Instance-Based Clustering for Databases

We present a method for automatically clustering similar attribute values in a database system spanning multiple domains. The method constructs a value abstraction hierarchy for each attribute using rules that are derived from the database instance. The rules have a confidence and popularity that combine to express the "usefulness" of the rule. Attribute values are clustered if they are used as the premise for rules with the same consequence. By iteratively applying the algorithm, a hierarchy of clusters can be found. The algorithm can be improved by allowing domain expen direction during the clustering process

Configurable indexing and ranking for XML information retrieval

Indexing and ranking are two key factors for efficient and effective XML information retrieval. Inappropriate indexing may result in false negatives and false positives, and improper ranking may lead to low precisions. In this paper, we propose a configurable XML information retrieval system, in which users can configure appropriate index types for XML tags and text contents. Based on users ’ index configurations, the system transforms XML structures into a compact tree representation, Ctree, and indexes XML text contents. To support XML ranking, we propose the concepts of “weighted term frequency ” and “inverted element frequency, ” where the weight of a term depends on its frequency and location within an XML element as well as its popularity among similar elements in an XML dataset. We evaluate the effectiveness of our system through extensive experiments on the INEX 03 dataset and 30 content and structure (CAS) topics. The experimental results reveal that our system has significantly high precision at low recall regions and achieves the highest average precision (0.3309) as compared with 38 official INEX 03 submissions using the strict evaluation metric

Integrated Multimedia Timeline of Medical Images and Data for Thoracic Oncology Patients

A prototype multimedia medical database has been developed to provide image and textual data for thoracic oncology patients undergoing treatment of advanced malignancies. The database integrates image data from the hospital pieture archiving and communication system with textual reports from the radiology information system, alphanumeric data contained in the hospital information system, and other electronic medical data. The database presents information in a timeline format and also contains visualization programs that permit the user to view and annotate radiographic measurements in tabular or graphic form. The database provides an efficient and intuitive display of the changing status of oncology patients. The ability to integrate, manage, and access relevant multimedia information may substantially enhance communication among distributed multidisciplinary health care providers and may ensure greater consistency and completeness of patient-related data

Pan-viral serology implicates enteroviruses in acute flaccid myelitis.

Since 2012, the United States of America has experienced a biennial spike in pediatric acute flaccid myelitis (AFM)1-6. Epidemiologic evidence suggests non-polio enteroviruses (EVs) are a potential etiology, yet EV RNA is rarely detected in cerebrospinal fluid (CSF)2. CSF from children with AFM (n = 42) and other pediatric neurologic disease controls (n = 58) were investigated for intrathecal antiviral antibodies, using a phage display library expressing 481,966 overlapping peptides derived from all known vertebrate and arboviruses (VirScan). Metagenomic next-generation sequencing (mNGS) of AFM CSF RNA (n = 20 cases) was also performed, both unbiased sequencing and with targeted enrichment for EVs. Using VirScan, the viral family significantly enriched by the CSF of AFM cases relative to controls was Picornaviridae, with the most enriched Picornaviridae peptides belonging to the genus Enterovirus (n = 29/42 cases versus 4/58 controls). EV VP1 ELISA confirmed this finding (n = 22/26 cases versus 7/50 controls). mNGS did not detect additional EV RNA. Despite rare detection of EV RNA, pan-viral serology frequently identified high levels of CSF EV-specific antibodies in AFM compared with controls, providing further evidence for a causal role of non-polio EVs in AFM

Sequencing of the Sea Lamprey (Petromyzon marinus) Genome Provides Insights into Vertebrate Evolution

Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ∼500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms