Database of host-pathogen and related species interactions, and their global distribution

Interactions between species, particularly where one is likely to be a pathogen of the other, as well as the geographical distribution of species, have been systematically extracted from various web-based, free-access sources, and assembled with the accompanying evidence into a single database. The database attempts to answer questions such as what are all the pathogens of a host, and what are all the hosts of a pathogen, what are all the countries where a pathogen was found, and what are all the pathogens found in a country. Two datasets were extracted from the database, focussing on species interactions and species distribution, based on evidence published between 1950–2012. The quality of their evidence was checked and verified against well-known, alternative, datasets of pathogens infecting humans, domestic animals and wild mammals. The presented datasets provide a valuable resource for researchers of infectious diseases of humans and animals, including zoonoses.

Validation of a rapid urine screening assay for cocaine use among pregnant emergency patients

OBJECTIVES

To determine the accuracy of the OnTrak rapid urine latex agglutination immunoassay (AIA) for testing pregnant ED patients for the cocaine metabolite benzoylecgonine (BE), and to determine the frequency of urine BE in pregnant ED patients and the association of test results with patient demographics.

METHODS

A test performance evaluation was conducted using an inception cohort of pregnant patients at an urban teaching hospital ED. Patients with positive urine chorionic gonadotropin tests who had adequate remaining urine samples were studied. Patient demographics, ED diagnoses, and assay results were recorded without patient identifiers. Urine was tested using the rapid AIA. The first 150 samples were confirmed using a second immunoassay and gas chromatography with a nitrogen phosphorus detector. All positive samples also were confirmed with thin-layer chromatography, and quantification by gas chromatography-mass spectrometry.

RESULTS

Twenty of 342 (5.9%, 95% CI 3.4-8.4%) pregnant patients had urine samples positive by AIA testing for BE. Confirmation testing demonstrated no false-positive or -negative AIA result. Positive test results were not associated with specific patient diagnoses or demographics.

CONCLUSIONS

ED screening for cocaine use among pregnant patients can be accurately performed using the OnTrak AIA for BE. In the ED population screened, 5.9% of the pregnant women had urine samples positive for BE.

Structure elucidation methodology for disaccharides based on carbon-13 nuclear magnetic resonance spectrum simulation

Molecular mechanics techniques are used to derive structural parameters that allow carbon-13 nuclear magnetic resonance spectra of disaccharides to be modeled. On the basis of a collection of 40 disaccharide spectra, four linear models are derived that allow complete spectra to be simulated. On the basis of these 40 compounds, the average difference between simulated and observed chemical shifts is +/- 0.45 ppm. The majority of structural parameters used are based on interatomic distances computed from modeled three-dimensional atomic coordinates. Found particularly useful in modeling the disaccharide spectra are the effects of oxygen electron lone pairs and encodings of the structural environments of hydrogens alpha to the carbon whose chemical shift is being predicted. The computed models are examined, and their predictive ability is assessed. The potential application of the methodology to the structure elucidation of disaccharides is demonstrated.