Integration of Biological Sources: Exploring the Case of Protein Homology

Data integration is a key issue in the domain of bioin- formatics, which deals with huge amounts of heteroge- neous biological data that grows and changes rapidly. This paper serves as an introduction in the field of bioinformatics and the biological concepts it deals with, and an exploration of the integration problems a bioinformatics scientist faces. We examine ProGMap, an integrated protein homology system used by bioin- formatics scientists at Wageningen University, and several use cases related to protein homology. A key issue we identify is the huge manual effort required to unify source databases into a single resource. Un- certain databases are able to contain several possi- ble worlds, and it has been proposed that they can be used to significantly reduce initial integration efforts. We propose several directions for future work where uncertain databases can be applied to bioinformatics, with the goal of furthering the cause of bioinformatics integration

An Integrated Approach for Characterizing Aerosol Climate Impacts and Environmental Interactions

Aerosols exert myriad influences on the earth's environment and climate, and on human health. The complexity of aerosol-related processes requires that information gathered to improve our understanding of climate change must originate from multiple sources, and that effective strategies for data integration need to be established. While a vast array of observed and modeled data are becoming available, the aerosol research community currently lacks the necessary tools and infrastructure to reap maximum scientific benefit from these data. Spatial and temporal sampling differences among a diverse set of sensors, nonuniform data qualities, aerosol mesoscale variabilities, and difficulties in separating cloud effects are some of the challenges that need to be addressed. Maximizing the long-term benefit from these data also requires maintaining consistently well-understood accuracies as measurement approaches evolve and improve. Achieving a comprehensive understanding of how aerosol physical, chemical, and radiative processes impact the earth system can be achieved only through a multidisciplinary, inter-agency, and international initiative capable of dealing with these issues. A systematic approach, capitalizing on modern measurement and modeling techniques, geospatial statistics methodologies, and high-performance information technologies, can provide the necessary machinery to support this objective. We outline a framework for integrating and interpreting observations and models, and establishing an accurate, consistent, and cohesive long-term record, following a strategy whereby information and tools of progressively greater sophistication are incorporated as problems of increasing complexity are tackled. This concept is named the Progressive Aerosol Retrieval and Assimilation Global Observing Network (PARAGON). To encompass the breadth of the effort required, we present a set of recommendations dealing with data interoperability; measurement and model integration; multisensor synergy; data summarization and mining; model evaluation; calibration and validation; augmentation of surface and in situ measurements; advances in passive and active remote sensing; and design of satellite missions. Without an initiative of this nature, the scientific and policy communities will continue to struggle with understanding the quantitative impact of complex aerosol processes on regional and global climate change and air quality

Geo-neutrinos and Earth Models

We present the current status of geo-neutrino measurements and their implications for radiogenic heating in the mantle. Earth models predict different levels of radiogenic heating and, therefore, different geo-neutrino fluxes from the mantle. Seismic tomography reveals features in the deep mantle possibly correlated with radiogenic heating and causing spatial variations in the mantle geo-neutrino flux at the Earth surface. An ocean-based observatory offers the greatest sensitivity to the mantle flux and potential for resolving Earth models and mantle features. Refinements to estimates of the geo-neutrino flux from continental crust reduce uncertainty in measurements of the mantle flux, especially measurements from land-based observatories. These refinements enable the resolution of Earth models using the combined measurements from multiple continental observatories.Comment: 9 pages, 4 figures; Contributed paper TAUP 201

A meta-analysis of studies of treatments for feline urine spraying

Feline urine spraying inside the home is a common problem behaviour that owners seek advice for from veterinarians. Individual trials relating to a variety of interventions produce variable results, and to date, no consensus on the value of different treatments has emerged. This study therefore aimed to meta-analyse, current data from appropriate published clinical trials that evaluate treatments for feline urine spraying. Inclusion and exclusion criteria for study selection were predefined and methodological quality was assessed by two independent reviewers. Ten studies in nine publications that either evaluated pharmacotherapy or pheromonatherapy (the use of a synthetic analogue of the F3 facial fraction in the cat) were suitable for analysis. There was a significant (P 0.001) association between the use of any intervention and the number of cats that ceased or reduced urine spraying by at least 90%. Analysis by intervention type indicated that fluoxetine, clomipramine and pheromonatherapy may each assist in managing urine spraying beyond a placebo based intervention. This is the first time meta-analytical techniques have been used and reported to evaluate the efficacy of interventions used in veterinary behavioural medicine, and it has established confidence in the value of both conventional treatments (pharmacotherapy) and a more recently developed treatment modality (pheromonatherapy) as an adjunct to the management of this problem. It is suggested that future research into treatment efficacy for this problem uses the benchmark standard of randomised, controlled trials lasting for at least 8 weeks, with the outcome criteria of cessation of feline urine spraying or reduction by at least 90%

The role of statins in prevention and treatment of community acquired pneumonia: a systematic review and meta-analysis.

BACKGROUND: Emerging epidemiological evidence suggests that statins may reduce the risk of community-acquired pneumonia (CAP) and its complications. PURPOSE: Performed a systematic review to address the role of statins in the prevention or treatment of CAP. DATA SOURCE: Ovid MEDLINE, Cochrane, EMBASE, ISI Web of Science, and Scopus from inception through December 2011 were searched for randomized clinical trials, cohort and case-control studies. STUDY SELECTION: Two authors independently reviewed studies that examined the role of statins in CAP. DATA EXTRACTION: Data about study characteristics, adjusted effect-estimates and quality characteristics was extracted. DATA SYNTHESIS: Eighteen studies corresponding to 21 effect-estimates (eight and 13 of which addressed the preventive and therapeutic roles of statins, respectively) were included. All studies were of good methodological quality. Random-effects meta-analyses of adjusted effect-estimates were used. Statins were associated with a lower risk of CAP, 0.84 (95% CI, 0.74-0.95), I(2) = 90.5% and a lower short-term mortality in patients with CAP, 0.68 (95% CI, 0.59-0.78), I(2) = 75.7%. Meta-regression did not identify sources of heterogeneity. A funnel plot suggested publication bias in the treatment group, which was adjusted by a novel regression method with a resultant effect-estimate of 0.85 (95% CI, 0.77-0.93). Sensitivity analyses using the rule-out approach showed that it is unlikely that the results were due to an unmeasured confounder. CONCLUSIONS: Our meta-analysis reveals a beneficial role of statins for the risk of development and mortality associated with CAP. However, the results constitute very low quality evidence as per the GRADE framework due to observational study design, heterogeneity and publication bias

Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine

Despite the tremendous success, pitfalls have been observed in every step of a clinical metabolomics workflow, which impedes the internal validity of the study. Furthermore, the demand for logistics, instrumentations, and computational resources for metabolic phenotyping studies has far exceeded our expectations. In this conceptual review, we will cover inclusive barriers of a metabolomics-based clinical study and suggest potential solutions in the hope of enhancing study robustness, usability, and transferability. The importance of quality assurance and quality control procedures is discussed, followed by a practical rule containing five phases, including two additional "pre-pre-" and "post-post-" analytical steps. Besides, we will elucidate the potential involvement of machine learning and demonstrate that the need for automated data mining algorithms to improve the quality of future research is undeniable. Consequently, we propose a comprehensive metabolomics framework, along with an appropriate checklist refined from current guidelines and our previously published assessment, in the attempt to accurately translate achievements in metabolomics into clinical and epidemiological research. Furthermore, the integration of multifaceted multi-omics approaches with metabolomics as the pillar member is in urgent need. When combining with other social or nutritional factors, we can gather complete omics profiles for a particular disease. Our discussion reflects the current obstacles and potential solutions toward the progressing trend of utilizing metabolomics in clinical research to create the next-generation healthcare system.11Ysciescopu

Electrical stimulation with non-implanted devices for stress urinary incontinence in women

The authors would like to thank Luke Vale, Imran Omar, Sheila Wallace and Suzanne MacDonald at the Cochrane Incontinence Group for their support. We would also like to thank Mette Frahm Olsen, Gavin Stewart, Miriam Brazelli, Anna Sierawska, and Beatriz Gualeo for help with translations.Peer reviewedPublisher PD