Vortex Holography

We show that the Abelian Higgs field equations in the four dimensional anti de Sitter spacetime have a vortex line solution. This solution, which has cylindrical symmetry in AdS$_4$, is a generalization of the flat spacetime Nielsen-Olesen string. We show that the vortex induces a deficit angle in the AdS$_4$ spacetime that is proportional to its mass density. Using the AdS/CFT correspondence, we show that the mass density of the string is uniform and dual to the discontinuity of a logarithmic derivative of correlation function of the boundary scalar operator.Comment: LaTeX, 20 pages, 4 eps figures, references and two paragraphs added, to appear in Nucl. Phys.

Meeting Report: Application of Genotyping Methods to Assess Risks from Cryptosporidium in Watersheds

A workshop titled "Application of Genotyping Methods to Assess Pathogen Risks from Cryptosporidium in Drinking Water Catchments" was held at the International Water Association biennial conference, Marrakech, Morocco, 23 September 2004. The workshop presented and discussed the findings of an interlaboratory trial that compared methods for genotyping Cryptosporidium oocysts isolated from feces. The primary goal of the trial and workshop was to assess the utility of current Cryptosporidium genotyping methods for determining the public health significance of oocysts isolated from feces in potable-water-supply watersheds. An expert panel of 16 watershed managers, public health practitioners, and molecular parasitologists was assembled for the workshop. A subordinate goal of the workshop was to educate watershed management and public health practitioners. An open invitation was extended to all conference delegates to attend the workshop, which drew approximately 50 interested delegates. In this report we summarize the peer consensus emerging from the workshop. Recommendations on the use of current methods by watershed managers and public health practitioners were proposed. Importantly, all the methods that were reported in the trial were mutually supporting and found to be valuable and worthy of further utility and development. Where there were choices as to which method to apply, the small-subunit ribosomal RNA gene was considered to be the optimum genetic locus to target. The single-strand conformational polymorphism method was considered potentially the most valuable for discriminating to the subtype level and where a large number of samples were to be analyzed. A research agenda for protozoan geneticists was proposed to improve the utility of methods into the future. Standardization of methods and nomenclature was promoted

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Genotyping Cryptosporidium parvum by single-strand conformation polymorphism analysis of ribosomal and heat shock gene regions

Polymerase chain reaction (PCR)-coupled single-strand conformation polymorphism (SSCP) approaches utilizing nuclear DNA regions of the small subunit (SSU) of ribosomal RNA and heat shock protein 70 gene (HSP70) were established for genotyping Cryptosporidium parvum. The regions were amplified (individually or in a multiplex reaction) by PCR from DNA extracted from oocysts from ruminant or human hosts, then denatured and subjected to electrophoresis in a mutation detection enhancement (nondenaturing) gel matrix. Single-strand profiles produced in SSCP allowed the unequivocal identification/differentiation of the two common (human, 1 and cattle, 2) genotypes of C. parvum and the direct display of sequence variability within some samples, reflecting population variation. As these are considered among the most closely related genotypes (based on SSU and HSP70 sequence data), these findings and other preliminary results for C. felis (from cat) C. serpentis (from snake) and C. baileyi (from bird) indicate that the SSCP approaches established could be employed to identify any of the currently recognised genotypes and species of Cryptosporidium

High resolution genotyping of cryptosporidium by mutation scanning

This chapter focuses on the high resolution genotyping of Cryptosporidium by mutation scanning. A range of different molecular approaches has been developed to characterize Cryptosporidium species and genotypes. Some of these approaches may not necessarily precisely resolve sequence variation because they depend on the size-separation of DNA molecules. Some methods are laborious and time-consuming to perform when the analysis of large numbers of samples is needed. Such limitations may be overcome by employing mutation detection methods, such as Single-Strand Conformation Polymorphism (SSCP). This chapter presents a study, the aim of that was to evaluate an SSCP approach for the genotyping of Cryptosporidium oocyst isolates. The present SSCP methods have advantages over some approaches to screen for genetic variation in Cryptosporidium. In contrast to arbitrarily primed-PCR, SSCP employs amplicons produced at higher stringency using specific primers, thus minimizing the co-amplification of extraneous DNA and maximizing reproducibility. SSCP can be used to screen relatively large numbers of samples for variation prior to selective DNA sequence analysis, which reduces considerably time, labor, and expense, and in contrast to PCR-coupled RFLP, which screens for sequence variation at a small number of endonuclease restriction sites, SSCP scans the entire length of an amplicon for variability. The results presented in this chapter indicate that the present approach can be used as a diagnostic tool to identify any of the currently recognized species and genotypes of Cryptosporidium. Combined with DNA sequencing, the approach also provides a powerful analytical tool