Peer reviewed: instrumental analysis at the university of kansas: an experiment in problem-based learning

Students work in groups to solve real-world problems.     

Elevated expression of eIF4E in confined early breast cancer lesions: possible role of hypoxia

The translation-initiation factor eIF4E is rate-limiting for protein synthesis, and its over-expression results in oncogenic transformation of mammalian cells. eIF4E facilitates the synthesis of several powerful tumor angiogenic factors (FGF-2 and VEGF) by selectively enhancing their translation. In breast carcinomas, eIF4E is commonly over-expressed, but the pathology where this elevation is initially manifested is presently unknown. To probe whether the elevation of eIF4E marks an early stage of cancer development, we focused our research on early cancerous lesions. We have analyzed 70 invasive ductal carcinomas (IDCs), 78 ductal carcinomas in situ (DCIS), 51 benign lesions and 4 model cell lines for elevated expression of eIF4E by several different methods: Northern/Western blots, immuno-histochemistry and in situ RT-PCR. eIF4E expression was markedly increased in IDC and in islets of viable cells in the center of poorly vascularized DCIS, which are not easily identifiable by standard histological stains. We also show that expression of eIF4E is increased by hypoxia and, presumably, in hypoxic areas of these lesions. We propose that clonal expansion of cancer cells, permanently over-expressing eIF4E, gives them a critical advantage to survive hypoxia and marks the transition toward the vascular phase of cancer progression. Hence, eIF4E may be useful in stratifying DCIS lesions according to their malignant stage.     

Organized cell swimming motions in Bacillus subtilis colonies: patterns of short-lived whirls and jets

The swimming motions of cells within Bacillus subtilis colonies, as well as the associated fluid flows, were analyzed from video films produced during colony growth and expansion on wet agar surfaces. Individual cells in very wet dense populations moved at rates between 76 and 116 microm/s. Swimming cells were organized into patterns of whirls, each approximately 1,000 microm2, and jets of about 95 by 12 microm. Whirls and jets were short-lived, lasting only about 0.25 s. Patterns within given areas constantly repeated with a periodicity of approximately 1 s. Whirls of a given direction became disorganized and then re-formed, usually into whirls moving in the opposite direction. Pattern elements were also organized with respect to one another in the colony. Neighboring whirls usually turned in opposite directions. This correlation decreased as a function of distance between whirls. Fluid flows associated with whirls and jets were measured by observing the movement of marker latex spheres added to colonies. The average velocity of markers traveling in whirls was 19 microm/s, whereas those traveling in jets moved at 27 microm/s. The paths followed by markers were aligned with the direction of cell motion, suggesting that cells create flows moving with them into whirls and along jets. When colonies became dry, swimming motions ceased except in regions close to the periphery and in isolated islands where cells traveled in slow whirls at about 4 microm/s. The addition of water resulted in immediate though transient rapid swimming (> 80 microm/s) in characteristic whirl and jet patterns. The rate of swimming decreased to 13 microm/s within 2 min, however, as the water diffused into the agar. Organized swimming patterns were nevertheless preserved throughout this period. These findings show that cell swimming in colonies is highly organized.     

Inversion of feedforward neural networks: algorithms andapplications

There are many methods for performing neural network inversion. Multi-element evolutionary inversion procedures are capable of finding numerous inversion points simultaneously. Constrained neural network inversion requires that the inversion solution belong to one or more specified constraint sets. In many cases, iterating between the neural network inversion solution and the constraint set can successfully solve constrained inversion problems. This paper surveys existing methodologies for neural network inversion, which is illustrated by its use as a tool in query-based learning, sonar performance analysis, power system security assessment, control, and generation of codebook vectors     

The transient response of ZrO2 oxygen sensors to step changes in gas composition

The transient voltage response of ZrO₂ oxygen sensors was examined following step changes in gas composition. The experiments were performed on a laboratory flow reactor at 600° C. Composition changes between (a) 100% and (b) 1% O₂ in N₂ produced response curves whose symmetry varied between composition steps (a) from low-to-high oxygen and (b) from high-to-low oxygen. This difference is due to the logarithmic dependence of sensor voltage on oxygen partial pressure. Corresponding oxygen partial pressure-time curves, derived from experimental voltage via the Nernst equation, are symmetric with respect to the direction of composition changes. Abrupt transitions are found in voltage-time curves at 600° C following step changes of reactive gases; e.g. from O₂/N₂ mixtures to CO/N₂, H₂/N₂ or D₂/N₂ mixtures. These voltage-steps represent transitions in stoichiometry of the surface boundary layer on the ZrO₂ sensor. Delay times before the transition also reflect reaction stoichiometry. Response times with O₂/CO, O₂/H₂ and O₂/D₂ follow trends predicted by the kinetic theory of gases. A limited number of experiments were performed to examine the relationships between sensor response and sensor catalytic activity. Poorer oxidation catalytic activity parallels slower response characteristics.     

Photoluminescent distinction among plant life forms using phosphate buffered saline extract solutions

Photoluminescence of plant extract solutions has been investigated for discrimination of plant life forms (grasses, forbs, and shrubs) using principal component analysis (PCA). Clippings from each of six plant species representing three different plant life forms potentially found in the diets of free-ranging herbivores in the Chihuahuan Desert of North America were investigated for possible discernment. These plants included Sporobolus flexuosus (mesa dropseed, a grass), Pleuraphis mutica (tobosa, a grass), Dimorphocarpa wislizenii (spectacle pod, a forb), Sphaeralcea incana (pale globemallow, a forb), Flourensia cernua leaves (tarbush, a shrub), and Atriplex canescens leaves and stems (fourwing saltbush, a shrub). Emission spectra (370-600 nm) from phosphate buffered saline (PBS) extract solutions (pH 2.2, 7.5 and 12.5) were recorded for each plant with excitation at 365 nm. Use of PBS minimized chlorophyll interference. Discernment among plant life forms within these plant species was achieved.     

Magnetic resonance compatibility of multichannel silicon microelectrode systems for neural recording and stimulation: design criteria, tests, and recommendations

Magnetic resonance (MR) compatibility of biomedical implants and devices represents a challenge for designers and potential risks for users. This paper addresses these problems and presents the first MR-compatible multichannel silicon chronic microelectrode system, used for recording and electrical stimulation of the central nervous system for animal models. A standard chronic assembly, from the Center for Neural Communication Technology at the University of Michigan, was tested on a 2 Tesla magnet to detect forces, heating, and image distortions, and modified to minimize or eliminate susceptibility artifacts, tissue damage, and electrode displacement, maintaining good image quality and safety to the animals. Multiple commercial connectors were tested for MR compatibility and several options for the reference electrode were also tested to minimize image artifacts and provide a stable biocompatible reference for shortand long-term neural recordings. Different holding screws were tested to anchor the microelectrode assembly on the top of the skull. The final selection of this part was based on MR-compatibility, biocompatibility, durability, and mechanical and chemical stability. The required adaptor to interconnect the MR-compatible microelectrode with standard data acquisition systems was also designed and fabricated. The final design is fully MR-compatible and has been successfully tested on guinea pigs.     

Nine-analyte detection using an array-based biosensor

A fluorescence-based multianalyte immunosensor has been developed for simultaneous analysis of multiple samples. While the standard 6 x 6 format of the array sensor has been used to analyze six samples for six different analytes, this same format has the potential to allow a single sample to be tested for 36 different agents. The method described herein demonstrates proof of principle that the number of analytes detectable using a single array can be increased simply by using complementary mixtures of capture and tracer antibodies. Mixtures were optimized to allow detection of closely related analytes without significant cross-reactivity. Following this facile modification of patterning and assay procedures, the following nine targets could be detected in a single 3 x 3 array: Staphylococcal enterotoxin B, ricin, cholera toxin, Bacillus anthracis Sterne, Bacillus globigii, Francisella tularensis LVS, Yersiniapestis F1 antigen, MS2 coliphage, and Salmonella typhimurium. This work maximizes the efficiency and utility of the described array technology, increasing only reagent usage and cost; production and fabrication costs are not affected.     

Comparison of PCR prescreening to two cultivation procedures with PCR confirmation for detection of Mycobacterium avium subsp. paratuberculosis in U.S. Department of Agriculture fecal check test samples

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent in Johne's disease in cattle and causes diarrhea, decreased milk production, emaciation, and frequently death. The ability to detect MAP rapidly and accurately is an integral part of herd management. However, detection of this bacterium is complicated due to its slow division time and its ability to enter dormancy. Culture methods are considered the "gold standard," but they have their limitations. Many enzyme-linked immunosorbent assay methods and conventional PCR methods have been used as diagnostic tools. The present study compares the results of a PCR prescreen to two culture methods of detection paired with confirmatory PCR to determine the most accurate, rapid, and sensitive method using U.S. Department of Agriculture (USDA) fecal check samples. This study involving two laboratories (Marshfield Clinic Laboratories, using solid culture medium [Herrold's egg yolk agar], and TREK Diagnostic Systems Research and Development, using liquid culture medium [ESP Culture System II]) showed that the PCR prescreening method used in this study lacked specificity and sensitivity as a stand-alone test in fecal samples. However, the combination of liquid enrichment culture using the ESP II system, and PCR confirmation with the hspX primer set, was not only 100% sensitive and specific but also correlated with viable MAP and USDA culture results.     

Efficient testing of segmented aspherical mirrors by use of a reference plate and computer-generated holograms. II. Case study, error analysis, and experimental validation

Segmented mirrors present unique challenges to fabrication and testing that are absent for monolithic optics. Since traditional asphere tests do not address segmented optics adequately, we validate a previously developed method to test large quantities of segments accurately, quickly, and economically. In this test, the aspheric shape of each segment is controlled to high accuracy by use of computer-generated holograms, and the radius of curvature is tightly controlled by use of the reference plate. In an adjoining paper [Appl Opt 43, 5303 (2004)] we developed the theory for this test, and now we present a complete system design and optimization for measuring the 1.4-m segments from a 30-m F/1 primary. A complete tolerance analysis predicts a test accuracy of 4.8-nm rms surface and excellent accuracy for controlling the geometry of the segment. In addition, a laboratory demonstration using 30-cm optics is presented that demonstrated 3.9-nm rms surface accuracy.