An evaluation resource for geographic information retrieval

In this paper we present an evaluation resource for geographic information retrieval developed within the Cross Language Evaluation Forum (CLEF). The GeoCLEF track is dedicated to the evaluation of geographic information retrieval systems. The resource encompasses more than 600,000 documents, 75 topics so far, and more than 100,000 relevance judgments for these topics. Geographic information retrieval requires an evaluation resource which represents realistic information needs and which is geographically challenging. Some experimental results and analysis are reported

GeoCLEF 2007: the CLEF 2007 cross-language geographic information retrieval track overview

GeoCLEF ran as a regular track for the second time within the Cross Language Evaluation Forum (CLEF) 2007. The purpose of GeoCLEF is to test and evaluate cross-language geographic information retrieval (GIR): retrieval for topics with a geographic specification. GeoCLEF 2007 consisted of two sub tasks. A search task ran for the third time and a query classification task was organized for the first. For the GeoCLEF 2007 search task, twenty-five search topics were defined by the organizing groups for searching English, German, Portuguese and Spanish document collections. All topics were translated into English, Indonesian, Portuguese, Spanish and German. Several topics in 2007 were geographically challenging. Thirteen groups submitted 108 runs. The groups used a variety of approaches. For the classification task, a query log from a search engine was provided and the groups needed to identify the queries with a geographic scope and the geographic components within the local queries

Challenges to evaluation of multilingual geographic information retrieval in GeoCLEF

This is the third year of the evaluation of geographic information retrieval (GeoCLEF) within the Cross-Language Evaluation Forum (CLEF). GeoCLEF 2006 presented topics and documents in four languages (English, German, Portuguese and Spanish). After two years of evaluation we are beginning to understand the challenges to both Geographic Information Retrieval from text and of evaluation of the results of geographic information retrieval. This poster enumerates some of these challenges to evaluation and comments on the limitations encountered in the first two evaluations

GeoCLEF 2006: the CLEF 2006 Ccross-language geographic information retrieval track overview

After being a pilot track in 2005, GeoCLEF advanced to be a regular track within CLEF 2006. The purpose of GeoCLEF is to test and evaluate cross-language geographic information retrieval (GIR): retrieval for topics with a geographic specification. For GeoCLEF 2006, twenty-five search topics were defined by the organizing groups for searching English, German, Portuguese and Spanish document collections. Topics were translated into English, German, Portuguese, Spanish and Japanese. Several topics in 2006 were significantly more geographically challenging than in 2005. Seventeen groups submitted 149 runs (up from eleven groups and 117 runs in GeoCLEF 2005). The groups used a variety of approaches, including geographic bounding boxes, named entity extraction and external knowledge bases (geographic thesauri and ontologies and gazetteers)

Mycosin-1, a subtilisin-like serine protease of Mycobacterium tuberculosis, is cell wall-associated and expressed during infection of macrophages

BACKGROUND: Exported proteases are commonly associated with virulence in bacterial pathogens, yet there is a paucity of information regarding their role in Mycobacterium tuberculosis. There are five genes (mycP1-5) present within the genome of Mycobacterium tuberculosis H37Rv that encode a family of secreted, subtilisin-like serine proteases (the mycosins). The gene mycP1 (encoding mycosin-1) was found to be situated 3700 bp (four ORF's) from the RD1 deletion region in the genome of the attenuated vaccine strain M. bovis BCG (bacille de Calmette et Guérin) and was selected for further analyses due to the absence of expression in this organism. RESULTS: Full-length, 50 kDa mycosin-1 was observed in M. tuberculosis cellular lysates, whereas lower-molecular-weight species were detected in culture filtrates. A similar lower-molecular-weight species was also observed during growth in macrophages. Mycosin-1 was localized to the membrane and cell wall fractions in M. tuberculosis by Western blotting, and to the cell envelope by electron microscopy. Furthermore, M. tuberculosis culture filtrates were shown to contain a proteolytic activity inhibited by mixed serine/cysteine protease inhibitors and activated by Ca(2+), features typical of the subtilisins. CONCLUSIONS: Mycosin-1 is an extracellular protein that is membrane- and cell wall-associated, and is shed into the culture supernatant. The protein is expressed after infection of macrophages and is subjected to proteolytic processing. Although proteolytically active mycosin-1 could not be generated recombinantly, serine protease activity containing features typical of the subtilisins was detected in M. tuberculosis culture filtrates

Supporting undergraduate research capacity development: A process evaluation of an Undergraduate Research Office at a South African Faculty of Medicine and Health Sciences

Background. University-based research capacity development (RCD) mechanisms tend to focus on staff and postgraduate students, with few structures targeted at undergraduate students. Support for undergraduate research must be tailored to the unique requirements of research at this level, while maintaining links with relevant structures in both the RCD and teaching and learning domains. Objective. To conduct a process evaluation of the Undergraduate Research Office (URO) in the Faculty of Medicine and Health Sciences at Stellenbosch University, South Africa, using RCD and characteristics of excellence in undergraduate research criteria as benchmarks. Methods. A process evaluation of URO’s first 6 years was conducted using a logic model of URO’s inputs, activities, and outputs. Through a retrospective document review, a descriptive analysis of URO’s inputs and activities (narrative) and URO’s outputs (statistical) was conducted. Results. Following a description of inputs and activities, results present URO’s outputs as a measure of the uptake of these activities. From 2015 to 2020, 259 undergraduate research projects were completed. Research consultations, workshops and undergraduate presentations at the faculty’s Annual Academic Day have more than doubled since URO’s inception. The Undergraduate Research Ethics Committee has reviewed 243 ethics applications since 2015, with a 1 - 2-week turnaround time. A total of 134 funding applications worth ZAR705 986 have been awarded for research project, conference presentation and publication costs. Conclusion. Results show the potential impact of a formal undergraduate research support entity on the undergraduate research outputs of a Faculty of Medicine and Health Sciences. This article highlights elements for success for formal undergraduate research support, and identifies gaps going forward

Bovine tuberculosis in African buffaloes : observations regarding Mycobacterium bovis shedding into water and exposure to environmental mycobacteria

Includes bibliographyBackground: African buffaloes are the maintenance host for Mycobacterium bovis in the endemically infected Kruger National Park (KNP). The infection is primarily spread between buffaloes via the respiratory route, but it is not known whether shedding of M. bovis in nasal and oral excretions may lead to contamination of ground and surface water and facilitate the transmission to other animal species. A study to investigate the possibility of water contamination with M. bovis was conducted in association with a BCG vaccination trial in African buffalo. Groups of vaccinated and nonvaccinated buffaloes were kept together with known infected in-contact buffalo cows to allow natural M. bovis transmission under semi-free ranging conditions. In the absence of horizontal transmission vaccinated and control buffaloes were experimentally challenged with M. bovis. Hence, all study buffaloes in the vaccination trial could be considered potential shedders and provided a suitable setting for investigating questions relating to the tenacity of M. bovis shed in water. Results: Serial water samples were collected from the drinking troughs of the buffaloes once per season over an eleven-month period and cultured for presence of mycobacteria. All water samples were found to be negative for M. bovis, but 16 non-tuberculous Mycobacterium spp. isolates were cultured. The non-tuberculous Mycobacterium species were further characterised using 5'-16S rDNA PCR-sequencing, resulting in the identification of M. terrae, M. vaccae (or vanbaalenii), M. engbaekii, M. thermoresistibile as well as at least two species which have not yet been classified. Conclusion: The absence of detectable levels of Mycobacterium bovis in the trough water suggests that diseased buffalo do not commonly shed the organism in high quantities in nasal and oral discharges. Surface water may therefore not be likely to play an important role in the transmission of bovine tuberculosis from buffalo living in free-ranging ecosystems. The study buffalo were, however, frequently exposed to different species of non-tuberculous, environmental mycobacteria, with an unknown effect on the buffaloes' immune response to mycobacteria.Peer Reviewe

The common ‘thermolabile' variant of methylene tetrahydrofolate reductase is a major determinant of mild hyperhomocysteinaemia

Mild hyperhomocysteinaemia is a major risk factor for vascular disease and neural tube defects (NTDs), conferring an approximately three-fold relative risk for each condition. It has several possible causes: heterozygosity for rare loss of function mutations in the genes for 5,10-methylene tetrahydrofolate reductase (MTHFR) or cystathionine-β-synthase (CBS); dietary insufficiency of vitamin co-factors B6, B12 or folates; or homozygosity for a common ‘thermolabile' mutation in the MTHFR gene which has also been associated with vascular disease and NTDs. We quantified the contribution of the thermolabile mutation to the hyperhomocysteinaemic phenotype in a working male population (625 individuals). Serum folate and vitamin B12 concentrations were also measured and their relationship with homocysteine status and MTHFR genotype assessed. The homozygous thermolabile genotype occurred in 48.4, 35.5, and 23.4% of the top 5,10, and 20% of individuals (respectively) ranked by plasma homocysteine levels, compared with a frequency of 11.5% in the study population as a whole, establishing that the mutation is a major determinant of homocysteine levels at the upper end of the range. Serum folate concentrations also varied with genotype, being lowest in thermolabile homozygotes. The MTHFR thermolabile genotype should be considered when population studies are designed to determine the effective homocysteine-lowering dose of dietary folate supplements, and when prophylactic doses of folate are recommended for individual

Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions

BACKGROUND: The PE and PPE multigene families of Mycobacterium tuberculosis comprise about 10% of the coding potential of the genome. The function of the proteins encoded by these large gene families remains unknown, although they have been proposed to be involved in antigenic variation and disease pathogenesis. Interestingly, some members of the PE and PPE families are associated with the ESAT-6 (esx) gene cluster regions, which are regions of immunopathogenic importance, and encode a system dedicated to the secretion of members of the potent T-cell antigen ESAT-6 family. This study investigates the duplication characteristics of the PE and PPE gene families and their association with the ESAT-6 gene clusters, using a combination of phylogenetic analyses, DNA hybridization, and comparative genomics, in order to gain insight into their evolutionary history and distribution in the genus Mycobacterium. RESULTS: The results showed that the expansion of the PE and PPE gene families is linked to the duplications of the ESAT-6 gene clusters, and that members situated in and associated with the clusters represent the most ancestral copies of the two gene families. Furthermore, the emergence of the repeat protein PGRS and MPTR subfamilies is a recent evolutionary event, occurring at defined branching points in the evolution of the genus Mycobacterium. These gene subfamilies are thus present in multiple copies only in the members of the M. tuberculosis complex and close relatives. The study provides a complete analysis of all the PE and PPE genes found in the sequenced genomes of members of the genus Mycobacterium such as M. smegmatis, M. avium paratuberculosis, M. leprae, M. ulcerans, and M. tuberculosis. CONCLUSION: This work provides insight into the evolutionary history for the PE and PPE gene families of the mycobacteria, linking the expansion of these families to the duplications of the ESAT-6 (esx) gene cluster regions, and showing that they are composed of subgroups with distinct evolutionary (and possibly functional) differences