historical controls was 78.1% ( 82 of 105) compared with 88.0% ( 389 of 442) for those patients who received the 5 pound payment (diff = 9.9%, 95% CI 2.3% to 19.1%). Direct payments significantly increased the odds of response ( adjusted odds ratio = 2.2, 95% CI 1.2 to 4.0, P = 0.009) with only 12 of 442 patients declining the payment. The incentive did not save costs to the trial - the extra cost per additional respondent was almost 50 pound. Conclusion: The direct payment of 5 pound significantly increased the completion of postal questionnaires at negligible increase in cost for an adequately powered study

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

BACKGROUND: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. RESULTS: The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. CONCLUSION: The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel

Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

Most signals detected by genome-wide association studies map to non-coding sequence and their tissue-specific effects influence transcriptional regulation. However, key tissues and cell-types required for functional inference are absent from large-scale resources. Here we explore the relationship between genetic variants influencing predisposition to type 2 diabetes (T2D) and related glycemic traits, and human pancreatic islet transcription using data from 420 donors. We find: (a) 7741 cis-eQTLs in islets with a replication rate across 44 GTEx tissues between 40% and 73%; (b) marked overlap between islet cis-eQTL signals and active regulatory sequences in islets, with reduced eQTL effect size observed in the stretch enhancers most strongly implicated in GWAS signal location; (c) enrichment of islet cis-eQTL signals with T2D risk variants identified in genome-wide association studies; and (d) colocalization between 47 islet cis-eQTLs and variants influencing T2D or glycemic traits, including DGKB and TCF7L2. Our findings illustrate the advantages of performing functional and regulatory studies in disease relevant tissues.Peer reviewe

Towards BioDBcore: a community-defined information specification for biological databases

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological database

Incidence, severity, aetiology and type of neck injury in men's amateur rugby union: a prospective cohort study

<p>Abstract</p> <p>Background</p> <p>There is a paucity of epidemiological data on neck injury in amateur rugby union populations. The objective of this study was to determine the incidence, severity, aetiology and type of neck injury in Australian men's amateur rugby union.</p> <p>Methods</p> <p>Data was collected from a cohort of 262 participants from two Australian amateur men's rugby union clubs via a prospective cohort study design. A modified version of the Rugby Union Injury Report Form for Games and Training was used by the clubs physiotherapist or chiropractor in data collection.</p> <p>Results</p> <p>The participants sustained 90 (eight recurrent) neck injuries. Exposure time was calculated at 31143.8 hours of play (12863.8 hours of match time and 18280 hours of training). Incidence of neck injury was 2.9 injuries/1000 player-hours (95%CI: 2.3, 3.6). As a consequence 69.3% neck injuries were minor, 17% mild, 6.8% moderate and 6.8% severe. Neck compression was the most frequent aetiology and was weakly associated with severity. Cervical facet injury was the most frequent neck injury type.</p> <p>Conclusions</p> <p>This is the first prospective cohort study in an amateur men's rugby union population since the inception of professionalism that presents injury rate, severity, aetiology and injury type data for neck injury. Current epidemiological data should be sought when evaluating the risks associated with rugby union football.</p

Efficient and Correct Stencil Computation via Pattern Matching and Static Typing

Stencil computations, involving operations over the elements of an array, are a common programming pattern in scientific computing, games, and image processing. As a programming pattern, stencil computations are highly regular and amenable to optimisation and parallelisation. However, general-purpose languages obscure this regular pattern from the compiler, and even the programmer, preventing optimisation and obfuscating (in)correctness. This paper furthers our work on the Ypnos domain-specific language for stencil computations embedded in Haskell. Ypnos allows declarative, abstract specification of stencil computations, exposing the structure of a problem to the compiler and to the programmer via specialised syntax. In this paper we show the decidable safety guarantee that well-formed, well-typed Ypnos programs cannot index outside of array boundaries. Thus indexing in Ypnos is safe and run-time bounds checking can be eliminated. Program information is encoded as types, using the advanced type-system features of the Glasgow Haskell Compiler, with the safe-indexing invariant enforced at compile time via type checking

Allogeneic haematopoietic stem cell transplantation for mitochondrial neurogastrointestinal encephalomyopathy

Mitochondrial neurogastrointestinal encephalopathy (MNGIE) is a rare fatal autorecessive disease. Halter et al. report outcomes from all known haematopoietic stem cell transplantations worldwide from sibling or unrelated donors for MNGIE between 2005 and 2011. In some of the recipients, correction of the underlying metabolic defect results in gradual clinical improvemen