Correlation indices : a new access method to exploit correlated attributes

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007.Includes bibliographical references (p. 69-71).In relational query processing, one generally chooses between two classes of access paths when performing a predicate lookup for which no clustered index is available. One option is to use an unclustered index. Another is to perform a complete sequential scan of the table. Online analytical processing (OLAP) workloads often do not benefit from the availability of unclustered indices; the cost of random disk I/O becomes prohibitive for all but the most selective queries. Unfortunately, this means that data warehouses and other OLAP systems frequently perform sequential scans, unless they can satisfy nearly all of the queries posed to them by a single clustered index [7], or unless they have available specialized data structures - like bitmap indices, materialized views, or cubes - to answer queries directly. This thesis presents a new index data structure called a correlation index (CI) that enables OLAP databases to answer a wider range of queries from a single clustered index or sorted file. The CI exploits correlations between the key attribute of a clustered index and other unclustered attributes in the table. In order to predict when CIs will exhibit wins over alternative access methods, the thesis describes an analytical cost model that is suitable for integration with existing query optimizers. An implementation compares CI performance against sequential scans and unclustered B+Tree indices in the popular Berkeley DB [22] library. Experimental results over three different data sets validate the accuracy of the cost model and establish numerous cases where CIs accelerate lookup times by 5 to 20 times over both unclustered B+Trees and sequential scans. The strong experimental results suggest that CIs offer practical and substantial benefits in a variety of useful query scenarios.by George Huo.M.Eng

Hollywood: a comparative relational database of alternative splicing

RNA splicing is an essential step in gene expression, and is often variable, giving rise to multiple alternatively spliced mRNA and protein isoforms from a single gene locus. The design of effective databases to support experimental and computational investigations of alternative splicing (AS) is a significant challenge. In an effort to integrate accurate exon and splice site annotation with current knowledge about splicing regulatory elements and predicted AS events, and to link information about the splicing of orthologous genes in different species, we have developed the Hollywood system. This database was built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags, and links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. Hollywood was implemented as a relational database and currently contains comprehensive information for human and mouse. It is accompanied by a web query tool that allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene. A streamlined graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser. The database is accessible at

CORADD: Correlation Aware Database Designer for Materialized Views and Indexes

We describe an automatic database design tool that exploits correlations between attributes when recommending materialized views (MVs) and indexes. Although there is a substantial body of related work exploring how to select an appropriate set of MVs and indexes for a given workload, none of this work has explored the effect of correlated attributes (e.g., attributes encoding related geographic information) on designs. Our tool identifies a set of MVs and secondary indexes such that correlations between the clustered attributes of the MVs and the secondary indexes are enhanced, which can dramatically improve query performance. It uses a form of Integer Linear Programming (ILP) called ILP Feedback to pick the best set of MVs and indexes for given database size constraints. We compare our tool with a state-of-the-art commercial database designer on two workloads, APB-1 and SSB (Star Schema Benchmark---similar to TPC-H). Our results show that a correlation-aware database designer can improve query performance up to 6 times within the same space budget when compared to a commercial database designer.National Science Foundation (U.S.) (Grant IIS-0704424)SAP Corporation (Grant

Meconium Atazanavir Concentrations and Early Language Outcomes in HIV-Exposed, Uninfected Infants with Prenatal Atazanavir Exposure

This is not the published version.OBJECTIVE: To investigate whether prenatal atazanavir (ATV) exposure, assessed by meconium antiretroviral quantification, predicts early child language outcomes. Prenatal ATV exposure previously was associated with poorer language development in one-year-olds. METHODS: Pregnant women with HIV and their uninfected infants enrolled in the SMARTT study. Meconium antiretroviral concentrations were quantified by liquid chromatography-tandem mass spectrometry. Language development at 1 year was assessed with MacArthur-Bates Communicative Development Inventory (CDI) and Bayley Scales of Infant and Toddler Development—Third Edition (Bayley-III). Late language emergence (LLE) was defined as ≥ one of four CDI scores ≤10th percentile for age. Associations between fetal ATV exposure timing and duration, meconium ATV concentration, and language outcomes were evaluated, adjusting for potential confounders. RESULTS: Through 2013, meconium samples were available from 175 of 432 infants with prenatal ATV exposure. Valid Bayley-III (n=93) and CDI (n=106) assessments also were available. After adjustment for potential confounders, higher ATV meconium concentrations were associated with lower LLE risk (P=0.04), and cumulative ATV exposure duration also was associated with higher Bayley-III Language scores (P=0.03). Maternal ATV duration and initiation week correlated with ATV meconium concentrations (positively and negatively, respectively). CONCLUSIONS: Higher meconium ATV concentrations were protective against developmental language delays at 1 year, suggesting the importance of fetal ATV detoxification into meconium. This information supports ATV exposure safety for infant language development. ATV is a preferred ARV for pregnant women with HIV, suggesting the importance of ATV safety investigations. Additionally, further pursuit of the influences on language development in HEU infants is required

Insulin and glucose play a role in foam cell formation and function

BACKGROUND: Foam cell formation in diabetic patients often occurs in the presence of high insulin and glucose levels. To test whether hyperinsulinemic hyperglycemic conditions affect foam cell differentiation, we examined gene expression, cytokine production, and Akt phosphorylation in human monocyte-derived macrophages incubated with two types of oxidized low density lipoprotein (LDL), minimally modified LDL (mmLDL) and extensively oxidized LDL (OxLDL). METHODS AND RESULTS: Using Affymetrix GeneChip(® )arrays, we found that several genes directly related to insulin signaling were changed. The insulin receptor and glucose-6-phosphate dehydrogenase were upregulated by mmLDL and OxLDL, whereas insulin-induced gene 1 was significantly down-regulated. In hyperinsulinemic hyperglycemic conditions, modified LDL upregulated Akt phosphorylation and expression of the insulin-regulated aminopeptidase. The level of proinflammatory cytokines, IL-lβ, IL-12, and IL-6, and of a 5-lipoxygenase eicosanoid, 5-hydroxyeicosatetraenoic acid (5-HETE), was also increased. CONCLUSION: These results suggest that the exposure of macrophages to modified low density lipoproteins in hyperglycemic hyperinsulinemic conditions affects insulin signaling and promotes the release of proinflammatory stimuli, such as cytokines and eicosanoids. These in turn may contribute to the development of insulin resistance

Geometric Control of Human Stem Cell Morphology and Differentiation

During tissue morphogenesis, stem cells and progenitor cells migrate, proliferate, and differentiate, with striking changes in cell shape, size, and acting mechanical stresses. The local cellular function depends on the spatial distribution of cytokines as well as local mechanical microenvironments in which the cells reside. In this study, we controlled the organization of human adipose derived stem cells using micro-patterning technologies, to investigate the influence of multi-cellular form on spatial distribution of cellular function at an early stage of cell differentiation. The underlying role of cytoskeletal tension was probed through drug treatment. Our results show that the cultivation of stem cells on geometric patterns resulted in pattern- and position-specific cell morphology, proliferation and differentiation. The highest cell proliferation occurred in the regions with large, spreading cells (such as the outer edge of a ring and the short edges of rectangles). In contrast, stem cell differentiation co-localized with the regions containing small, elongated cells (such as the inner edge of a ring and the regions next to the short edges of rectangles). The application of drugs that inhibit the formation of actomyosin resulted in the lack of geometrically specific differentiation patterns. This study confirms the role of substrate geometry on stem cell differentiation, through associated physical forces, and provides a simple and controllable system for studying biophysical regulation of cell function