bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crystallization of truncated human apolipoprotein A-I in a novel conformation
Authors: Borhani David W. , Engler Jeffrey A. , Brouillette Christie G. 
Published: July 2002

The crystallization of recombinant human apolipoprotein A-I (apo A-I), the major protein component of high-density lipoprotein, in a new crystal form is described. The fragment crystallized, residues 44–243 of native apo A-I [apo Δ(1–43)A-I], is very similar to intact native apo A-I in its ability to bind lipid, to be incorporated into high-density lipoproteins and to activate lecithin–cholesterol acyl transferase. Apo Δ(1–43)A-I crystallizes, in the presence of β-D-octylglucopyranoside, in space group I222 or I212121, with unit-cell parameters a = 37.11, b = 123.62, c = 164.65 Å and a diffraction limit of 3.2 Å. These form II crystals grow under conditions of significantly lower ionic strength than the original form I crystals (space group P212121, a = 97.47, b = 113.87, c = 196.19 Å, diffraction limit 3.0 Å). Packing arguments show that the unusual open conformation of apo Δ(1–43)A-I found in the form I crystals cannot be packed into the smaller oddly proportioned form II unit cell. Monomeric apo Δ(1–43)A-I, as either a four-helix bundle (∼75 × 30 × 30 Å) or an extended helical rod (∼150 × 20 × 20 Å), can be packed into the form II unit cell. It is concluded, therefore, that apo Δ(1–43)A-I may have crystallized in one of these distinct conformations in the form II crystals.
Crystallization and preliminary X-ray diffraction studies of human catalase
Authors: Nagem R. A. P. , Martins E. A. L. , Gonçalves V. M. , Aparício R. , Polikarpov I. 
Published: July 2002

The enzyme catalase (H2O2–H2O2 oxidoreductase; E.C. 11.1.6) was purified from haemolysate of human placenta and crystallized using the vapour-diffusion technique. Synchrotron-radiation diffraction data have been collected to 1.76 Å resolution. The enzyme crystallized in the space group P212121, with unit-cell dimensions a = 83.6, b = 139.4, c = 227.5 Å. A molecular-replacement solution of the structure has been obtained using beef liver catalase (PDB code 4blc) as a search model.
Actinide coordination sphere in various U, Np and Pu nitrato coordination complexes
Authors: Den Auwer C. , Revel R. , Charbonnel M. C. , Presson M. T. , Conradson S. D. , Simoni E. , Le Du J. F. , Madic C. 
Published: July 2002

Waste management of nuclear fuel represents one of the major environmental concerns of the decade. To recycle fissile valuable materials, intimate knowledge of complexation mechanisms involved in the solvent extraction processes is indispensable. Evolution of the actinide coordination sphere of AnO2(NO3)2TBP-type complexes (An = U, Np, Pu; TBP = tributylphosphate) with the actinide valence state have been probed by XAS at the metal L
III edge. Dramatic changes in the actinide coordination sphere appeared when the An(VI) metal is reduced to An(IV). However, no significant evolution in the actinide environment has been noticed across the series UO2
2+, NpO2
2+ and PuO2
2+.
2-[N-(tert-Butoxycarbonyl)tyrosyl]-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid nitromethane solvate
Authors: Deschamps Jeffrey R. , Flippen-Anderson Judith L. , George Clifford 
Published: July 2002

The title compound, C24H28N2O6·0.825CH3NO2, is a member of the TIPP (i.e.Try–Tic–Phe–Phe) family of opioid ligands. The asymmetric unit contains one peptide molecule and one nitromethane molecule. Unlike other members of this familiy, this dipeptide has an extended conformation [i.e.ϕ1 = −103.6 (6)°, ω1 = 168.1 (4)°, ψ1 = 152.4 (5)°]. This conformation was further examined with the programCHEM3D. No significant energy difference was found between the energy-minimized conformation and a more tightly folded model conformation.
Enzyme specificity under dynamic control II: Principal component analysis of α‐lytic protease using global and local solvent boundary conditions
Authors: Ota Nobuyuki , Agard David A. 
Published: July 2002

AbstractThe contributions of conformational dynamics to substrate specificity have been examined by the application of principal component analysis to molecular dynamics trajectories of α‐lytic protease. The wild‐type α‐lytic protease is highly specific for substrates with small hydrophobic side chains at the specificity pocket, while the Met190→Ala binding pocket mutant has a much broader specificity, actively hydrolyzing substrates ranging from Ala to Phe. Based on a combination of multiconformation analysis of cryo‐X‐ray crystallographic data, solution nuclear magnetic resonance (NMR), and normal mode calculations, we had hypothesized that the large alteration in specificity of the mutant enzyme is mainly attributable to changes in the dynamic movement of the two walls of the specificity pocket. To test this hypothesis, we performed a principal component analysis using 1‐nanosecond molecular dynamics simulations using either a global or local solvent boundary condition. The results of this analysis strongly support our hypothesis and verify the results previously obtained by in vacuo normal mode analysis. We found that the walls of the wild‐type substrate binding pocket move in tandem with one another, causing the pocket size to remain fixed so that only small substrates are recognized. In contrast, the M190A mutant shows uncoupled movement of the binding pocket walls, allowing the pocket to sample both smaller and larger sizes, which appears to be the cause of the observed broad specificity. The results suggest that the protein dynamics of α‐lytic protease may play a significant role in defining the patterns of substrate specificity. As shown here, concerted local movements within proteins can be efficiently analyzed through a combination of principal component analysis and molecular dynamics trajectories using a local solvent boundary condition to reduce computational time and matrix size.
A Demonstration of Artificial Neural-Networks-Based Data Mining for
Gas-Turbine-Driven Compressor Stations
Authors: Botros K. K. , Kibrya G. , Glover A. 
Published: July 2002

Abstract
This paper presents a successful demonstration of application of neural networks to perform various data mining functions on an RB211 gas-turbine-driven compressor station. Radial basis function networks were optimized and were capable of performing the following functions: (a) backup of critical parameters, (b) detection of sensor faults, (c) prediction of complete engine operating health with few variables, and (d) estimation of parameters that cannot be measured. A Kohonen SOM technique has also been applied to recognize the correctness and validity of any data once the network is trained on a good set of data. This was achieved by examining the activation levels of the winning unit on the output layer of the network. Additionally, it would also be possible to determine the suspicious, faulty or corrupted parameter(s) in the cases which are not recognized by the network by simply examining the activation levels of the input neurons.
Gas-phase evolution and convective heat transfer in closed-cell vapor transport of organic thin films in microgravity and unit gravity
Authors: Debe M. K. , Poirier R. J. , Cook E. L. , Miller L. R. , Spiering M. S. , Floeder S. P. 
Published: July 2002

The completed first phase of the analyses of a series of physical vapor transport experiments conducted both in low earth orbit on the Space Shuttle Orbiter and in the laboratory is presented. The experiments are the first to use physical vapor transport as a process to grow oriented organic thin films on epitaxially active substrates sealed within demountable ampoules. It was found that the films grown in the microgravity environment were smoother, optically more homogeneous and denser than their unit gravity grown counterparts, and contained predominantly a new polymorph of copper phthalocyanine (CuPc). In this report the gas-phase evolution within the ampoules and resulting convective effects on the substrate temperature have been characterized for four microgravity processed cells and over twenty ground control experiments. The nitrogen-equivalent total pressures and partial pressures of nine common gases are measured within the processed ampoules and the relationships determined empirically among the gas pressures, compositions, and the orientation of the ampoule relative to the earth’s gravitational field.
Significant gas evolution amounting to several times the original backfilled buffer gas is found in all the ampoules, and attributed to hydrogen evolution from stainless-steel components and the thermal decomposition of as little as 0.06% of the starting source material. The amounts and compositions are found to be very consistent among the different experiments, leading to the conclusion that this is not a significant variable in the comparisons of microstructure differences observed between the microgravity grown and laboratory grown films. It is observed that the substrate temperature is sensitive not only to the ampoule gas pressure and composition, but also to the ampoule orientation and its external gas environment during the thermal processing. It is concluded that enhanced convective heat transfer to the substrate occurs not only with the hotter end of the ampoule below the cooler end but also when the hotter end is above the cooler end under unit gravity conditions.
Finally, estimates of the thermophysical parameters are calculated for a representative ampoule gas composition, including the mixture kinetic viscosity, thermal conductivity, heat capacity, binary diffusivity of the CuPc, and the effective vapor pressure of the CuPc above the substrate.
Thermal relaxation kinetics of strained Si/Si1−xGex heterostructures determined by direct measurement of mosaicity and lattice parameter variations
Authors: Sardela M. R. , Hansson G. V. 
Published: July 2002

The thermal stability of strained Si1−xGex/Si heterostructures grown by molecular-beam epitaxy was investigated. Alloy structures with Ge fractions between 5% and 23% and thicknesses from 160 to 200 nm, corresponding to excess stress from 112 to 712 MPa, were grown at 450 °C. X-ray high-resolution reciprocal lattice mapping (HRRLM) was employed as the major analysis tool to investigate the status of the strain and the material quality of the structures prior to and after high-temperature furnace annealing between 700 and 1000 °C. By this technique, the variations of the alloy lattice parameters parallel and perpendicular to the growth direction were independently determined as functions of the annealing temperature (Ta) within an accuracy ≊10−5. In addition, the annealing-induced variations in the shape of the x-ray scattering distributions were used to investigate the material quality and the changes in the mosaic character of the structures. For 700≤Ta≤800 °C, a strong increase in the strain relaxation with an activation energy of (2.3±0.2) eV was observed. The relaxation dependence on the excess stress was determined to follow a power of (1.9±0.2) law. In addition, strong broadening of the diffraction peaks was observed in the direction orthogonal to the scattering vector, demonstrating that the formation of strain-relieving dislocations introduces significant mosaicity in the structures.
At Ta≳800 °C, the levels of strain relaxation and mosaicity were found to be high, but the rate of increase was clearly reduced. The contribution to this effect owing to the dislocation–dislocation interaction was evaluated and was shown to be an important mechanism in limiting the maximum attainable relaxation in the structures. Effects of Ge diffusion were estimated and were shown to be relevant at Ta=1000 °C. The relaxation was significantly higher for structures with a higher Ge fraction but, in a structure with 5.67% Ge, a low-intensity diffuse scattering probably related to local strain fields from the initial stages of relaxation and dislocation formation, was observed. The use of HRRLM in the characterization of this important heterostructure system appeared to be appropriate not only for providing an accurate determination of lattice parameter variations as a function of Ta but, in addition, for differentiating between the effects of strain character and those of defect-related contributions to Bragg reflections.
Metrology package for electron beam exposure tool evaluation: Application to EBES4
Authors: Kung E.H. , Kostelak R. L. , Biddick C. J. , Vaidya S. 
Published: July 2002

Throughout the stages of electron beam (e-beam) exposure tool development and application, the machine performance needs to be accurately characterized. A series of tests have been developed and implemented to diagnose and optimize the AT&T in-house EBES4 system for both mask making and direct wafer writing. The techniques employed for these tests will be described, and the evaluation results and how they lend themselves to machine diagnostics will be illustrated for EBES4.
The tests consist of a complement of optical inspection, scanning electron microscopy (SEM) imaging, MARKET analysis, and electrical probe metrology. Optical and SEM techniques served to examine the machine writing characteristics and exposure pattern quality. Partially developed images in positive resists accentuated errors due to improper exposure. Electrical probe metrology was used to quantify and optimize machine accuracy. Compared to conventional optical and SEM measurement techniques, electrical metrology offers the advantages of higher throughput, superior resolution and sensitivity, much better accuracy and precision, and abundant statistics. The standard manufacturing electron beam exposure system (MEBES) MARKET program was utilized to measure pattern misplacement due to intrafield and interfield distortions. The magnitude of stripe shear and butting errors was quantified by electrical linewidth measurement. The 256 μm stripe butting error on EBES4 has a mean value of 0.011 μm and 3 σ of 0.066 μm. Employing simple electrical testers such as box-in-box and bridge resistors, EBES4 demonstrated pattern placement precision of 0.069 and 0.066 μm, ‘‘‖mean‖+3σ,’’ in the x and y directions, respectively. Aligning globally to zero-level fiducial marks, machine level to level registration capability for direct writing was determined to be 0.093 and 0.110 μm, ‖mean‖+3σ, in the x and y directions, respectively. Again, with the aid of electrical testers, linewidth control across a 90 mm square writing area at 20 kV on EBES4 was measured to be 0.027 μm (3σ) for 0.375 μm isolated features. Such machine evaluation data can be used to prove-in system specifications, and can be fed back to both the machine designers and the users for system optimization and integrated circuits design rule development, respectively.
Axial radio frequency electric field intensity and ion density during low to high mode transition in argon electron cyclotron resonance discharges
Authors: Carl D. A. , Williamson M. C. , Lieberman M. A. , Lichtenberg A. J. 
Published: July 2002

To investigate the transition from the low density mode to the high density mode in an electron cyclotron resonance (ECR) discharge, a Langmuir probe and an E field probe were used to measure ion density and E field intensity as functions of axial position and power. The experiments were performed in argon at 0.13 Pa in a 7.9 cm diam cyclindrical source chamber propagating TE11 mode 2.45 GHz microwave power. Low mode was characterized by a standing wave throughout the plasma chamber and minimal power absorption. High mode exhibited nearly complete power absorption and no standing wave past the ECR zone. A sliding short (ss) was used to determine if the position of an E field null in the source chamber affected the transition between these two modes for various magnetic field configurations. The ss position had little effect on mode transition, relative power absorption or ion density when positioned downstream from a broad, large volume resonance zone (resonance near the mirror midplane). However, the plasma could not be ignited if the short was placed at or upstream from the large volume resonance zone.
If the magnetic field was adjusted to yield a sharp, small volume resonance zone (resonance midway between the midplane and the throat), then positioning the ss to force an E field null at the resonance zone would prevent plasma ignition, even at 800 W forward power. The ion density exhibited a hysteresis (i.e., a direct jump from no plasma to a plasma density observed at other sliding short positions for that same forward power, thereafter following the ion density versus forward power dependence observed at nearby ss positions) on power cycling when the sliding short was within ∼1 cm of the broad resonance zone or within ∼1 cm of forcing a null in the sharp resonance zone caes. The ion density versus power curve for the broad volume case exhibited a change in slope over the transition region (Pforward ≊40 W) when the ion density at the resonance zone was ≊1×1011 cm−3. For the narrow zone cases, a region of bistability (i.e., rapid plasma density fluctuations between low and high mode with little or no change in external input power) was observed for which the ion density fluctuated between a value near 5×1010 cm−3 in low mode and 5×1011 cm−3 in high mode. Similar transitions were observed in a 14.6 cm diam ECR source with a TM01 mode, indicating that the effect is not solely dependent on the microwave field structure in the ECR chamber.
Mechanisms of Artemisinin Resistance in the Rodent Malaria Pathogen
Plasmodium yoelii
Authors: Walker Daniel J. , Pitsch Jessica L. , Peng Michael M. , Robinson Brian L. , Peters Wallace , Bhisutthibhan Jamaree , Meshnick Steven R. 
Published: July 2002

ABSTRACT

Artemisinin and its derivatives are important new antimalarials which are now used widely in Southeast Asia. Clinically relevant artemisinin resistance has not yet been reported but is likely to occur. In order to understand how the malaria parasite might become resistant to this drug, we studied artemisinin resistance in the murine malaria parasite
Plasmodium yoelii
. The artemisinin-resistant strain (ART), which is approximately fourfold less sensitive to artemisinin than the sensitive NS strain, accumulated 43% less radiolabeled drug in vitro (
P
< 0.01). Within the parasite, the drug appeared to react with the same parasite proteins in both strains. The translationally controlled tumor protein, one of the artemisinin target proteins, did not differ between the strains. No DNA sequence difference was found, but the resistant strain was found to express 2.5-fold-more protein than the sensitive strain (
P
< 0.01). Thus, the phenotype of artemisinin resistance in
P. yoelii
appears to be multifactorial.
Tolerance and Pharmacokinetic Interactions of Rifabutin and Azithromycin
Authors: Hafner Richard , Bethel James , Standiford Harold C. , Follansbee Stephen , Cohn David L. , Polk Ronald E. , Mole Larry , Raasch Ralph , Kumar Princy , Mushatt David , Drusano George 
Published: July 2002

ABSTRACTThis multicenter study evaluated the tolerance and potential pharmacokinetic interactions between azithromycin and rifabutin in volunteers with or without human immunodeficiency virus infection. Daily dosing with the combination of azithromycin and rifabutin was poorly tolerated, primarily because of gastrointestinal symptoms and neutropenia. No significant pharmacokinetic interactions were found between these drugs.
Correlation between Antifungal Susceptibilities of
Coccidioides immitis
In Vitro and Antifungal Treatment with Caspofungin in a Mouse Model
Authors: González Gloria M. , Tijerina Rolando , Najvar Laura K. , Bocanegra Rosie , Luther Michael , Rinaldi Michael G. , Graybill John R. 
Published: July 2002

ABSTRACT

Caspofungin (Merck Pharmaceuticals) was tested in vitro against 25 clinical isolates of
Coccidoides immitis.
In vitro susceptibility testing was performed in accordance with the National Committee for Clinical Laboratory Standards document M38-P guidelines. Two
C. immitis
isolates for which the caspofungin MICs were different were selected for determination of the minimum effective concentration (MEC), and these same strains were used for animal studies. Survival and tissue burdens of the spleens, livers, and lungs were used as antifungal response markers. Mice infected with strain 98-449 (48-h MIC, 8 μg/ml; 48-h MEC, 0.125 μg/ml) showed 100% survival to day 50 when treated with caspofungin at ≥1 mg/kg. Mice infected with strain 98-571 (48-h MIC, 64 μg/ml; 48-h MEC, 0.125 μg/ml) displayed ≥80% survival when the treatment was caspofungin at ≥5 mg/kg. Treatment with caspofungin at 0.5, 1, 5, or 10 mg/kg was effective in reducing the tissue fungal burdens of mice infected with either isolate. When tissue fungal burden study results were compared between strains, caspofungin showed no statistically significant difference in efficacy in the organs of the mice treated with both strains. A better in vitro-in vivo correlation was noted when we used the MEC instead of the MIC as the endpoint for antifungal susceptibility testing. Caspofungin may have a role in the treatment of coccidioidomycosis.
Isolation and Characterization of a New Denitrifying Spirillum Capable of Anaerobic Degradation of Phenol
Authors: Shinoda Yoshifumi , Sakai Yasuyoshi , Ué Makiko , Hiraishi Akira , Kato Nobuo 
Published: July 2002

ABSTRACT

Two kinds of phenol-degrading denitrifying bacteria,
Azoarcus
sp. strain CC-11 and spiral bacterial strain CC-26, were isolated from the same enrichment culture after 1 and 3 years of incubation, respectively. Both strains required ferrous ions for growth, but strain CC-26 grew better than strain CC-11 grew under iron-limited conditions, which may have resulted in the observed change in the phenol-degrading bacteria during the enrichment process. Strain CC-26 grew on phenol, benzoate, and other aromatic compounds under denitrifying conditions. Phylogenetic analysis of 16S ribosomal DNA sequences revealed that this strain is most closely related to a
Magnetospirillum
sp., a member of the α subclass of the class
Proteobacteria
, and is the first strain of a denitrifying aromatic compound-degrading bacterium belonging to this group. Unlike previously described
Magnetospirillum
strains, however, this strain did not exhibit magnetotaxis. It grew on phenol only under denitrifying conditions. Other substrates, such as acetate, supported aerobic growth, and the strain exhibited microaerophilic features.
Secretion of Recombinant Proteins via the Chaperone/Usher Pathway in
Escherichia coli
Authors: Zavialov Anton V. , Batchikova Natalia V. , Korpela Timo , Petrovskaya Lada E. , Korobko Vyacheslav G. , Kersley Joanne , MacIntyre Sheila , Zav'yalov Vladimir P. 
Published: July 2002

ABSTRACT

F1 antigen (Caf1) of
Yersinia pestis
is assembled via the Caf1M chaperone/Caf1A usher pathway. We investigated the ability of this assembly system to facilitate secretion of full-length heterologous proteins fused to the Caf1 subunit in
Escherichia coli
. Despite correct processing of a chimeric protein composed of a modified Caf1 signal peptide, mature human interleukin-1β (hIL-1β), and mature Caf1, the processed product (hIL-1β:Caf1) remained insoluble. Coexpression of this chimera with a functional Caf1M chaperone led to the accumulation of soluble hIL-1β:Caf1 in the periplasm. Soluble hIL-1β:Caf1 reacted with monoclonal antibodies directed against structural epitopes of hIL-1β. The results indicate that Caf1M-induced release of hIL-1β:Caf1 from the inner membrane promotes folding of the hIL-1β domain. Similar results were obtained with the fusion of Caf1 to hIL-1β receptor antagonist or to human granulocyte-macrophage colony-stimulating factor. Following coexpression of the hIL-1β:Caf1 precursor with both the Caf1M chaperone and Caf1A outer membrane protein, hIL-1β:Caf1 could be detected on the cell surface of
E. coli
. These results demonstrate for the first time the potential application of the chaperone/usher secretion pathway in the transport of subunits with large heterogeneous N-terminal fusions. This represents a novel means for the delivery of correctly folded heterologous proteins to the periplasm and cell surface as either polymers or cleavable monomeric domains.