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Biomedical subjects

R M Levy

Publications and source records attributed to R M Levy.

At least 37 records · Page 2Linked to original sources
PubMed1998

Predictive factors for prolonged survival in acquired immunodeficiency syndrome-associated progressive multifocal leukoencephalopathy.

Progressive multifocal leukoencephalopathy (PML) complicating the acquired immunodeficiency syndrome (AIDS) is typically inexorably progressive with death usually occurring within 6 months of symptom onset. Occasional patients have been observed to survive longer than 1 year, often with remission of clinical features. In this study, we identify predictive factors for prolonged survival in patients with biopsy proven, AIDS-associated PML, by comparing 7 patients with survival exceeding 12 months from symptom onset with 45 patients with shorter survivals. PML was the presenting manifestation of AIDS in 5 (71.4%) of 7 long-term survivors compared with 8 (17.8%) of 45 short-term survivors. CD4 T-lymphocyte counts were substantially higher in the long-term survivors, with 3 (42.9%) of 7 having counts exceeding 300 cells/mm3 in comparison with only 1 (4.3%) of 23 short-term survivors. Contrast enhancement on radiographic imaging was observed in 3 (50%) of 6 long-term survivors in comparison with 4 (8.9%) of 45 short-term survivors. Neurological recovery and radiographic improvement were not observed in any short-term survivors but were seen in 5 (71.4%) long-term survivors. There was no association between treatment modalities and survival. Predictors of long-term survival in AIDS patients with PML include PML as the heralding manifestation of AIDS, high CD4 T-lymphocyte count at disease onset, lesion enhancement on computed tomographic scan or magnetic resonance imaging, and evidence of recovery of neurological function.

AIDS-Associated Nephropathy↗
PubMed1998

Protein hydration and unfolding--insights from experimental partial specific volumes and unfolded protein models.

BACKGROUND: The partial specific volume of a protein is an experimental quantity containing information about solute-solvent interactions and protein hydration. We use a hydration-shell model to partition the partial specific volume into an intrinsic volume occupied by the protein and a change in the volume occupied by the solvent resulting from the solvent interactions with the protein. We seek to extract microscopic information about protein hydration and unfolding from experimental volume measurements without using computer simulations. We employ the idea that the protein-solvent interaction will be proportional to the surface area of the protein. RESULTS: A linear relationship is obtained when the difference between the experimental protein partial specific volume and its intrinsic volume is plotted as a function of the protein solvent-accessible surface area. The effect of using different protein volume definitions on the analysis of protein volumetric properties is discussed. Volumetric data are used to test a model for the unfolded state of proteins and to make predictions about the denatured state. CONCLUSIONS: The linear relationship between hydration-shell volume change and accessible surface area reflects the similar surface properties (fractional composition of nonpolar, polar and charged surface) among a diverse set of proteins. This linear relationship is found to be independent of how the solution is partitioned into solute and solvent components. The interpretation of hydration shell versus bulk water properties is found to be very model dependent, however. The maximally exposed unfolded protein model is found to be inconsistent with experimental volume changes of unfolding.

Algorithms↗
PubMed1998

Propagation of experimental uncertainties using the Lipari-Szabo model-free analysis of protein dynamics.

In this paper we make use of the graphical procedure previously described [Jin, D. et al. (1997) J. Am. Chem. Soc., 119, 6923-6924] to analyze NMR relaxation data using the Lipari-Szabo model-free formalism. The graphical approach is advantageous in that it allows the direct visualization of the experimental uncertainties in the motional parameter space. Some general 'rules' describing the relationship between the precision of the relaxation measurements and the precision of the model-free parameters and how this relationship changes with the overall tumbling time (tau m) are summarized. The effect of the precision in the relaxation measurements on the detection of internal motions not close to the extreme narrowing limit is analyzed. We also show that multiple timescale internal motions may be obscured by experimental uncertainty, and that the collection of relaxation data at very high field strength can improve the ability to detect such deviations from the simple Lipari-Szabo model.

Models, Theoretical↗
PubMed1998

Tertiary contacts in alpha-lactalbumin at pH 7 and pH 2: a molecular dynamics study.

Molecular dynamics simulations of alpha-lactalbumin were performed under conditions of neutral pH and low pH in order to study the acid-induced molten globule state. Through the use of experimental techniques such as NMR and CD spectroscopy, molten globules have been characterized as being compact intermediates with secondary structure similar to that of the native protein but with tertiary structure that is disordered. The detailed structure of the molten globule state is unknown, however. Through the use of computer simulations we can study the structural changes which occur upon lowering pH. The simulations presented here differ from previous unfolding simulations in two important ways: the electrostatic interactions are treated more accurately than ever before, and artificially high temperatures are not used to force the protein to unfold. Simulations of 880 psec each were run at pH 7 (control simulation) and pH 2. We concentrate on the interesting changes in the tertiary interactions within the protein with lowering of pH. In particular, there is a loss of native tertiary contacts in the beta domain and interdomain region, and a large decrease in interdomain hydrogen bonds.

Computer Simulation↗
PubMed1998

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

This review focuses on recent progress in two areas in which computer simulations with explicit solvent are being applied: the thermodynamic decomposition of free energies, and modeling electrostatic effects. The computationally intensive nature of these simulations has been an obstacle to the systematic study of many problems in solvation thermodynamics, such as the decomposition of solvation and ligand binding free energies into component enthalpies and entropies. With the revolution in computer power continuing, these problems are ripe for study but require the judicious choice of algorithms and approximations. We provide a critical evaluation of several numerical approaches to the thermodynamic decomposition of free energies and summarize applications in the current literature. Progress in computer simulations with explicit solvent of charge perturbations in biomolecules was slow in the early 1990s because of the widespread use of truncated Coulomb potentials in these simulations, among other factors. Development of the sophisticated technology described in this review to handle the long-range electrostatic interactions has increased the predictive power of these simulations to the point where comparisons between explicit and continuum solvent models can reveal differences that have their true physical origin in the inherent molecularity of the surrounding medium.

Computer Simulation↗
PubMed1997

Quantitative, crossover, double-blind trial paradigm for patient screening for chronic intraspinal narcotic administration.

Careful preoperative screening of candidates for indwelling drug administration systems for the relief of intractable pain can help to exclude patients who will not benefit from this technology and predict efficacy in others. Unfortunately, bias on the part of both the treating physician and the patient can inappropriately skew the results of subjective or improperly controlled trials and lead to the implantation of drug administration systems in patients who will not benefit from chronic intrathecal narcotic administration. The author and his coworkers have designed a quantitative, crossover, double-blind paradigm for screening patients who might otherwise be deemed eligible for chronic intraspinal narcotic administration. This paradigm has been used 31 times in 30 patients; based on the outcome of this testing, 22 patients (73%) underwent implantation of chronic infusion systems. Sixteen (80%) of 20 patients with pain related to cancer underwent pump implantation, whereas only six (60%) of the 10 patients with pain of nonmalignant origin were so treated. Sixteen of the patients (72%) have reported good to excellent relief after pump implantation; this includes 12 (75%) of the 16 patients with pain related to cancer and four (66%) of the six patients with pain of nonmalignant origin. This screening paradigm thus appears to be both reliable and easily applied and promises to be of assistance in the selection of patients appropriate for this mode of therapy.

Journal Article↗
PubMed1997

Radiofrequency trigeminal rhizolysis for the treatment of trigeminal neuralgia secondary to brainstem infarction. Report of two cases.

Although percutaneous radiofrequency trigeminal rhizolysis (RFL) has been used to treat idiopathic trigeminal neuralgia thought secondary to multiple sclerosis, the use of RFL for trigeminal neuralgia caused by brainstem infarction has not been advocated. The authors report two patients with trigeminal neuralgia following pontine infarction in whom aggressive medical management failed, but who were successfully treated with RFL. Pain relief has persisted for the 3- and 6-year duration of follow-up examinations. Descending trigeminal reticular fibers may be affected by brainstem infarction and result in trigeminal neuralgia; thus, treatment by rhizotomy may be effective in decreasing the peripheral afferent input into the spinal trigeminal nucleus thus decreasing the pain. These two cases demonstrate the utility of RFL in the relief of ischemia-induced trigeminal neuralgia and lead the authors to suggest that its use be broadened to include this indication.

Journal Article↗
PubMed1997

Estimating articulation scores.

The ability of listeners to estimate articulation scores for lists of nonsense syllables was evaluated. Normal-hearing subjects were presented with lists of from 50 to 60 nonsense syllables that were degraded with various amounts of noise or filtering and were instructed to estimate consonant-correct scores for each condition. To provide a reference for estimating, subjects were shown the accurate orthographic representation of the syllable on a computer monitor to compare with the auditory presentation. The printed version was displayed either simultaneously with the auditory presentation or 500 ms after the offset of the syllable. Estimates were collected on two occasions to examine test-retest reliability, and actual percent-correct scores were obtained to check the accuracy of the estimates. Most subjects overestimated actual scores when the printed representation was provided simultaneously, but estimates were strikingly similar to actual scores when the printed representation was delayed. The delay appeared to prevent the printed representation from favorably biasing the reception of the syllable. The average of two or three estimates gave highly repeatable results for both visual displays. Crossover frequencies derived from the filtered-speech conditions were within the range reported in the literature. This supports the conclusion that subjects based their estimates on the recognition of speech sounds rather than other percepts associated with the speech-in-noise conditions such as loudness of the noise. The estimation procedure permits the collection of articulation scores in much less time than required by traditional test procedures.

Adult↗
PubMed1997

The entry of antiviral and antiretroviral drugs into the central nervous system.

The ability of antiviral and antiretroviral drugs to enter the brain is a critical issue in the treatment of many viral brain diseases, including HIV-related neurologic disease. Much of the literature concerning nucleoside analog entry into the nervous system focuses on drug levels in the cerebrospinal fluid (CSF), equating these with drug levels in the brain extracellular fluid (ECF) as though the two compartments intermix freely. We review the anatomic and physiologic aspects of drug entry into CSF and into brain ECF, as well as the exchange processes between these two compartments. In most instances drug concentrations in the CSF and ECF compartments bear little relationship to one another and using CSF concentrations to extrapolate brain ECF concentrations may significantly overestimate the latter. Accepted terminology and methodology for making measurements of blood-brain barrier function are discussed. Studies of brain uptake that express results as brain:plasma ratios, or that have used microdialysis, may overestimate the amount of drug reaching the brain. Using published data, we present an estimate of the time course of Zidovudine (AZT) concentrations in brain ECF and show that brain concentrations of AZT will likely be below that necessary to inhibit HIV-1 replication when AZT is administered systemically. Antiviral nucleosides and oligonucleotides appear to have limited entry into the brain when given systemically, which may hinder therapy of viral brain diseases, while some of the protease inhibitors may enter the brain more readily. Alternative methods for increasing antiviral and antiretroviral drug delivery to brain are discussed.

Anti-HIV Agents↗
PubMed1997

HIV-1-related neurologic disorders. Neurosurgical implications.

It has become important for clinicians to increase their understanding of the breadth, mechanism, and neurosurgical implications of viral illnesses of the central nervous system. These needs can now be more safely and accurately addressed using stereotactic neurosurgical techniques. This article provides an introduction to these disease and identifies the neurosurgical issues that may be raised in their diagnosis and treatment.

AIDS Dementia Complex↗
PubMed1996

Cytomorphology of progressive multifocal leukoencephalopathy (PML): review of sixteen cases occurring in HIV-positive patients.

Progressive multifocal leukoencephalopathy (PML) is a fatal demyelinating disorder of the central nervous system (CNS) resulting from infection of oligodendrocytes by JC virus. Although all patients immunocompromised by any congenital, acquired, or iatrogenic condition are at risk, the population which currently accounts for the majority of new cases is that infected with the human immunodeficiency virus (HIV). Though the clinical/radiologic presentation is characteristic, biopsy confirmation is necessary, as these patients are at risk for other primary CNS disorders which may produce similar clinical findings. Immediate assessment of tissue adequacy by cytologic smear is generally preferred in these specimens due to its relative reduced risk of disease transmission when compared to conventional frozen section. We report here the cytologic findings seen in touch imprints and squash preparations of 16 cases of PML, all occurring in HIV-positive patients and obtained by stereotactic guided needle biopsy. Typical cytomorphologic findings are described and correlated with histologic sections. In addition, features useful in the exclusion of other differential diagnostic possibilities are discussed.

Adult↗
PubMed1996

Cytomorphology of primary CNS lymphoma: review of 23 cases and evidence for the role of EBV.

Primary non-Hodgkin's lymphoma of the central nervous system (PCNSL) has recently increased in incidence, due primarily to an enlarging immunosuppressed patient population. The pathogenetic role of Epstein-Barr virus (EBV) is of interest due to its established role in other lymphoproliferative disorders in immunosuppressed patients. Twenty-three cases of histologically confirmed PCNSL with corresponding cytology were identified, all obtained under stereotactic guidance. Twenty patients were human immunodeficiency virus (HIV) positive, two were HIV negative, and one was of unknown status. Papanicolaou-stained slides were selected from each case and evaluated for the presence of EBV RNA via in situ hybridization (ISH) utilizing a biotinylated probe specific for EBER 1 RNA, and detected by a conventional streptavidin-peroxidase system. The cases included immunoblastic (12), large cell (10), and mixed small and large cell lymphoma (1). The predominant immunophenotype was B-cell (19), although T-cell (2) and biphenotypic (1) cases were also identified. ISH showed nuclear positivity for EBV RNA in 19 of 23 cases (83%). This study confirms the presence of EBV in PCNSL in immunosuppressed patients and implies a potential etiologic role. The ability to demonstrate EBV RNA in cytologic preparations by ISH also raises the possibility of early identification of high-risk patients through detection of EBV-infected lymphocytes in CSF specimens.

Adult↗
PubMed1995

A relaxation-matrix analysis of distance-constraint ranges for NOEs in proteins at long mixing times.

Long-mixing-time data (tau m > 200 ms) from NOE spectra have largely been ignored as a source of protein structural information due to the effects of spin diffusion on calculated interproton distances when using the two-spin approximation. An effective approach for incorporating spin-diffusion effects in an average way into refinements is to choose distance bounds based on distributions of distances observed in NOE back calculations on homologous proteins from a protein structure database. We have determined distributions of interproton distances characteristic of newly observed NOE cross peaks for the proteins crambin, PTI, and echistatin at long mixing times. A relaxation-matrix analysis was used to model the effects of spin diffusion. Constraint ranges were constructed from the interproton distance distributions which can be used in standard protein-refinement programs based on the two-spin approximation. Back calculations are also used to analyze constraint ranges typically used for protein structure determinations based on NOE spectra at shorter mixing times.

Electron Spin Resonance Spectroscopy↗
PubMed1995

Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-alpha transforming growth factor.

Order parameters for the backbone N-H and C alpha-H bond vectors have been calculated from a 150 ps molecular dynamics (MD) simulation of human type-alpha transforming growth factor in H2O solvent. Two kinds of 'crankshaft motions' of the polypeptide backbone are observed in this MD trajectory. The first involves small-amplitude rocking of the rigid peptide bond due to correlated changes in the backbone dihedral angles psi i-1 and phi i. These high-frequency 'librational crankshaft' motions are correlated with systematically smaller values of motional order parameters for backbone N-H bond vectors compared to C alpha-H bond vectors. In addition, infrequent 'crankshaft flips' of the peptide bond from one local minimum to another are observed for several amino acid residues. These MD simulations demonstrate that comparisons of N-H and C alpha-H order parameters provide a useful approach for identifying crankshaft librational motions in proteins.

Amino Acid Sequence↗
PubMed1995

A comparison of intrathecally administered narcotic and nonnarcotic analgesics for experimental chronic neuropathic pain.

The antinociceptive actions of morphine and tizanidine (an alpha 2-adrenergic agonist) administered intrathecally in a rat model of mononeuropathic pain were investigated. Tizanidine increased to normal levels the intensity of a noxious pressure stimulus required to induce paw withdrawal (p < 0.01) and decreased the duration of limb withdrawal from both normal-temperature and cooled floors in a dose-dependent manner (p < 0.01). Tizanidine had virtually no effect on the latency of paw withdrawal from a noxious heat stimulus. In comparison, morphine significantly decreased, in a dose-dependent manner, limb withdrawal from the normal-temperature and cooled floors and increased to cutoff values the withdrawal latencies of both noxious heat and pressure stimuli (p < 0.01). The effect of tizanidine was limited to the hyperalgesic limb and served to normalize reactive latencies, whereas morphine affected both hindlimbs and increased latencies to supranormal cutoff values. These data suggest that intrathecal tizanidine may be more specific than morphine in reversing the allodynia and hyperpathia associated with neuropathic pain states and may be of value in the management of patients with these clinical syndromes.

Analgesics↗
PubMed1994

Intrinsic pKas of ionizable residues in proteins: an explicit solvent calculation for lysozyme.

Molecular dynamics simulations of triclinic hen egg white lysozyme in aqueous solution were performed to calculate the intrinsic pKas of 14 ionizable residues. An all-atom model was used for both solvent and solute, and a single 180 ps simulation in conjunction with a Gaussian fluctuation analysis method was used. An advantage of the Gaussian fluctuation method is that it only requires a single simulation of the system in a reference state to calculate all the pKas in the protein, in contrast to multiple simulations for the free energy perturbation method. pKint shifts with respect to reference titratable residues were evaluated and compared to results obtained using a finite difference Poisson-Boltzmann (FDPB) method with a continuum solvent model; overall agreement with the direction of the shifts was generally observed, though the magnitude of the shifts was typically larger with the explicit solvent model. The contribution of the first solvation shell to the total charging free energies of the titratable groups was explicitly evaluated and found to be significant. Dielectric shielding between pairs of titratable groups was examined and found to be smaller than expected. The effect of the approximations used to treat the long-range interactions on the pKint shifts is discussed.

Amino Acids↗
PubMed1994

Three-dimensional structure of echistatin and dynamics of the active site.

The snake venom protein echistatin contains the cell recognition sequence Arg-Gly-Asp and is a potent inhibitor of platelet aggregation. The three-dimensional structure of echistatin and the dynamics of the active RGD site are presented. A set of structures was determined using the Distance Geometry method and subsequently refined by Molecular Dynamics and energy minimization. Disulfide pairings are suggested, based on violations of experimental constraints. The structures satisfy 230 interresidue distance constraints, derived from nuclear Overhauser effect measurements, five hydrogen-bonding constraints, and 21 torsional constraints from vicinal spin-spin coupling constants. The segment from Gly5 to Cys20 and from Asp30 to Asn42 has a well-defined conformation and the Arg-Gly-Asp sequence, which adopts a turn-like structure, is located at the apex of a nine-residue loop connecting the two strands of a distorted beta-sheet. The mobility of the Arg-Gly-Asp site has been quantitatively characterized by 15N relaxation measurements. The overall correlation time of echistatin was determined from fluorescence measurements, and was used in a model-free analysis to determine internal motional parameters. The active site has order parameters of 0.3-0.5, i.e., among the smallest values ever observed at the active site of a protein. Correlation of the flexible region of the protein as characterized by relaxation experiments and the NMR solution structures was made by calculating generalized order parameters from the ensemble of three-dimensional structures. The motion of the RGD site detected experimentally is more extensive than a simple RGD loop 'wagging' motional model, suggested by an examination of superposed solution structures.

Amino Acid Sequence↗