High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology

The worldwide threat of tuberculosis to human health emphasizes the need to develop novel approaches to a global epidemiological surveillance. The current standard for Mycobacterium tuberculosis typing based on IS6110 restriction fragment length polymorphism (RFLP) suffers from the difficulty of comparing data between independent laboratories. Here, we propose a high-resolution typing method based on variable number tandem repeats (VNTRs) of genetic elements named mycobacterial interspersed repetitive units (MIRUs) in 12 human minisatellite-like regions of the M. tuberculosis genome. MIRU-VNTR profiles of 72 different M. tuberculosis isolates were established by PCR analysis of all 12 loci. From 2 to 8 MIRU-VNTR alleles were identified in the 12 regions in these strains, which corresponds to a potential of over 16 million different combinations, yielding a resolution power close to that of IS6110-RFLP. All epidemiologically related isolates tested were perfectly clustered by MIRU-VNTR typing, indicating that the stability of these MIRU-VNTRs is adequate to track outbreak episodes. The correlation between genetic relationships inferred from MIRU-VNTR and IS6110-RFLP typing was highly significant. Compared with IS6110-RFLP, high-resolution MIRU-VNTR typing has the considerable advantages of being fast, appropriate for all M. tuberculosis isolates, including strains that have a few IS6110 copies, and permitting easy and rapid comparison of results from independent laboratories. This typing method opens the way to the construction of digital global databases for molecular epidemiology studies of M. tuberculosis.

NOMAD: a versatile strategy for in vitro DNA manipulation applied to promoter analysis and vector design.

Molecular analysis of complex modular structures, such as promoter regions or multi-domain proteins, often requires the creation of families of experimental DNA constructs having altered composition, order, or spacing of individual modules. Generally, creation of every individual construct of such a family uses a specific combination of restriction sites. However, convenient sites are not always available and the alternatives, such as chemical resynthesis of the experimental constructs or engineering of different restriction sites onto the ends of DNA fragments, are costly and time consuming. A general cloning strategy (nucleic acid ordered assembly with directionality, NOMAD; WWW resource locator http:@Lmb1.bios.uic.edu/NOMAD/NOMAD.htm l) is proposed that overcomes these limitations. Use of NOMAD ensures that the production of experimental constructs is no longer the rate-limiting step in applications that require combinatorial rearrangement of DNA fragments. NOMAD manipulates DNA fragments in the form of "modules" having a standardized cohesive end structure. Specially designed "assembly vectors" allow for sequential and directional insertion of any number of modules in an arbitrary predetermined order, using the ability of type IIS restriction enzymes to cut DNA outside of their recognition sequences. Studies of regulatory regions in DNA, such as promoters, replication origins, and RNA processing signals, construction of chimeric proteins, and creation of new cloning vehicles, are among the applications that will benefit from using NOMAD.

From local to global in quasiconformal structures.

We exhibit a large class of metric spaces whose infinitesimal quasiconformal structure is strong enough to capture the global quasiconformal structure. A sufficient condition for this to happen is described in terms of a Poincaré-type inequality.

Disposable electrochromic polyaniline sensor based on a redox response using a conventional camera: A first approach to handheld analysis

We present a disposable optical sensor for Ascorbic Acid (AA). It uses a polyaniline based electrochromic sensing film that undergoes a color change when exposed to solutions of ascorbic acid at pH 3.0. The color is monitored by a conventional digital camera working with the hue (H) color coordinate. The electrochromic film was deposited on an Indium Tin Oxide (ITO) electrode by cyclic voltammetry and then characterized by atomic force microscopy, electrochemical and spectroscopic techniques. An estimation of the initial rate of H, as ΔH/Δt, is used as the analytical parameter and resulted in the following logarithmic relationship: ΔH/Δt = 0.029 log[AA] + 0.14, with a limit of detection of 17 μM. The relative standard deviation when using the same membrane 5 times was 7.4% for the blank, and 2.6% (for n = 3) on exposure to ascorbic acid in 160 μM concentration. The sensor is disposable and its applicability to pharmaceutical analysis was demonstrated. This configuration can be extended for future handheld configurations.

Ethnography’s Contribution to Newspaper Analysis: Claims-Making Revisited. CES Papers - Open Forum #12, 2012

Newspaper data are a popular data source for studies across the social sciences. This paper empirically examines the widespread criticisms that this data is hampered by selection, description and researcher bias. It does so by taking one of the most authoritative European comparative research projects ‘Mobilisation on Ethnic Relations, Citizenship and Immigration’ (MERCI) as its case study given that the resulting publications have inspired many researches on both sides of the Atlantic to apply the so-called ‘claims-making’ method (e.g. Koopmans, Statham, Giugni and Passy 2005). Drawing on the author’s familiarity with the Dutch part of the data set and field specific expertise, this paper qualitatively re-analyses the claims recorded for Surinamese, Turkish and Kurdish migrants in the Netherlands and reviews the conclusions for migrant transnationalism and integration in particular. It reveals how an ethnographic approach can tackle description bias and researcher unreliability and brings selection bias into full view. While offering concrete suggestions for incorporating ethnography into newspaper analysis, it also exposes the limits of these methods for the study of cross-border activities such as migrant transnationalism.

ANOGI: Stata module to generate Analysis of Gini

anogi computes the "Analysis of Gini" for population sub-groups proposed by Frick et al. (2006; Sociological Methods and Research 34/4).

Introduction to advanced analysis /

Caption title.

A to zero of refrigeration; a simple story of man-made cold.

Rev. 1956.

Application of the ion exchange separation of uranium to the analysis of ores /

"Date Declassified: September 23, 1955."

Word-book of English spelling, oral and written. Designed to attain practical results in the acquisition of the ordinary English vocabulary, and to serve as an introduction to word-analysis.

Mode of access: Internet.

Supplement to special analysis D : a report required by the Federal Capital Investment Program Information Act of 1984 (Title II of Public Law 98-501).

"February 11, 1985."

Introduction to numerical analysis.

Mode of access: Internet.