Spreadsheet macro for setting up PCR assay tubes

This article describes a Microsoft Excel macro designed to calculate PCR master mix amounts based on variations in the DNA template amounts added to each tube, the total number of PCR assay tubes being set up or both. This macro uses a dynamic dialog box to quickly calculate and display the new component volumes after changes in one or both of the variables. The PCR assay mix protocol can then be printed in a format suitable for record keeping. This macro was designed for use with the Windows version of Excel but will also run on Macintosh computers.     

Beginnings and endings: keys to better engineering technicalwriting

Engineers face many technical writing tasks that have many features in common: title, abstract, introduction, problem formulation, methods, results, and conclusions. But it is often very difficult to actually write these segments in the same order they appear in the finished product. Instead of this linear approach, we recommend a modular approach starting with the core sections, the methods and results that researchers know best, and working backward and forward to pick up the beginnings and endings. We show how the beginning and ending sections build on the core sections and offer strategies to improve them     

Magnetic resonance imaging of bovine ovaries in vitro

A sample of 20 bovine ovaries were imaged in vitro using nuclear magnetic resonance (NMR) techniques to determine the visibility of various physiologic structures. In particular, the possibility of using NMR imaging to differentiate atretic follicles from physiologically selected and ovulatory follicles was examined. Five of the 20 ovaries were preserved in formalin, whereas the remaining 15 were preserved in a saline solution and imaged within 18 hours of death. Images weighted by T₁ and T₂ proton spin relaxation rates were obtained along with some three-dimensional (3-D) data sets acquired via a fast imaging with steady-state precession technique. Physiologically different structures were easily identified in the images from their morphology, especially in the 3-D images. Weighting by T₁ and T₂ was able to separate structures in the fresh ovaries in the following manner. Atretic and cohort follicles appear dark in T₁-weighted images and bright in T₂-weighted images. Ovulatory follicles appear bright in both T₁-and T₂-weighted images, whereas prephysiologic selection follicles present an intermediate brightness in T₁-weighted images and appear dark in T₂-weighted images. The corpus luteum appears bright in T₁-weighted images and dark in T₂-weighted images, whereas cysts in the corpus luteum appear dark in T₁-weighted images and bright in T₂-weighted images. The varying brightness of the follicles at different stages of development is hypothesized to be related to different hormone and protein concentrations in the follicular fluid. For example, it is known that physiologically selected preovulatory follicles contain high concentrations of estrogens in a viscous follicular fluid. The increased viscosity may occur only when the follicle fluid contains high concentrations of estrogen and contributes to bright T₁-weighted images. The possibility of using nuclear relaxation-weighted NMR imaging for the study of follicular dynamics and other ovarian biology therefore shows great promise.     

Medical Images Simulation, Storage, and Processing on the European DataGrid Testbed

The European 1ST DataGrid project was a pioneer in identifying the medical imaging field as an application domain that can benefit from Grid technologies. This paper describes how and for which purposes medical imaging applications can be Grid-enabled. Applications that have been deployed on the DataGrid testbed and middleware are described. They relate to medical image manipulation, including image production, secured image storage, and image processing. Results show that Grid technologies are still in their youth to address all issues related to complex medical imaging applications. If the benefit of Grid enabling for some medical applications is clear, there remain opened research and technical issues to develop and integrate all necessary services.     

Numerical analysis of a laterally loaded shaft constructed within an MSE wall

Drilled shafts have been widely used to support lateral loads from superstructures. For typical applications, design methods are available to generate lateral load versus displacement curves and to estimate ultimate lateral capacity and displacement of the drilled shaft under a certain lateral load. However, occasionally drilled shafts have to be constructed within the reinforced zones of MSE walls, for instance drilled shafts supporting sound walls, traffic signs, billboards, and other superstructures. Under these circumstances, existing design methods are not applicable because of: (1) the limited horizontal extent of the soil mass; (2) the resistance from reinforcement; and (3) the influence of MSE wall facing. In this regard, a full-scale field study was conducted to investigate the behavior of shafts within the MSE wall, subjected to lateral loads. The test wall was 43 m long and 6 m high and constructed with layers of uniaxial geogrid and selected backfill. Three-dimensional numerical analyses were performed prior to the construction of this test wall (i.e., Class-A prediction) to guide its design and after the field test using the actual material properties (i.e., Class-C prediction). The selected test shaft for the analyses in this study was located at 1.8 m behind the wall facing. The numerical results from the Class-A and Class-C predictions are compared with the field data. The study showed that the Class-A prediction provided useful information for the design of the test wall and development of field test details. The Class-C prediction improved the overall accuracy of the calculations and could serve as a reference for future study.     

Microbiological quality and safety of quahog clams, Mercenaria mercenaria, during refrigeration and at elevated storage temperatures

The effects of storage temperatures and times on the microbiological quality and safety of hard-shelled quahog clams (Mercenaria mercenaria) were examined. Samples were stored at four different incubation temperatures (3.3, 7.2, 10.0, and 12.8 degrees C) for a period of 3 weeks, following their harvest from summer growing waters (> or = 27 degrees C) and winter waters (< or = 4 degrees C). Clams were analyzed for two naturally occurring pathogens, Vibrio parahaemolyticus and Vibrio vulnificus. During the summer, V. parahaemolyticus was isolated from 56% of the stored samples, with the highest concentration, 6,100/g, occurring on day 12 at 12.8 degrees C. Also, during the summer, V. vulnificus was isolated from 11% of the stored samples, with the highest concentration of 1,500/g occurring on day 15 at 7.2 degrees C. No Vibrio spp. were detected during the winter. During summer storage, aerobic mesophilic counts on plate count agar (PCA) containing 2% NaCl ranged from 10(4) to 10(8) CFU/g, and during storage of the winter samples, aerobic mesophilic PCA (with added NaCl) counts ranged from <100 to 10(4) CFU/g. Comparatively, summer storage mesophilic counts on PCA containing no added NaCl ranged from <100 to 10(5) CFU/g, and for the winter samples the range was <100 to 10(2) CFU/g. Coliform and fecal coliform counts ranged from <0.3 to 61.1/g and <0.3 to 24.4/g, respectively. There was no statistical correlation between the length of storage or the temperature of incubation and the presence of V. parahaemolyticus, V. vulnificus, coliforms, or fecal coliforms. However, storage time and incubation temperature affected the PCA counts (P < or = 0.05) in quahog clams.     

Sudden deaths in yearling feedlot cattle

A survey of the causes for fatal diseases of yearling feedlot cattle was conducted on more than 407,000 cattle during a 14-month period. Of the 4,260 (1%) cattle that died during this period, 1,358 (32%) were categorized as cases of "sudden death syndrome." Of the 11 most frequent causes of the syndrome, as determined at necropsy, only 4--bloat, pulmonary aneurysms, riding injury, and hemopericardium--were considered as short-course problems and true causes of sudden death. The largest number of cases of sudden death were attributed to pneumonia (113 animals). Consequently, the sudden death syndrome is a misnomer for many long-course diseases and, in some instances, a mask for neglect because, as clinically used, the name frequently includes cattle that have been sick, often with pneumonia, for several days.