Querying distributed heterogeneous structured and semi-structured data sources

The continuing growth and widespread popularity of the internet means that the collection of useful data available for public access is rapidly increasing both in number and size. These data are spread over distributed heterogeneous data sources like traditional databases or sources of various forms containing unstructured and semi-structured data. Obviously, the value of these data sources would in many cases be greatly enhanced if the data they contain could be combined and queried in a uniform manner. The research work reported in this dissertation is concerned with querying and integrating a multiplicity of distributed heterogeneous structured data residing in relational databases and semi-structured data held in well- formed XML documents produced by internet applications or human- coded. In particular, we have addressed the problems of: (1) specifying the mappings between a global schema and the local data sources' schemas, and resolving the heterogeneity which can occur between data models, schemas or schema concepts (2) processing queries that are expressed on a global schema into local queries. We have proposed an approach to combine and query the data sources through a mediation layer. Such a layer is intended to establish and evolve an XML Metadata Knowledge Base (XMKB) incrementally which assists the Query Processor in mediating between user queries posed over the global schema and the queries on the underlying distributed heterogeneous data sources. It translates such queries into sub-queries -called local queries- which are appropriate to each local data source. The XMKB is built in a bottom-up fashion by extracting and merging incrementally the metadata of the data sources. It holds the data source's information (names, types and locations), descriptions of the mappings between the global schema and the participating data source schemas, and function names for handling semantic and structural discrepancies between the representations. To demonstrate our research, we have designed and implemented a prototype system called SISSD (System to Integrate Structured and Semi- structured Databases). The system automatically creates a GUI tool for meta-users (who do the metadata integration) which they use to describe mappings between the global schema and local data source schemas. These mappings are used to produce the XMKB. The SISSD allows the translation of user queries into sub-queries fitting each participating data source, by exploiting the mapping information stored in the XMKB. The major results of the thesis are: (1) an approach that facilitates building structured and semi-structured data integration systems (2) a method for generating mappings between a global and local schemas' paths, and resolving the conflicts caused by the heterogeneity of the data sources such as naming, structural, and semantic conflicts which, may occur between the schemas (3) a method for translating queries in terms of a global schema into sub-queries in terms of local schemas. Hence, the presented approach shows that: (a) mapping of the schemas' paths can only be partially automated, since the logical heterogeneity problems need to be resolved by human judgment based on the application requirements (b) querying distributed heterogeneous structured and semi-structured data sources is possible.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Querying distributed heterogeneous structured and semi-structured data sources

The continuing growth and widespread popularity of the internet means that the collection of useful data available for public access is rapidly increasing both in number and size. These data are spread over distributed heterogeneous data sources like traditional databases or sources of various forms containing unstructured and semi-structured data. Obviously, the value of these data sources would in many cases be greatly enhanced if the data they contain could be combined and queried in a uniform manner. The research work reported in this dissertation is concerned with querying and integrating a multiplicity of distributed heterogeneous structured data residing in relational databases and semi-structured data held in well- formed XML documents produced by internet applications or human- coded. In particular, we have addressed the problems of: (1) specifying the mappings between a global schema and the local data sources' schemas, and resolving the heterogeneity which can occur between data models, schemas or schema concepts (2) processing queries that are expressed on a global schema into local queries. We have proposed an approach to combine and query the data sources through a mediation layer. Such a layer is intended to establish and evolve an XML Metadata Knowledge Base (XMKB) incrementally which assists the Query Processor in mediating between user queries posed over the global schema and the queries on the underlying distributed heterogeneous data sources. It translates such queries into sub-queries -called local queries- which are appropriate to each local data source. The XMKB is built in a bottom-up fashion by extracting and merging incrementally the metadata of the data sources. It holds the data source's information (names, types and locations), descriptions of the mappings between the global schema and the participating data source schemas, and function names for handling semantic and structural discrepancies between the representations. To demonstrate our research, we have designed and implemented a prototype system called SISSD (System to Integrate Structured and Semi- structured Databases). The system automatically creates a GUI tool for meta-users (who do the metadata integration) which they use to describe mappings between the global schema and local data source schemas. These mappings are used to produce the XMKB. The SISSD allows the translation of user queries into sub-queries fitting each participating data source, by exploiting the mapping information stored in the XMKB. The major results of the thesis are: (1) an approach that facilitates building structured and semi-structured data integration systems (2) a method for generating mappings between a global and local schemas' paths, and resolving the conflicts caused by the heterogeneity of the data sources such as naming, structural, and semantic conflicts which, may occur between the schemas (3) a method for translating queries in terms of a global schema into sub-queries in terms of local schemas. Hence, the presented approach shows that: (a) mapping of the schemas' paths can only be partially automated, since the logical heterogeneity problems need to be resolved by human judgment based on the application requirements (b) querying distributed heterogeneous structured and semi-structured data sources is possibl

Managing patient expectations through understanding health service experiences

The ever-increasing demand for health care services, together with heightened expectations for quality care, continue to put pressures on health care professionals. In this editorial, we introduce our perspective on managing patient expectations through gaining research insights on health service experiences of patients and their support network. Drawing upon research from social psychology, we examine the types of threat that typically confront patients during health care service experiences, and their subsequent coping strategies. We call for enhanced focus on social science research for effective delivery of high-quality health care services

Mangroves and Their Response to a Heavy Metal Polluted Wetland in the North Coast of Puerto Rico

Peninsula La Esperanza is part of the San Juan Bay Estuary and located in the north coast of Puerto Rico. Mangroves are the predominant type of vegetation; that can exhibit diverse external and internal mechanisms allowing them to tolerate and to act as phytoremediators of heavy metals (HM) in surrounding soils. This study was focused in three mangrove species that can be found in La Esperanza: Rhizophora mangle (RM), Laguncularia racemosa (LR) and Avicennia germinans (AG). Arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), mercury (Hg), lead (Pb), and zinc (Zn) were selected to be identified, measure concentrations in sediments, in green (GL) and senescent (SL) leaves, and study phytoremediation potential as a mitigation alternative calculating bioconcentration afctors (BCFs) and retranslocation percents (RT%). For this, Peninsula La Esperanza was divided in three main research sites. Our results show a significant difference among all heavy metals and their distribution in each site. Moreover, the mangrove species, A. germinans, showed lower RT% for Hg in all three sites, which could be considered the best species for phytoextraction of this heavy metal. The results suggest that the three species have a synergistic effect in the way they manage the heavy metal in surrounding polluted soils, although each species have a different capacity to manage each heavy metal

Impact of Health Policy Changes on Emergency Medicine in Maryland Stratified by Socioeconomic Status

Introduction: On January 1, 2014, the financing and delivery of healthcare in the state of Maryland (MD) profoundly changed. The insurance provisions of the Patient Protection and Affordable Care Act (ACA) began implementation and a major revision of MD’s Medicare waiver ushered in a Global Budget Revenue (GBR) structure for hospital reimbursement. Our objective was to analyze the impact of these policy changes on emergency department (ED) utilization, hospitalization practices, insurance profiles, and professional revenue. We stratified our analysis by the socioeconomic status (SES) of the ED patient population. Methods: We collected monthly mean data including patient volume, hospitalization percentages, payer mix, and professional revenue from January 2013 through December 2015 from a convenience sample of 11 EDs in Maryland. Using regression models, we compared each of the variables 18 months after the policy changes and a six-month washout period to the year prior to ACA/GBR implementation. We included the median income of each ED’s patient population as an explanatory variable and stratified our results by SES. Results:Our 11 EDs saw an annualized volume of 399,310 patient visits during the study period. This ranged from a mean of 41 daily visits in the lowest volume rural ED to 171 in the highest volume suburban ED. After ACA/GBR, ED volumes were unchanged (95% confidence interval [CI] [-1.58- 1.24], p=.817). Hospitalization percentages decreased significantly by 1.9% from 17.2% to 15.3% (95% CI [-2.47%-1.38%], p Conclusion: Health policy changes at the federal and state levels have resulted in significant changes to emergency medicine practice and finances in MD. Admission and observation percentages have been reduced, fewer patients are uninsured, and professional revenue has increased. All changes are significantly more pronounced in EDs with patients of lower SES. [West J Emerg Med. 2017;18(3)356-365.

Longitudinal liver stiffness assessment in patient with chronic hepatitis C undergoing antiviral therapy.

BACKGROUND/AIMS:Liver stiffness (LS) measurement by means of transient elastography (TE) is accurate to predict fibrosis stage. The effect of antiviral treatment and virologic response on LS was assessed and compared with untreated patients with chronic hepatitis C (CHC). METHODS: TE was performed at baseline, and at weeks 24, 48, and 72 in 515 patients with CHC. RESULTS: 323 treated (62.7%) and 192 untreated patients (37.3%) were assessed. LS experienced a significant decline in treated patients and remained stable in untreated patients at the end of study (P<0.0001). The decline was significant for patients with baseline LS ≥ 7.1 kPa (P<0.0001 and P 0.03, for LS ≥ 9.5 and ≥ 7.1 kPa vs lower values, respectively). Sustained virological responders and relapsers had a significant LS improvement whereas a trend was observed in nonresponders (mean percent change -16%, -10% and -2%, for SVR, RR and NR, respectively, P 0.03 for SVR vs NR). In multivariate analysis, high baseline LS (P<0.0001) and ALT levels, antiviral therapy and non-1 genotype were independent predictors of LS improvement. CONCLUSIONS: LS decreases during and after antiviral treatment in patients with CHC. The decrease is significant in sustained responders and relapsers (particularly in those with high baseline LS) and suggests an improvement in liver damage

Identification of the decumbenone biosynthetic gene cluster in and the importance for production of calbistrin

Background: Filamentous fungi are important producers of secondary metabolites, low molecular weight molecules that often have bioactive properties. Calbistrin A is a secondary metabolite with an interesting structure that was recently found to have bioactivity against leukemia cells. It consists of two polyketides linked by an ester bond: a bicyclic decalin containing polyketide with structural similarities to lovastatin, and a linear 12 carbon dioic acid structure. Calbistrin A is known to be produced by several uniseriate black Aspergilli, Aspergillus versicolor-related species, and Penicillia. Penicillium decumbens produces calbistrin A and B as well as several putative intermediates of the calbistrin pathway, such as decumbenone A-B and versiol. Results: A comparative genomics study focused on the polyketide synthase (PKS) sets found in three full genome sequence calbistrin producing fungal species, P. decumbens, A. aculeatus and A. versicolor, resulted in the identification of a novel, putative 13-membered calbistrin producing gene cluster (calA to calM). Implementation of the CRISPR/Cas9 technology in P. decumbens allowed the targeted deletion of genes encoding a polyketide synthase (calA), a major facilitator pump (calB) and a binuclear zinc cluster transcription factor (calC). Detailed metabolic profiling, using UHPLC-MS, of the ∆calA (PKS) and ∆calC (TF) strains confirmed the suspected involvement in calbistrin productions as neither strains produced calbistrin nor any of the putative intermediates in the pathway. Similarly analysis of the excreted metabolites in the ∆calB (MFC-pump) strain showed that the encoded pump was required for efficient export of calbistrin A and B. Conclusion: Here we report the discovery of a gene cluster (calA-M) involved in the biosynthesis of the polyketide calbistrin in P. decumbens. Targeted gene deletions proved the involvement of CalA (polyketide synthase) in the biosynthesis of calbistrin, CalB (major facilitator pump) for the export of calbistrin A and B and CalC for the transcriptional regulation of the cal-cluster. This study lays the foundation for further characterization of the calbistrin biosynthetic pathway in multiple species and the development of an efficient calbistrin producing cell factory

The Effect of Epstein-Barr Virus Latent Membrane Protein 2 Expression on the Kinetics of Early B Cell Infection

Infection of human B cells with wild-type Epstein-Barr virus (EBV) in vitro leads to activation and proliferation that result in efficient production of lymphoblastoid cell lines (LCLs). Latent Membrane Protein 2 (LMP2) is expressed early after infection and previous research has suggested a possible role in this process. Therefore, we generated recombinant EBV with knockouts of either or both protein isoforms, LMP2A and LMP2B (Δ2A, Δ2B, Δ2A/Δ2B) to study the effect of LMP2 in early B cell infection. Infection of B cells with Δ2A and Δ2A/Δ2B viruses led to a marked decrease in activation and proliferation relative to wild-type (wt) viruses, and resulted in higher percentages of apoptotic B cells. Δ2B virus infection showed activation levels comparable to wt, but fewer numbers of proliferating B cells. Early B cell infection with wt, Δ2A and Δ2B viruses did not result in changes in latent gene expression, with the exception of elevated LMP2B transcript in Δ2A virus infection. Infection with Δ2A and Δ2B viruses did not affect viral latency, determined by changes in LMP1/Zebra expression following BCR stimulation. However, BCR stimulation of Δ2A/Δ2B cells resulted in decreased LMP1 expression, which suggests loss of stability in viral latency. Long-term outgrowth assays revealed that LMP2A, but not LMP2B, is critical for efficient long-term growth of B cells in vitro. The lowest levels of activation, proliferation, and LCL formation were observed when both isoforms were deleted. These results suggest that LMP2A appears to be critical for efficient activation, proliferation and survival of EBV-infected B cells at early times after infection, which impacts the efficient long-term growth of B cells in culture. In contrast, LMP2B did not appear to play a significant role in these processes, and long-term growth of infected B cells was not affected by the absence of this protein. © 2013 Wasil et al

TP53 status and taxane-platinum versus platinum-based therapy in ovarian cancer patients: A non-randomized retrospective study

<p>Abstract</p> <p>Background</p> <p>Taxane-platinum therapy (TP) has replaced platinum-based therapy (PC or PAC, DNA damaging chemotherapy) in the postoperative treatment of ovarian cancer patients; however, it is not always effective. TP53 protein plays a differential role in response to DNA-damaging agents and taxanes. We sought to define profiles of patients who benefit the most from TP and also of those who can be treated with PC.</p> <p>Methods</p> <p>We compared the effectiveness of PC/PAC (n = 253) and TP (n = 199) with respect to tumor TP53 accumulation in ovarian cancer patients with FIGO stage IIB-IV disease; this was a non-randomized retrospective study. Immunohistochemical analysis was performed on 452 archival tumors; univariate and multivariate analysis by the Cox's and logistic regression models was performed in all patients and in subgroups with [TP53(+)] and without TP53 accumulation [TP53(-)].</p> <p>Results</p> <p>The advantage of taxane-platinum therapy over platinum-based therapy was seen in the TP53(+), and not in the TP53(-) group. In the TP53(+) group taxane-platinum therapy enhanced the probability of complete remission (p = .018), platinum sensitivity (p = .014), platinum highly sensitive response (p = .038) and longer survival (OS, p = .008). Poor tumor differentiation diminished the advantage from taxane-platinum therapy in the TP53(+) group. In the TP53(-) group PC/PAC was at least equally efficient as taxane-platinum therapy and it enhanced the chance of platinum highly sensitive response (p = .010). However, in the TP53(-) group taxane-platinum therapy possibly diminished the risk of death in patients over 53 yrs (p = .077). Among factors that positively interacted with taxane-platinum therapy in some analyses were endometrioid and clear cell type, FIGO III stage, bulky residual tumor, more advanced age of patient and moderate tumor differentiation.</p> <p>Conclusion</p> <p>Our results suggest that taxane-platinum therapy is particularly justified in patients with TP53(+) tumors or older than 53 years. In the group of patients ≤53 yrs and with TP53(-) tumors platinum-based therapy is possibly equally efficient. We provide hints for planning randomized trials to verify these observations.</p