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  • 1
    ISSN: 0948-5023
    Keywords: HIV-1 reverse transcriptase ; Minor groove binding track ; Particle-mesh Ewald
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract We have built a molecular dynamics model for human immunodeficiency virus (HIV-1) reverse transcriptase (RT) complexed with a 19/18-mer template/primer by combining the structural information of a low resolution crystal structure of a HIV-1 RT/DNA complex (1hmi) with that of a high resolution crystal structure of unliganded HIV-1 RT (1rtj). The process involved slow forcing of the α-carbons of 1rtj onto those of 1hmi using constrained MD simulations, while immersing the protein in aqueous solution. A similar technique was used to build the bent all-atom DNA duplex, which was then docked into the modeled protein. The resulting model complex was refined using molecular dynamics simulation with the Particle-mesh Ewald method employed to accommodate long-range electrostatic interactions. New parameters of the Amber force field that affect DNA twist are tested and largely validated. The model has been used successfully to explain the results of vertical scanning mutagenesis of residue 266 (Trp266). Recently, the low resolution crystal structure of the HIV-1 RT/DNA complex has been refined to a 2.8 Å resolution (2hmi) and a crystal structure of a HIV-1/RT/dTTP ternary complex has been determined at 3.2 Å resolution (1rtd). A detailed structural comparison of the prior model structure and the two experimental structures becomes possible. Overall, the three structures share many similarities. The root mean square deviations of the α-carbons for the individual subdomains among the three structures are within the same ranges. The secondary structure assignments in the three structures are nearly identical. Key protein-DNA contacts such as those in the region of the primer grip are also similar in the three structures.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Boston, USA and Oxford, UK : Blackwell Publishers Inc.
    Risk analysis 20 (2000), S. 0 
    ISSN: 1539-6924
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Notes: Driven by differing statutory mandates and programmatic separation of regulatory responsibilities between federal, state, and tribal agencies, distinct chemical and radiation risk management strategies have evolved. In the field this separation poses real challenges since many of the major environmental risk management decisions we face today require the evaluation of both types of risks. Over the last decade, federal, state, and tribal agencies have continued to discuss their different approaches and explore areas where their activities could be harmonized. The current framework for managing public exposures to chemical carcinogens has been referred to as a ‘bottom up approach.’ Risk between 10−4 and 10−6 is established as an upper bound goal. In contrast, a ‘top down’ approach that sets an upper bound dose limit and couples with site specific As Low As Reasonably Achievable Principle (ALARA), is in place to manage individual exposure to radiation. While radiation risk are typically managed on a cumulative basis, exposure to chemicals is generally managed on a chemical-by-chemical, medium-by-medium basis. There are also differences in the nature and size of sites where chemical and radiation contamination is found. Such differences result in divergent management concerns. In spite of these differences, there are several common and practical concerns among radiation and chemical risk managers. They include 1) the issue of cost for site redevelopment and long-term stewardship, 2) public acceptance and involvement, and 3) the need for flexible risk management framework to address the first two issues. This article attempts to synthesize key differences, opportunities for harmonization, and challenges ahead.
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1524-475X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: We have previously shown that positively charged beads (DEAE A25) increase wound breaking strength in linear incisions in rats and nonhuman primates at days 10–14 post-wounding. The increased wound strength may result in part from a stimulation of cells adjacent to the DEAE A25 beads to produce growth factors important for wound healing. In this report, we investigate this hypothesis by comparing the relative expression levels of transforming growth factor-β1 and its receptor transforming growth factor-β receptor type I in DEAE A25-treated and contralateral untreated rat linear incisions. DEAE A25-treated incisions were stronger than untreated control wounds at 3 days post-wounding, and the difference in breaking strength reached statistical significance at days 5, 7 and 10. Immunohistochemical analysis revealed a significant increase in transforming growth factor-β1 and transforming growth factor-β receptor type I expression in DEAE A25-treated incisions, up to 7 days post-wounding, as compared to untreated control wounds. FACS analysis revealed that macrophage cell lines exposed to DEAE A25 in vitro upregulate transforming growth factor-β1 and transforming growth factor-β receptor type I expression by 2–3 fold. Therefore, the increase in expression of transforming growth factor-β1 and transforming growth factor-β receptor type I in DEAE A25-treated incisions may be due to an increase in the concentration of macrophages adjacent to DEAE A25 beads, as well as the stimulation of individual macrophages to produce greater amounts of transforming growth factor-β1 and transforming growth factor-β receptor type I. This study also supports the significance of transforming growth factor-β1 in wound healing.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Clinical psychology 7 (2000), S. 0 
    ISSN: 1468-2850
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Psychology
    Notes: Scheel's critique (this issue) of the empirical support for dialectical behavior therapy (DBT) should be of considerable benefit to DBT research. Too often in the history of clinical psychology there has been an excessive embracing of a particular clinical perspective. Scheel's critique is at times itself excessive, but the need for dismantling research to pinpoint the most effective and necessary features of DBT is well established. Nevertheless, as Scheel states, “DBT should not be held to a research standard higher than other treatments for the same condition, and at this time it meets and probably exceeds those criteria.”
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 112 (2000), S. 2265-2273 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Quantum mechanical calculations on the vibrational predissociation dynamics of NeBr2 in the B electronic state have been performed and the results compared with both experimental data and other computational studies. For vibrational levels with v≤20 we find that the vibrational state dependence of the predissociation lifetimes is in qualitative agreement with experimental measurements, as are the calculated Br2 fragment rotational distributions. For higher vibrational levels, the B←X excitation profiles are well represented by a sum of two Lorentzian line shapes. We attribute this result to the presence of long-lived resonances in the dissociative continuum that are reminiscent of long-lived dissociative trajectories in previous classical studies of NeBr2. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 113 (2000), S. 707-718 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The rotationally resolved spectrum of a fundamental band of hydrogen fluoride tetramer has been recorded using a pulsed slit-jet, diode laser spectrometer. The band has a parallel rotational structure and is assigned as the H–F out-of-plane libration fundamental with Au symmetry. Ninety-five ground state combination differences were fit to a symmetric top Hamiltonian to give the following ground state rotational constants: B″=0.132 081(7) cm−1, DJ″=7.1(7)×10−7 cm−1, DJK″=−9(2)×10−7 cm−1, HJJJ″=6(2)×10−10 cm−1, HJJK″=9(7)×10−10 cm−1, HJKK″=−1.3(8)×10−10 cm−1. A total of 190 transitions were fit to determine the upper state spectroscopic constants: v4=714.7849(1) cm−1, B′=0.129 634(5) cm−1, Δ(C−B)=0.001 344 cm−1, DJ′=6.4(5)×10−7 cm−1, DJK′=−4.5(6)×10−7 cm−1, ΔDK=2.92(8)×10−6 cm−1, HJJJ′=3(1)×10−10 cm−1, HJKK′=−1.55(6)×10−8 cm−1; ΔHKKK=−4.65(6)×10−8 cm−1. Furthermore, a perpendicular band centered at 752.7 cm−1 was observed. The band has a rotational line spacing that gives an approximate B″ value of 0.132 cm−1; it has been assigned as the Eu symmetry, H–F in-plane libration fundamental of the HF tetramer. Finally, a parallel band was observed at 741.0 cm−1 with B″=0.076 cm−1 and has been assigned as the A″ symmetry, H–F out-of-plane libration fundamental of the HF pentamer. Structural parameters and harmonic vibrational frequencies are estimated from first-principles, correlated MP2 and CCSD(T) calculations. These are the largest calculations performed to date for this system with respect to both orbital basis set and level of electron correlation. The CCSD(T) harmonic frequencies are, in particular, the first reported for the tetramer at this level of theory. Based on our results, we suggest "best estimates" of RFF=2.51 Å, rHF=0.947 Å, and θHFF=9.7° for the structural parameters and a range for De of 27.4 to 28.1 kcal/mol (D0=19.7 to 20.4 kcal/mol) for the parameters and for the energy of the tetramer dissociating into four monomers. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Oxford : Blackwell Science Ltd
    Anaesthesia 55 (2000), S. 0 
    ISSN: 1365-2044
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: We tried to determine if a blood conservation pressure transducer system reduced blood transfusions, increased haemoglobin concentration or reduced line infections in critically ill patients. One hundred patients were randomly allocated to conventional or blood conserving systems attached to systemic and pulmonary arterial catheters. Intravascular lines were cultured after removal. There were no significant differences in transfusions or haemoglobin concentration. Blood conservation: median units transfused, 2 (range 0–19); mean haemoglobin at 7 days, 11.2 g.dl−1 (SD, 1.0). Conventional: median units, 2 (range 0–34); mean haemoglobin at 7 days, 11.1 g.dl−1 (SD 1.0). Thirty-seven of 99 arterial lines were colonised in the controls compared with 29 of 96 in the blood conservation group. Patients who required haemofiltration in both groups had significantly increased transfusion requirements. Haemofiltration: median 6 units (range 0–34) vs. non-haemofiltered: median 1 (range 0–14; p 〈 0.001). There were no significant differences in transfusions, haemoglobin concentration or line colonisation with the blood conservation system. There is considerable potential for blood conservation during haemofiltration.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Science Ltd
    Anaesthesia 55 (2000), S. 0 
    ISSN: 1365-2044
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 69 (2000), S. 497-529 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract DNA replication fidelity is a key determinant of genome stability and is central to the evolution of species and to the origins of human diseases. Here we review our current understanding of replication fidelity, with emphasis on structural and biochemical studies of DNA polymerases that provide new insights into the importance of hydrogen bonding, base pair geometry, and substrate-induced conformational changes to fidelity. These studies also reveal polymerase interactions with the DNA minor groove at and upstream of the active site that influence nucleotide selectivity, the efficiency of exonucleolytic proofreading, and the rate of forming errors via strand misalignments. We highlight common features that are relevant to the fidelity of any DNA synthesis reaction, and consider why fidelity varies depending on the enzymes, the error, and the local sequence environment.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 113 (2000), S. 2263-2269 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The collisional dependence of polarization spectroscopy (PS) with a picosecond-pulse laser is investigated theoretically with a perturbative treatment and experimentally by probing hydroxyl (OH) in a flow cell with a buffer gas of argon. Using a frequency-doubled distributed-feedback dye laser (DFDL), the PS signal strength is monitored as a function of pressure using a nonsaturating pump beam and a saturating pump beam. The collisional dependence of the PS signal is found to decrease significantly with a saturating pump beam. Increasing the flow-cell pressure by a factor of 50 (from 10 torr to 500 torr), the PS signal strength produced with a nonsaturating pump beam decreases by a factor of 18 while that produced with a saturating pump decreases by only a factor of 3. A third-order perturbative (weak-field) approach is used to develop an analytical expression for the PS signal generated by single-mode, exponentially decaying laser pulses. This expression correctly predicts the experimental results acquired with the nonsaturating pump beam. The analytical solution is used to examine the effects of pulse length on the collisional dependence of the weak-field PS signal strength. Results are also presented for a numerical simulation of the time-dependent density matrix equations for the high intensity case. © 2000 American Institute of Physics.
    Type of Medium: Electronic Resource
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