The NESTOR Framework: how to Handle Hierarchical Data Structures

Περιέχει το πλήρες κείμενοIn this paper we study the problem of representing, managing and exchanging hierarchically structured data in the context of a Digital Library (DL). We present the NEsted SeTs for Object hieRarchies (NESTOR) framework defining two set data models that we call: the “Nested Set Model (NS-M)” and the “Inverse Nested Set Model (INSM)” based on the organization of nested sets which enable the representation of hierarchical data structures. We present the mapping between the tree data structure to NS-M and to INS-M. Furthermore, we shall show how these set data models can be used in conjunction with Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) adding new functionalities to the protocol without any change to its basic functioning. At the end we shall present how the couple OAI-PMH and the set data models can be used to represent and exchange archival metadata in a distributed environment

Expression of selected proteins in breast cancer brain metastases

 The aim of the study was to assess the immunohistochemical (IHC) profiles of SRC3, Pax2, ER, PgR, Her2, EGFR, CK5/6, and Ki67 proteins in breast-cancer brain metastasis. The study utilized tumor samples from 30 metastatic patients and calculated correlations between all IHC variables. In fourteen cases, primary breast cancers paired with secondary deposits were analyzed. We evaluated the association between IHC status in the primary and secondary deposits, grade, and histotype of the tumors. The examination of the metastatic deposits in all 30 patients resulted in positive detection in the following cases: SRC3 in 20 cases (66.6%), Pax2 in 22 (73.3%), ER in 22 (73.3%), PgR in 25 (83.3%), Her2 in 10 (33.3%), EGFR in 12 (40%), CK5/6 in 7 (23.3%), and Ki67 in 23 (76.6%). Grade 2 was found in 13.3% of all patients, and grade 3 in 86.7%. SRC3 and Pax2 were positive in both G2 and G3. Invasive lobular carcinoma and invasive ductal carcinoma were diagnosed in 23.3% and 76.7% of cases, respectively. There were no differences between the IHC expression of the studied proteins in either grading or histotype of the tumors. In the IHC profiles, which included SRC3, Pax2, ER, PgR, Her2, CK5/6, Ki67, and EGFR, we found no statistically significant differences between the primary cancer and the brain metastasis. In our study of metastatic breast carcinoma deposits, there was no correlation between SRC3, Pax2 status and histotype, and tumor grade. The IHC status of the paired primary and metastatic deposits did not differ in a statistically significant manner.

Plasma-sprayed thermal barrier coatings: numerical study on damage localization and evolution

Thermal barrier coatings (TBCs) are advanced material systems used to enhance performance and in-service life of components operated at high temperatures in gas turbines and other power-generation devices. Because of complexity, numerical methods became important tools both for design of these coatings and for in-service life estimations and optimization. In this contribution, two main features that affect the TBCs’ performance, namely the roughness of the bond coat and the microstructure of the ceramic top coat, are discussed based on Finite Element Method (FEM) and Finite Element Microstructure MEshfree (FEMME) simulations that were used to calculate stresses and assess damage within the coating. Roughness data obtained from plasma-sprayed CoNiCrAlY + YSZ coated samples are supplemented to discuss assumptions and results of employed numerical models

Autologous tooth graft after endodontical treated used for socket preservation: A multicenter clinical study.

The aim of the study was to evaluate the tooth extracted use as autologous tooth graft after endodontic root canal therapies used for socket preservation. To this purpose, the Tooth Transformer shredding and decontamination machine has been used. The graft obtained in this way, was inserted at the time of the extraction or at a second surgery altogether with the chosen regenerative therapy. This clinical trial enrolled patients with post-estractive defects requiring the restoration bone dimension and shape in the maxillary and mandibular zone. In addition, 98 patients with 119 extraction sockets were enrolled across 10 standardized centers. An innovative preparation method, using the dedicated automated device Tooth Transformer, able to transform autologous teeth in suitable grafting material, has been used. The extracted tooth was cleaned and treated using a Tooth Transformer and made a socket preservation. Thirteen Biopsies were realized to analyze the histologic outcomes at the average time of four months to demonstrate that the autologous tooth graft made from root after endodontic therapy should be used in human bone regeneration as graft for dental implant placement

The temporal pattern of respiratory and heart disease mortality in response to air pollution.

Short-term changes in ambient particulate matter with aerodynamic diameters < 10 micro m (PM10) have been associated with short-term fluctuations in mortality or morbidity in many studies. In this study, we tested whether those deaths are just advanced by a few days or weeks using a multicity hierarchical modeling approach for all-cause, respiratory, and cardiovascular deaths, for all ages and stratifying by age groups, within the APHEA-2 (Air Pollution and Health: A European Approach) project. We fit a Poisson regression and used an unconstrained distributed lag to model the effect of PM10 exposure on deaths up to 40 days after the exposure. In baseline models using PM10 the day of and day before the death, we found that the overall PM10 effect (per 10 micro g/m3) was 0.74% [95% confidence interval (95% CI), -0.17 to 1.66] for respiratory deaths and 0.69% (95% CI, 0.31-1.08) for cardiovascular deaths. In unrestricted distributed lag models, the effect estimates increased to 4.2% (95% CI, 1.08-7.42) for respiratory deaths and to 1.97% (95% CI, 1.38-2.55) for cardiovascular deaths. Our study confirms that most of the effect of air pollution is not simply advanced by a few weeks and that effects persist for more than a month after exposure. The effect size estimate for PM10 doubles when we considered longer-term effects for all deaths and for cardiovascular deaths and becomes five times higher for respiratory deaths. We found similar effects when stratifying by age groups. These larger effects are important for risk assessment

The taxonomic name resolution service : an online tool for automated standardization of plant names

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 14 (2013): 16, doi:10.1186/1471-2105-14-16.The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ webcite and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/ webcite.BJE was supported by NSF grant DBI 0850373 and TR by CSIRO Marine and Atmospheric Research, Australia,. BB and BJE acknowledge early financial support from Conservation International and TEAM who funded the development of early prototypes of taxonomic name resolution. The iPlant Collaborative (http://www.iplantcollaborative.org) is funded by a grant from the National Science Foundation (#DBI-0735191)

Interpenetrated Magnesium–Tricalcium Phosphate Composite: Manufacture, Characterization and In Vitro Degradation Test

Magnesium and calcium phosphates composites are promising biomaterials to create biodegradable load-bearing implants for bone regeneration. The present investigation is focused on the design of an interpenetrated magnesium–tricalcium phosphate (Mg–TCP) composite and its evaluation under immersion test. In the study, TCP porous preforms were fabricated by robocasting to have a prefect control of porosity and pore size and later infiltrated with pure commercial Mg through current-assisted metal infiltration (CAMI) technique. The microstructure, composition, distribution of phases and degradation of the composite under physiological simulated conditions were analysed by scanning electron microscopy, elemental chemical analysis and X-ray diffraction. The results revealed that robocast TCP preforms were full infiltrated by magnesium through CAMI, even small pores below 2 lm have been filled with Mg, giving to the composite a good interpenetration. The degradation rate of the Mg–TCP composite displays lower value compared to the one of pure Mg during the first 24 h of immersion test.Magnesium and calcium phosphates composites are promising biomaterials to create biodegradable load-bearing implants for bone regeneration. The present investigation is focused on the design of an interpenetrated magnesium–tricalcium phosphate (Mg–TCP) composite and its evaluation under immersion test. In the study, TCP porous preforms were fabricated by robocasting to have a prefect control of porosity and pore size and later infiltrated with pure commercial Mg through current-assisted metal infiltration (CAMI) technique. The microstructure, composition, distribution of phases and degradation of the composite under physiological simulated conditions were analysed by scanning electron microscopy, elemental chemical analysis and X-ray diffraction. The results revealed that robocast TCP preforms were full infiltrated by magnesium through CAMI, even small pores below 2 lm have been filled with Mg, giving to the composite a good interpenetration. The degradation rate of the Mg–TCP composite displays lower value compared to the one of pure Mg during the first 24 h of immersion test