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.     

The flavin-containing monooxygenase 2 gene (FMO2) of humans, but not of other primates, encodes a truncated, nonfunctional protein

Flavin-containing monooxygenases (FMOs) are NADPH-dependent flavoenzymes that catalyze the oxidation of heteroatom centers in numerous drugs and xenobiotics. FMO2, or "pulmonary" FMO, one of five forms of the enzyme identified in mammals, is expressed predominantly in lung and differs from other FMOs in that it can catalyze the N-oxidation of certain primary alkylamines. We describe here the isolation and characterization of cDNAs for human FMO2. Analysis of the sequence of the cDNAs and of a section of the corresponding gene revealed that the major FMO2 allele of humans encodes a polypeptide that, compared with the orthologous protein of other mammals, lacks 64 amino acid residues from its C terminus. Heterologous expression of the cDNA revealed that the truncated polypeptide was catalytically inactive. The nonsense mutation that gave rise to the truncated polypeptide, a C --> T transition in codon 472, is not present in the FMO2 gene of closely related primates, including gorilla and chimpanzee, and must therefore have arisen in the human lineage after the divergence of the Homo and Pan clades. Possible mechanisms for the fixation of the mutation in the human population and the potential significance of the loss of functional FMO2 in humans are discussed.     

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.     

Sliding Mode Control with Adaptive Fuzzy Dead-Zone Compensation of an Electro-hydraulic Servo-System

Electro-hydraulic servo-systems are widely employed in industrial applications such as robotic manipulators, active suspensions, precision machine tools and aerospace systems. They provide many advantages over electric motors, including high force to weight ratio, fast response time and compact size. However, precise control of electro-hydraulic systems, due to their inherent nonlinear characteristics, cannot be easily obtained with conventional linear controllers. Most flow control valves can also exhibit some hard nonlinearities such as dead-zone due to valve spool overlap. This work describes the development of an adaptive fuzzy sliding mode controller for an electro-hydraulic system with unknown dead-zone. The boundedness and convergence properties of the closed-loop signals are proven using Lyapunov stability theory and Barbalat’s lemma. Numerical results are presented in order to demonstrate the control system performance.     

An adaptive fuzzy sliding mode controller for remotely operated underwater vehicles

Sliding mode control is a very attractive control scheme because of its robustness against both structured and unstructured uncertainties as well as external disturbances. In this way, it has been widely employed for the dynamic positioning of remotely operated underwater vehicles. Nevertheless, in such situations the discontinuities in the control law must be smoothed out to avoid the undesirable chattering effects. The adoption of properly designed boundary layers has proven effective in completely eliminating chattering, however, leading to an inferior tracking performance. This work describes the development of a dynamic positioning system for remotely operated underwater vehicles. The adopted approach is primarily based on the sliding mode control strategy and enhanced by an adaptive fuzzy algorithm for uncertainty/disturbance compensation. Using the Lyapunov stability theory and Barbalat’s lemma, the boundedness and convergence properties of the closed-loop signals are analytically proven. The performance of the proposed control scheme is also evaluated by means of numerical simulations.     

Slicing the metric space to provide quick indexing of complex data in the main memory

Searching in a dataset for elements that are similar to a given query element is a core problem in applications that manage complex data, and has been aided by metric access methods (MAMs). A growing number of applications require indices that must be built faster and repeatedly, also providing faster response for similarity queries. The increase in the main memory capacity and its lowering costs also motivate using memory-based MAMs. In this paper, we propose the Onion-tree, a new and robust dynamic memory-based MAM that slices the metric space into disjoint subspaces to provide quick indexing of complex data. It introduces three major characteristics: (i) a partitioning method that controls the number of disjoint subspaces generated at each node; (ii) a replacement technique that can change the leaf node pivots in insertion operations; and (iii) range and k-NN extended query algorithms to support the new partitioning method, including a new visit order of the subspaces in k-NN queries. Performance tests with both real-world and synthetic datasets showed that the Onion-tree is very compact. Comparisons of the Onion-tree with the MM-tree and a memory-based version of the Slim-tree showed that the Onion-tree was always faster to build the index. The experiments also showed that the Onion-tree significantly improved range and k-NN query processing performance and was the most efficient MAM, followed by the MM-tree, which in turn outperformed the Slim-tree in almost all the tests.     

Spatial data warehouses and spatial OLAP come towards the cloud: design and performance

Cloud computing systems handle large volumes of data by using almost unlimited computational resources, while spatial data warehouses (SDWs) are multidimensional databases that store huge volumes of both spatial data and conventional data. Cloud computing environments have been considered adequate to host voluminous databases, process analytical workloads and deliver database as a service, while spatial online analytical processing (spatial OLAP) queries issued over SDWs are intrinsically analytical. However, hosting a SDW in the cloud and processing spatial OLAP queries over such database impose novel obstacles. In this article, we introduce novel concepts as cloud SDW and spatial OLAP as a service, and afterwards detail the design of novel schemas for cloud SDW and spatial OLAP query processing over cloud SDW. Furthermore, we evaluate the performance to process spatial OLAP queries in cloud SDWs using our own query processor aided by a cloud spatial index. Moreover, we describe the cloud spatial bitmap index to improve the performance to process spatial OLAP queries in cloud SDWs, and assess it through an experimental evaluation. Results derived from our experiments revealed that such index was capable to reduce the query response time from 58.20 up to 98.89 %.