A system for automated lexical mapping

Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2005.Includes bibliographical references (leaves 19-20).Merging of clinical systems and medical databases, or aggregation of information from disparate databases, frequently requires a process where vocabularies are compared and similar concepts are mapped. Using a normalization phase followed by a novel alignment stage inspired by DNA sequence alignment methods, automated lexical mapping can map terms from various databases to standard vocabularies such as UMLS (Unified Medical Language System) and SNOMED (the Systematized Nomenclature of Medicine). This automated lexical mapping was evaluated using a real-world database of consultation letters from Children's Hospital Boston. The first phase involved extracting the reason for referral from the consultation letters. The reasons for referral were then mapped to SNOMED. The alignment algorithm was able to map 72% of equivalent concepts through lexical mapping alone. Lexical mapping can facilitate the integration of data from diverse sources and decrease the time and cost required for manual mapping and integration of clinical systems and medical databases.by Jennifer Y. Sun.S.M

Molecular Investigation of the Bioluminescent Fungus Mycena chlorophos: Comparison between a Vouchered Museum Specimen and Field Samples from Taiwan

There are 71 species of bioluminescent fungi belonging to at least three distinct evolutionary lineages. Mycena chlorophos is a bioluminescent species that is distributed in tropical climates, especially in Southeastern Asia, and the Pacific. This research examined Mycena chlorophos from Taiwan using molecular techniques to compare the identity of a named museum specimens and field samples. For this research, field samples were collected in Taiwan and compared with a specimen provided by the National Museum of Natural Science, Taiwan (NMNS). Specific locations for collection were chosen based on previous GIS data provided by NMNS. FTA DNA extraction cards were used to collect fresh DNA from fruiting bodies. The samples were brought back to the lab at SUNY-ESF located in Syracuse, N. Y. where DNA extraction, PCR amplification and restriction fragment length polymorphism (RFLP) analysis of the nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS region) were performed. The ITS region, or fungal barcode was sequenced from these PCR products. The RFLP patterns and ITS sequences showed that the field samples and museum specimen were probably the same species, supported by BLAST search in Genbank. This study has raised questions about the mechanisms of long distance fungal spore dispersal, and suggests possible future research in taxonomic and interdisciplinary study of Mycena chlorophos

A Narrative Review of Protective Factors that Predict Enculturation Processes for Latinx Individuals in the U.S.

A Narrative Review of Protective Factors that Predict Enculturation Processes for Latinx Individuals in the U.S. Jane Sun, Dept. of Psychology, Jennifer Rodriguez, Alanna Cason, Yessica Flores, Karl Villareal, Arlenis Santana, Dept. of Psychology Graduate Student, & Chloe Walker, Dept. of Psychology Graduate Student, with Dr. Chelsea D. Williams, Dept. of Psychology According to the 2010 U.S. Census, the rise of immigration led the Latinx community to experience the largest population growth amongst all ethnic-racial groups (Sanchez et al., 2012). Enculturation is the process of preserving heritage cultural values while enduring the influence of the current, surrounding culture (Schwartz et al., 2013). Enculturation is a subcomponent in the broad spectrum of acculturation, the process through which the introduction of two differing cultures induces cultural changes (Rodriguez et al., 2002). While current research has focused on the protective factors involved in the acculturative process, minimal research has centered on the protective factors in enculturation amongst the Latinx community. The aim of the current narrative review was to identify the protective factors (e.g., language, values, generational differences, group membership) associated with enculturation of Latinx U.S. citizens. Implications will discuss the promotion of social awareness within the Latinx community.https://scholarscompass.vcu.edu/uresposters/1333/thumbnail.jp

RAPTOR: Routing Attacks on Privacy in Tor

The Tor network is a widely used system for anonymous communication. However, Tor is known to be vulnerable to attackers who can observe traffic at both ends of the communication path. In this paper, we show that prior attacks are just the tip of the iceberg. We present a suite of new attacks, called Raptor, that can be launched by Autonomous Systems (ASes) to compromise user anonymity. First, AS-level adversaries can exploit the asymmetric nature of Internet routing to increase the chance of observing at least one direction of user traffic at both ends of the communication. Second, AS-level adversaries can exploit natural churn in Internet routing to lie on the BGP paths for more users over time. Third, strategic adversaries can manipulate Internet routing via BGP hijacks (to discover the users using specific Tor guard nodes) and interceptions (to perform traffic analysis). We demonstrate the feasibility of Raptor attacks by analyzing historical BGP data and Traceroute data as well as performing real-world attacks on the live Tor network, while ensuring that we do not harm real users. In addition, we outline the design of two monitoring frameworks to counter these attacks: BGP monitoring to detect control-plane attacks, and Traceroute monitoring to detect data-plane anomalies. Overall, our work motivates the design of anonymity systems that are aware of the dynamics of Internet routing

Two RNA-binding motifs in eIF3 direct HCV IRES-dependent translation.

The initiation of protein synthesis plays an essential regulatory role in human biology. At the center of the initiation pathway, the 13-subunit eukaryotic translation initiation factor 3 (eIF3) controls access of other initiation factors and mRNA to the ribosome by unknown mechanisms. Using electron microscopy (EM), bioinformatics and biochemical experiments, we identify two highly conserved RNA-binding motifs in eIF3 that direct translation initiation from the hepatitis C virus internal ribosome entry site (HCV IRES) RNA. Mutations in the RNA-binding motif of subunit eIF3a weaken eIF3 binding to the HCV IRES and the 40S ribosomal subunit, thereby suppressing eIF2-dependent recognition of the start codon. Mutations in the eIF3c RNA-binding motif also reduce 40S ribosomal subunit binding to eIF3, and inhibit eIF5B-dependent steps downstream of start codon recognition. These results provide the first connection between the structure of the central translation initiation factor eIF3 and recognition of the HCV genomic RNA start codon, molecular interactions that likely extend to the human transcriptome