Measurement of amide hydrogen exchange by MALDI-TOF mass spectrometry

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) was used to determine amide proton/deuteron (H/D) exchange rates. The method has broad application to the study of protein conformation and folding and to the study of protein-ligand interactions and requires no modifications of the instrument. Amide protons were allowed to exchange with deuterons in buffered D2O at room temperature, pD 7.25. Exchanged deuterons were "frozen" in the exchanged state by quenching at pH 2.5, 0 degree C and analyzed by MALDI-TOF MS. The matrix mixture consisted of 5 mg/mL alpha-cyano-4-hydroxycinnamic acid, acetonitrile, ethanol, and 0.1% TFA. The matrix was adjusted to pH 2.5, and the chilled MALDI target was rapidly dried. Deuteration of amide protons on cyclic AMP-dependent protein kinase was measured after short times of incubation in deuterium by pepsin protein digestion and MALDI-TOF MS analysis. The unseparated peptic digest was analyzed in a single spectrum of the mixture. From five spectra, H/D exchange rates were determined for some 40 peptides covering 65% of the protein sequence.     

Isoseparation curves: a mechanism for optimizing off-axis dose homogeneity of intact breast irradiation

The purpose of this paper is to determine whether using off-axis isoseparation curves to optimize the collimator rotation angle improves dose homogeneity. Eleven intact breast irradiation patients underwent computerized tomography (CT) treatment planning with 1 cm abutting slices. Central plane treatment planning, using 6 MV photons, tissue inhomogeneity corrections, and isocentric opposed tangent treatment fields, was performed. Collimators were rotated to match chest wall slope through the use of a beam's-eye-view setting. Patient separations were measured from the apex of the breast to the posterior field border on each axial CT slice. Sagittal-plane isoseparation curves were constructed from these measurements. Using these curves, the collimator rotation that minimized off-axis separation differences was determined. A comparison of off-axis dose inhomogeneity was performed for patients with a > or =10 degrees difference between this optimized collimator angle and the angle determined by chest wall slope. These comparative treatment plans differed only with respect to collimator angle rotation. The mean optimal collimator rotation angle differed significantly from the mean rotation angle which matched the chest wall slope (5.4 degrees vs. 11 degrees, respectively, P < 0.001). Four of the 11 patients had rotation angle differences of 10 degrees. In these patients, the optimization of collimator angle reduced the percentage of breast volume to "that" received > or =110% of the prescribed dose. For the patient with the largest breast size to the patient with the smallest breast size the decreases were, respectively, 5% (15% to 10%), 3% (24% to 21%), 1% (4% to 3%), and 1% (0.9% to 0%). The mean reduction in dose inhomogeneity was greatest in the inferior breast quadrants. At 6 cm and 4 cm off axis, the mean reductions in the percentages of the breast tissue to "that" received 110% of the prescribed dose were respectively 15.1% and 5.3 %. Optimizing the collimator angle through the use of isoseparation curves decreases dose inhomogeneity. The greatest improvements are in the inferior quadrants of the intact breast. The improved dose homogeneity may have clinical relevance in the treatment of patients with large breast sizes.     

Discriminating constant from variable angular velocities in structure from motion

We investigated accuracy in discriminating between constant and variable angular velocities for orthographic projections of three-dimensional rotating objects. The reported judgments of "constant" or "variable" angular velocity were only slightly influenced by the projected angular velocities, but they were greatly affected by the variations of the deformation, a first-order component of the optic flow. When viewing either a rotating ellipsoidal volume or a planar surface that accelerated and decelerated over the course of rotation, observers' tendencies to report a variable angular velocity were increased when the temporal phase of the acceleration pattern increased the range of variation of the median deformation; the tendencies were decreased when the same acceleration pattern was used to decrease the range of variation of the median deformation. These results provide evidence contrary to the hypothesis that the visual system performs a mathematically correct analysis of the optic flow.     

Fiber-optic probes with improved excitation and collection efficiency for deep-UV Raman and resonance Raman spectroscopy

The ability of ultraviolet resonance Raman spectroscopy (UVRRS) to determine structural, environmental, and analytical information concerning low-concentration aqueous biomolecules makes it a powerful bioanalytical and biophysical technique. Unfortunately, its utility has been limited by experimental requirements that preclude in situ or in vivo studies in most cases. We have developed the first high-performance fiber-optic probes suitable for long-term use in pulsed UVRRS applications in the deep- UV (DUV, 205-250 nm). The probes incorporate recently developed improved ultraviolet (IUV) fibers that do not exhibit the rapid solarization and throughput decay that previously hampered the use of optical fibers for delivering pulsed, DUV light. A novel 90 degrees mirrored collection geometry is used to overcome the inner-filtering effects that plague flush-probe geometries. The IUV fibers are characterized with respect to their efficacy at transmitting pulsed, DUV laser light, and prototype probes are used to obtain pulsed UVRRS data of aromatic amino acids, proteins, and hormones at low concentrations with 205-240-nm pulsed excitation. Efficient probe geometries and fabrication methods are presented. The performance of the probes in examining resonance-enhanced Raman signals from absorbing chromophores is investigated, and the optimal excitation wavelength is shown to be significantly red-shifted from the maximum of the resonance Raman enhancement profile. Generally applicable procedures for determining optimal experimental conditions are also introduced.     

Analogues of capsaicin with agonist activity as novel analgesic agents: structure-activity studies. 4. Potent, orally active analgesics

Structural features of three regions of the capsaicin molecule necessary for agonist properties were delineated by a previously reported modular approach. These in vitro agonist effects were shown to correlate with analgesic potency in rodent models. Combination of optimal structural features from each of these regions of the capsaicin molecule have led to highly potent agonists (eg., 1b). Evaluation in vivo established that 1b had analgesic properties but poor oral activity, short duration of action, and excitatory side effects which precluded further development of this compound. Preliminary metabolism studies had shown that the phenol moiety of 1b was rapidly glucuronidated in vivo, providing a possible explanation for the poor pharmacokinetic profile. Subsequent specific modification of the phenol group led to compounds 2a-j, which retained in vitro potency. The in vivo profiles of two representatives of this series, 2a,h, were much improved over the "parent" phenol series, and they are candidates for development as analgesic agents.     

Supramalleolar osteotomy for ankle valgus in myelomeningocele

Oral fibroblasts stimulated invasion of oral-carcinoma cells into the collagen matrix. The mechanisms of the fibroblast-induced stimulation of invasiveness was further investigated by examining cell motility and proteolytic activity of tumor cells, using mainly an adenoid-cystic-carcinoma cell line (ACCS) and normal fibroblasts from gingival tissues. Conditioned medium from the fibroblasts grown in serum-free medium was fractionated on a Superdex 200 pg column, and Peak 1 eluted at 200 to 300 kDa and Peak 2 eluted at 50 to 100 kDa were found to contain different specific activity. Treatment of ACCS cells with Peak 1 resulted in an increase in the production of proteolytic enzymes. Peak 2 stimulated both chemotaxis and chemokinesis of ACCS cells. A chemotactic factor was purified from the heparin-unbound fraction of Peak 2 by anion exchange and hydrophobic chromatography, and was named "fibroblast-derived motility factor (FDMF)". At 1 microg/ml, FDMF stimulated chemotaxis of ACCS cells by 4-fold compared with unstimulated controls. Characterization of the physicochemical properties of FDMF suggested that it might be different from any known motility factors. Exposure of ACCS cells to FDMF resulted in reduced amounts of actin stress fiber in the cytoplasm and induction of tyrosine phosphorylation of several cellular proteins detectable 30 to 60 min after treatment. These FDMF-induced changes were blocked by pre-treatment either with genistein or with pertussis toxin. These findings suggest that FDMF may be a novel protein which stimulates cell motility via a signaling pathway mediated by a pertussis-toxin-sensitive G protein and tyrosine phosphorylation.     

Perinuclear antineutrophil cytoplasmic antibodies in patients with Crohn's disease define a clinical subgroup

BACKGROUND & AIMS: Antineutrophil cytoplasmic antibodies (ANCA) have been consistently detected in a subgroup of patients with Crohn's disease (CD). This study was designed to determine whether serum ANCA expression in patients with CD characterizes an identifiable clinical subgroup. METHODS: The study population consisted of 69 consecutive patients with an established diagnosis of CD as determined by a combination of characteristic clinical, radiographic, endoscopic, and histopathologic criteria. Sera from the patients were analyzed for the presence of ANCAs using the fixed neutrophil enzyme-linked immunosorbent assay (ELISA) assay. Perinuclear ANCA (pANCA)-positive and cytoplasmic ANCA (cANCA)-positive results by ELISA were confirmed by indirect immunofluorescence staining. Clinical profiles of the ANCA-positive patients with CD were compared with those of patients with CD not expressing ANCA (ANCA-negative). RESULTS: pANCA-positive patients with CD have endoscopically and/or histopathologically documented left-sided colitis and symptoms of left-sided colonic inflammation, clinically reflected by rectal bleeding and mucus discharge, urgency, and treatment with topical agents. One hundred percent of patients with CD expressing pANCA had "UC-like" features. CONCLUSIONS: In patients with CD, serum pANCA expression characterizes a UC-like clinical phenotype. Stratification of CD by serum pANCA provides evidence of heterogeneity within CD and suggests a common intestinal mucosal inflammatory process among a definable subgroup of patients with CD and UC expressing this marker.     

Shape optimization for tumor location

In non-invasive thermal diagnostics, accurate correlations between the thermal image at skin surface and interior human physiology are desired. In this work, an estimation methodology to determine unknown geometrical parameters of an embedded tumor is proposed. We define a functional that represents the mismatch between a measured experimental temperature profile, which may be obtained by infrared thermography on the skin surface, and the solution of an appropriate boundary problem. This functional is related to the geometrical parameters through the solution of the boundary problem, in such a way that finding the minimum of this functional form also means finding the unknown geometrical parameters of the embedded tumor. Sensitivity analysis techniques coupled with the adjoint method were considered to compute the shape derivative of the functional. Then, a nonmonotone spectral projected gradient method was implemented to solve the optimization problem of finding the optimal geometric parameters.     

Amperometric biosensor for formic acid in air

The possibility of developing a simple, inexpensive and specific personal passive “real-time” air sampler incorporating a biosensor for formic acid was investigated. The sensor is based on the enzymatic reaction between formic acid and formate dehydrogenase (FDH) with nicotinamide adenine dinucleotide (NAD⁺) as a co-factor and Meldola's blue as mediator. An effective way to immobilise the enzyme, co-factor and Meldola's blue on screen-printed, disposable, electrodes was found to be in a mixture of glycerol and phosphate buffer covered with a gas-permeable membrane. Steady-state current was reached after 4–15 min and the limit of detection was calculated to be below 1 mg/m³. However, the response decreased by 50% after storage at −15°C for 1 day.     

Supporting command and control training functions in the emergency management domain using cognitive systems engineering

The design and implementation of MERMAIDS, a computer-based training system in the domain of emergency command and control, is described. The research investigates the use of cognitive systems engineering and information management tools for modelling and representing training knowledge of emergency system operators. We propose a decision-centric human-computer interface as a new method of supporting computer-based modelling in the domain of emergency systems. Several interacting themes in information management relevant to emergency response planning are discussed.