A PROCESS FOR ACHIEVING COMPARABLE DATA FROM HETEROGENEOUS DATABASES

The current state of health and biomedicine includes an enormity of heterogeneous data ‘silos’, collected for different purposes and represented differently, that are presently impossible to share or analyze in toto. The greatest challenge for large-scale and meaningful analyses of health-related data is to achieve a uniform data representation for data extracted from heterogeneous source representations. Based upon an analysis and categorization of heterogeneities, a process for achieving comparable data content by using a uniform terminological representation is developed. This process addresses the types of representational heterogeneities that commonly arise in healthcare data integration problems. Specifically, this process uses a reference terminology, and associated "maps" to transform heterogeneous data to a standard representation for comparability and secondary use. The capture of quality and precision of the “maps” between local terms and reference terminology concepts enhances the meaning of the aggregated data, empowering end users with better-informed queries for subsequent analyses. A data integration case study in the domain of pediatric asthma illustrates the development and use of a reference terminology for creating comparable data from heterogeneous source representations. The contribution of this research is a generalized process for the integration of data from heterogeneous source representations, and this process can be applied and extended to other problems where heterogeneous data needs to be merged.

The Web KnowARR Framework: Orchestrating Computational Intelligence with Graph Databases

This chapter presents fuzzy cognitive maps (FCM) as a vehicle for Web knowledge aggregation, representation, and reasoning. The corresponding Web KnowARR framework incorporates findings from fuzzy logic. To this end, a first emphasis is particularly on the Web KnowARR framework along with a stakeholder management use case to illustrate the framework’s usefulness as a second focal point. This management form is to help projects to acceptance and assertiveness where claims for company decisions are actively involved in the management process. Stakeholder maps visually (re-) present these claims. On one hand, they resort to non-public content and on the other they resort to content that is available to the public (mostly on the Web). The Semantic Web offers opportunities not only to present public content descriptively but also to show relationships. The proposed framework can serve as the basis for the public content of stakeholder maps.

Characteristics and comprehensiveness of adult HIV care and treatment programmes in Asia-Pacific, sub-Saharan Africa and the Americas: results of a site assessment conducted by the International epidemiologic Databases to Evaluate AIDS (IeDEA) Collaboration

INTRODUCTION HIV care and treatment programmes worldwide are transforming as they push to deliver universal access to essential prevention, care and treatment services to persons living with HIV and their communities. The characteristics and capacity of these HIV programmes affect patient outcomes and quality of care. Despite the importance of ensuring optimal outcomes, few studies have addressed the capacity of HIV programmes to deliver comprehensive care. We sought to describe such capacity in HIV programmes in seven regions worldwide. METHODS Staff from 128 sites in 41 countries participating in the International epidemiologic Databases to Evaluate AIDS completed a site survey from 2009 to 2010, including sites in the Asia-Pacific region (n=20), Latin America and the Caribbean (n=7), North America (n=7), Central Africa (n=12), East Africa (n=51), Southern Africa (n=16) and West Africa (n=15). We computed a measure of the comprehensiveness of care based on seven World Health Organization-recommended essential HIV services. RESULTS Most sites reported serving urban (61%; region range (rr): 33-100%) and both adult and paediatric populations (77%; rr: 29-96%). Only 45% of HIV clinics that reported treating children had paediatricians on staff. As for the seven essential services, survey respondents reported that CD4+ cell count testing was available to all but one site, while tuberculosis (TB) screening and community outreach services were available in 80 and 72%, respectively. The remaining four essential services - nutritional support (82%), combination antiretroviral therapy adherence support (88%), prevention of mother-to-child transmission (PMTCT) (94%) and other prevention and clinical management services (97%) - were uniformly available. Approximately half (46%) of sites reported offering all seven services. Newer sites and sites in settings with low rankings on the UN Human Development Index (HDI), especially those in the President's Emergency Plan for AIDS Relief focus countries, tended to offer a more comprehensive array of essential services. HIV care programme characteristics and comprehensiveness varied according to the number of years the site had been in operation and the HDI of the site setting, with more recently established clinics in low-HDI settings reporting a more comprehensive array of available services. Survey respondents frequently identified contact tracing of patients, patient outreach, nutritional counselling, onsite viral load testing, universal TB screening and the provision of isoniazid preventive therapy as unavailable services. CONCLUSIONS This study serves as a baseline for on-going monitoring of the evolution of care delivery over time and lays the groundwork for evaluating HIV treatment outcomes in relation to site capacity for comprehensive care.

The effects of anti-infective preventive measures on the occurrence of biologic implant complications and implant loss: a systematic review.

PURPOSE To systematically appraise whether anti-infective protocols are effective in preventing biologic implant complications and implant loss after a mean observation period ≥ 10 years after loading. MATERIALS AND METHODS An electronic search of Medline via PubMed and Embase via Ovid databases complemented by manual search was conducted up to October 31, 2012. Studies were included provided that they were published in English, German, French, or Italian, and conducted on ≥ 20 partially and fully edentulous patients with dental implants and regular (≥ 1×/year) supportive periodontal therapy (SPT) over a mean observation period ≥ 10 years. Assessment of the identified studies and data extraction were performed independently by two reviewers. Authors were contacted if required. Collected data were reported by descriptive methods. RESULTS The initial electronic search resulted in the identification of 994 titles from Medline via PubMed and 531 titles from Embase via Ovid databases, respectively. After elimination of duplicate titles and exclusion of 60 full-text articles, 143 articles were analyzed, resulting in 15 studies eligible for qualitative analysis. The implant survival rate ranged from 85.7% to 99.2% after a mean observation period ≥ 10 years. One comparative study assessed the effects of regular SPT on the occurrence of biologic complications and implant loss. Overall, regular diagnosis and implementation of anti-infective therapeutic protocols were effective in the management of biological complications and prevention of implant loss. Residual probing depths at the end of active periodontal therapy and development of reinfection during supportive periodontal therapy (SPT) represented a significant risk for the onset of peri-implantitis and implant loss. Comparative studies indicated that implant survival and success rates were lower in periodontally compromised vs noncompromised patients. CONCLUSIONS In order to achieve high long-term survival and success rates of dental implants and their restorations, enrollment in regular SPT including anti-infective preventive measures should be implemented. Therapy of peri-implant mucositis should be considered as a preventive measure for the onset of peri-implantitis. Completion of active periodontal therapy should precede implant placement in periodontally compromised patients.

Effectiveness of Personal Protective Equipment for Healthcare Workers Caring for Patients with Filovirus Disease: A Rapid Review.

BACKGROUND A rapid review, guided by a protocol, was conducted to inform development of the World Health Organization's guideline on personal protective equipment in the context of the ongoing (2013-present) Western African filovirus disease outbreak, with a focus on health care workers directly caring for patients with Ebola or Marburg virus diseases. METHODS Electronic databases and grey literature sources were searched. Eligibility criteria initially included comparative studies on Ebola and Marburg virus diseases reported in English or French, but criteria were expanded to studies on other viral hemorrhagic fevers and non-comparative designs due to the paucity of studies. After title and abstract screening (two people to exclude), full-text reports of potentially relevant articles were assessed in duplicate. Fifty-seven percent of extraction information was verified. The Grading of Recommendations Assessment, Development and Evaluation framework was used to inform the quality of evidence assessments. RESULTS Thirty non-comparative studies (8 related to Ebola virus disease) were located, and 27 provided data on viral transmission. Reporting of personal protective equipment components and infection prevention and control protocols was generally poor. CONCLUSIONS Insufficient evidence exists to draw conclusions regarding the comparative effectiveness of various types of personal protective equipment. Additional research is urgently needed to determine optimal PPE for health care workers caring for patients with filovirus.

Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants

Background Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) have been widely used as SSR source for plants of economic relevance but their application to non-model species is still modest. Methods Here, we explored the use of publicly available ESTs (GenBank at the National Center for Biotechnology Information-NCBI) for SSRs development in non-model plants, focusing on genera listed by the International Union for the Conservation of Nature (IUCN). We also search two model genera with fully annotated genomes for EST-SSRs, Arabidopsis and Oryza, and used them as controls for genome distribution analyses. Overall, we downloaded 16 031 555 sequences for 258 plant genera which were mined for SSRsand their primers with the help of QDD1. Genome distribution analyses in Oryza and Arabidopsis were done by blasting the sequences with SSR against the Oryza sativa and Arabidopsis thaliana reference genomes implemented in the Basal Local Alignment Tool (BLAST) of the NCBI website. Finally, we performed an empirical test to determine the performance of our EST-SSRs in a few individuals from four species of two eudicot genera, Trifolium and Centaurea. Results We explored a total of 14 498 726 EST sequences from the dbEST database (NCBI) in 257 plant genera from the IUCN Red List. We identify a very large number (17 102) of ready-to-test EST-SSRs in most plant genera (193) at no cost. Overall, dinucleotide and trinucleotide repeats were the prevalent types but the abundance of the various types of repeat differed between taxonomic groups. Control genomes revealed that trinucleotide repeats were mostly located in coding regions while dinucleotide repeats were largely associated with untranslated regions. Our results from the empirical test revealed considerable amplification success and transferability between congenerics. Conclusions The present work represents the first large-scale study developing SSRs by utilizing publicly accessible EST databases in threatened plants. Here we provide a very large number of ready-to-test EST-SSR (17 102) for 193 genera. The cross-species transferability suggests that the number of possible target species would be large. Since trinucleotide repeats are abundant and mainly linked to exons they might be useful in evolutionary and conservation studies. Altogether, our study highly supports the use of EST databases as an extremely affordable and fast alternative for SSR developing in threatened plants.

Photometric monitoring of non-resolved space debris and databases of optical light curves.

The population of space debris increased drastically during the last years. Collisions involving massive objects may produce large number of fragments leading to significantly growth of the space debris population. An effective remediation measure in order to stabilize the population in LEO, is therefore the removal of large, massive space debris. To remove these objects, not only precise orbits, but also more detailed information about their attitude states will be required. One important property of an object targeted for removal is its spin period and spin axis orientation. If we observe a rotating object, the observer sees different surface areas of the object which leads to changes in the measured intensity. Rotating objects will produce periodic brightness vari ations with frequencies which are related to the spin periods. Photometric monitoring is the real tool for remote diagnostics of the satellite rotation around its center of mass. This information is also useful, for example, in case of contingency. Moreover, it is also important to take into account the orientation of non-spherical body (e.g. space debris) in the numerical integration of its motion when a close approach with the another spacecr aft is predicted. We introduce the two databases of light curves: the AIUB data base, which contains about a thousand light curves of LEO, MEO and high-altitude debris objects (including a few functional objects) obtained over more than seven years, and the data base of the Astronomical Observatory of Odessa University (Ukraine), which contains the results of more than 10 years of photometric monitoring of functioning satellites and large space debris objects in low Earth orbit. AIUB used its 1m ZIMLAT telescope for all light curves. For tracking low-orbit satellites, the Astronomical Observatory of Odessa used the KT-50 telescope, which has an alt-azimuth mount and allows tracking objects moving at a high angular velocity. The diameter of the KT-50 main mirror is 0.5 m, and the focal length is 3 m. The Odessa's Atlas of light curves includes almost 5,5 thousand light curves for ~500 correlated objects from a time period of 2005-2014. The processing of light curves and the determination of the rotation period in the inertial frame is challenging. Extracted frequencies and reconstructed phases for some interesting targets, e.g. GLONASS satellites, for which also SLR data were available for confirmation, will be presented. The rotation of the Envisat satellite after its sudden failure will be analyzed. The deceleration of its rotation rate within 3 years is studied together with the attempt to determine the orientation of the rotation axis.

Effect of chin-cup treatment on the temporomandibular joint: a systematic review

AIM To systematically search the literature and assess the available evidence for the influence of chin-cup therapy on the temporomandibular joint regarding morphological adaptations and appearance of temporomandibular disorders (TMD). MATERIALS AND METHODS Electronic database searches of published and unpublished literature were performed. The following electronic databases with no language and publication date restrictions were searched: MEDLINE (via Ovid and PubMed), EMBASE (via Ovid), the Cochrane Oral Health Group's Trials Register, and CENTRAL. Unpublished literature was searched on ClinicalTrials.gov, the National Research Register, and Pro-Quest Dissertation Abstracts and Thesis database. The reference lists of all eligible studies were checked for additional studies. Two review authors performed data extraction independently and in duplicate using data collection forms. Disagreements were resolved by discussion or the involvement of an arbiter. RESULTS From the 209 articles identified, 55 papers were considered eligible for inclusion in the review. Following the full text reading stage, 12 studies qualified for the final review analysis. No randomized clinical trial was identified. Eight of the included studies were of prospective and four of retrospective design. All studies were assessed for their quality and graded eventually from low to medium level of evidence. Based on the reported evidence, chin-cup therapy affects the condylar growth pattern, even though two studies reported no significance changes in disc position and arthrosis configuration. Concerning the incidence of TMD, it can be concluded from the available evidence that chin-cup therapy constitutes no risk factor for TMD. CONCLUSION Based on the available evidence, chin-cup therapy for Class III orthodontic anomaly seems to induce craniofacial adaptations. Nevertheless, there are insufficient or low-quality data in the orthodontic literature to allow the formulation of clear statements regarding the influence of chin-cup treatment on the temporomandibular joint.

Coastal Survey Maps: From Historical Documents to Digital Databases

This paper describes the spatial data handling procedures used to create a vector database of the Connecticut shoreline from Coastal Survey Maps. The appendix contains detailed information on how the procedures were implemented using Geographic Transformer Software 5 and ArcGIS 8.3. The project was a joint project of the Connecticut Department of Environmental Protection and the University of Connecticut Center for Geographic Information and Analysis.

A systematic review of the methods used to assess race and racial disparities in uterine fibroid research

Context: Black women are reported to have a higher prevalence of uterine fibroids, and a threefold higher incidence rate and relative risk for clinical uterine fibroid development as compared to women of other races. Uterine fibroid research has reported that black women experience greater uterine fibroid morbidity and disproportionate uterine fibroid disease burden. With increased interest in understanding uterine fibroid development, and race being a critical component of uterine fibroid assessment, it is imperative that the methods used to determine the race of research participants is defined and the operational definition of the use of race as a variable is reported for methodological guidance, and to enable the research community to compare statistical data and replicate studies. ^ Objectives: To systematically review and evaluate the methods used to assess race and racial disparities in uterine fibroid research. ^ Data Sources: Databases searched for this review include: OVID Medline, NML PubMed, Ebscohost Cumulative Index to Nursing and Allied Health Plus with Full Text, and Elsevier Scopus. ^ Review Methods: Articles published in English were retrieved from data sources between January 2011 and March 2011. Broad search terms, uterine fibroids and race, were employed to retrieve a comprehensive list of citations for review screening. The initial database yield included 947 articles, after duplicate extraction 485 articles remained. In addition, 771 bibliographic citations were reviewed to identify additional articles not found through the primary database search, of which 17 new articles were included. In the first screening, 502 titles and abstracts were screened against eligibility questions to determine citations of exclusion and to retrieve full text articles for review. In the second screening, 197 full texted articles were screened against eligibility questions to determine whether or not they met full inclusion/exclusion criteria. ^ Results: 100 articles met inclusion criteria and were used in the results of this systematic review. The evidence suggested that black women have a higher prevalence of uterine fibroids when compared to white women. None of the 14 studies reporting data on prevalence reported an operational definition or conceptual framework for the use of race. There were a limited number of studies reporting on the prevalence of risk factors among racial subgroups. Of the 3 studies, 2 studies reported prevalence of risk factors lower for black women than other races, which was contrary to hypothesis. And, of the three studies reporting on prevalence of risk factors among racial subgroups, none of them reported a conceptual framework for the use of race. ^ Conclusion: In the 100 uterine fibroid studies included in this review over half, 66%, reported a specific objective to assess and recruit study participants based upon their race and/or ethnicity, but most, 51%, failed to report a method of determining the actual race of the participants, and far fewer, 4% (only four South American studies), reported a conceptual framework and/or operational definition of race as a variable. However, most, 95%, of all studies reported race-based health outcomes. The inadequate methodological guidance on the use of race in uterine fibroid studies, purporting to assess race and racial disparities, may be a primary reason that uterine fibroid research continues to report racial disparities, but fails to understand the high prevalence and increased exposures among African-American women. A standardized method of assessing race throughout uterine fibroid research would appear to be helpful in elucidating what race is actually measuring, and the risk of exposures for that measurement. ^

Ordinary and duplicate analysis from major and trace elements of ODP Holes 146-888B and 168-1027B

Oceanic sediments deposited at high rate close to continents are dominated by terrigenous material. Aside from dilution by biogenic components, their chemical compositions reflect those of nearby continental masses. This study focuses on oceanic sediments coming from the juvenile Canadian Cordillera and highlights systematic differences between detritus deriving from juvenile crust and detritus from old and mature crust. We report major and trace element concentrations for 68 sediments from the northernmost part of the Cascade forearc, drilled at ODP Sites 888 and 1027. The calculated weighted averages for each site can then be used in the future to quantify the contribution of subducted sediments to Cascades volcanism. The two sites have similar compositions but Site 888, located closer to the continent, has higher sandy turbidite contents and displays higher bulk SiO2/Al2O3 with lower bulk Nb/Zr, attributed to the presence of zircons in the coarse sands. Comparison with published data for other oceanic sedimentary piles demonstrates the existence of systematic differences between modern sediments deriving from juvenile terranes (juvenile sediments) and modern sediments derived from mature continental areas (cratonic sediments). The most striking systematic difference is for Th/Nb, Th/U, Nb/U and Th/Rb ratios: juvenile sediments have much lower ratios than cratonic sediments. The small enrichment of Th over Nb in cratonic sediments may be explained by intracrustal magmatic and metamorphic differentiation processes. In contrast, their elevated Th/U and Nb/U ratios (average values of 6.87 and 7.95, respectively) in comparison to juvenile sediments (Th/U ~ 3.09, Nb/U ~ 5.15) suggest extensive U and Rb losses on old cratons. Uranium and Rb losses are attributed to long-term leaching by rain and river water during exposure of the continental crust at the surface. Over geological times, the weathering effects create a slow but systematic increase of Th/U with exposure time.