Differentiation of promonocytic U937 subclones into macrophagelike phenotypes regulates a cellular factor(s) which modulates fusion/entry of macrophagetropic human immunodeficiency virus type 1

Monocytes/macrophages (M/M) and CD4+ T cells are two important targets of human immunodeficiency virus (HIV) infection. Different strains of HIV-1 vary markedly in their abilities to infect cells belonging to the M/M lineage. Macrophagetropic (M-tropic) HIV-1 strains replicate well in primary lymphocytes as well as in primary macrophages; however, they generally infect T-cell lines poorly, if at all. Although promonocytic cell lines such as U937 have been used as in vitro models of HIV-1 infection of M/M, these cell lines are susceptible to certain T-cell-tropic (T-tropic) HIV-1 strains but are resistant to M-tropic HIV-1. In this study, we demonstrate that (i) certain U937 clones ("plus" clones), which are susceptible only to T-tropic HIV-1, become highly susceptible to M-tropic HIV-1 upon differentiation with retinoic acid (RA); (ii) other U937 clones ("minus" clones), which are resistant to both T- and M-tropic HIV-1, remain resistant to both viruses; and (iii) RA treatment induces expression of CCR5, a fusion/entry cofactor for M-tropic HIV-1 in both types of U937 clones, and yet enhances the fusogenicity of the plus clones, but not the minus clones, with M-tropic Env's. These results indicate that the major restriction of M-tropic HIV-1 infection in promonocytic cells occurs at the fusion/entry level, that differentiation into macrophage-like phenotypes renders some of these cells highly susceptible to infection with M-tropic HIV-1, and that CD4 and CCR5 may not be the only determinants of fusion/entry of M-tropic HIV-1 in these cells.     

Refining the level for anticipated hepatotoxicity in acetaminophen poisoning

Treatment of an acetaminophen overdose with N-acetyl cysteine usually is based on the position of the 4-h acetaminophen (APAP) level on the Rumack-Matthew nomogram; however, there is disagreement on the level at which clinically relevant hepatotoxicity occurs. A retrospective review of all acute adult formulation APAP exposures reported to our poison center between 1986 and 1993 was performed and cases corresponding to the "possible risk or toxicity" range on the nomogram were identified. Our current poison center protocol for APAP poisoning does not recommend treatment with N-acetylcysteine (NAC) in low-risk patients if the 4-h serum APAP level or the extrapolated equivalent falls within the possible toxicity range on the nomogram. Seventeen cases met the inclusion criteria for the study and received no NAC; six additional patients met inclusion criteria but received one or two doses of NAC before therapy was discontinued. No patients in either group demonstrated clinical evidence of hepatotoxicity. This pilot study suggests that patients with no risk factors and APAP levels in the "possible risk" range may not require NAC therapy.     

Hamstrings and psoas lengths during normal and crouch gait: implications for muscle-tendon surgery

OBJECTIVE: To study the relative contribution of the lung and the chest wall on the total respiratory system mechanics, gas exchange, and work of breathing in sedated-paralyzed normal subjects and morbidly obese patients, in the postoperative period. SETTING: Policlinico Hospital, University of Milan, Italy. METHODS: In ten normal subjects (normal) and ten morbidly obese patients (obese), we partitioned the total respiratory mechanics (rs) into its lung (L) and chest wall (w) components using the esophageal balloon technique together with airway occlusion technique, during constant flow inflation. We measured, after abdominal surgery, static respiratory system compliance (Cst,rs), lung compliance (Cst,L), chest wall compliance (Cst,w), total lung (Rmax,L) and chest wall (Rmax,w) resistance. Rmax,L includes airway (Rmin,L) and "additional" lung resistance (DR,L). DR,L represents the component due to viscoelastic phenomena of the lung tissue and time constant inequalities (pendelluft). Functional residual capacity (FRC) was measured by helium dilution technique. RESULTS: We found that morbidly obese patients compared with normal subjects are characterized by the following: (1) reduced Cst,rs (p < 0.01), due to lower Cst,L (55.3 +/- 15.3 mL x cm H2O-1 vs 106.6 +/- 31.7 mL x cm H2O-1; p < 0.01) and Cst,w (112.4 +/- 47.4 mL x cm H2O-1 vs 190.7 +/- 45.1 mL x cm H2O-1; p < 0.01); (2) increased Rmin,L (4.7 +/- 3.1 mL x cm H2O x L-1 x s; vs 1.0 +/- 0.8 mL x cm H2O x L-1 x s; p < 0.01) and DR,L (4.9 +/- 2.6 mL x cm H2O x L-1 x s; vs 1.5 +/- 0.8 mL x cm H2O x L-1 x s; p < 0.01); (3) reduced FRC (0.665 +/- 0.191 L vs 1.691 +/- 0.325 L; p < 0.01); (4) increased work performed to inflate both the lung (0.91 +/- 0.25 J/L vs 0.34 +/- 0.08 J/L; p < 0.01) and the chest wall (0.39 +/- 0.13 J/L vs 0.18 +/- 0.04 J/L; p < 0.01); and (5) a reduced pulmonary oxygenation index (PaO2/PAO2 ratio). CONCLUSION: Sedated-paralyzed morbidly obese patients, compared with normal subjects, are characterized by marked derangements in lung and chest wall mechanics and reduced lung volume after abdominal surgery. These alterations may account for impaired arterial oxygenation in the postoperative period.     

Classification Based on Hybridization of Parametric and Nonparametric Classifiers

Parametric methods of classification assume specific parametric models for competing population densities (e.g., Gaussian population densities can lead to linear and quadratic discriminant analysis) and they work well when these model assumptions are valid. Violation in one or more of these parametric model assumptions often leads to a poor classifier. On the other hand, nonparametric classifiers (e.g., nearest-neighbor and kernel-based classifiers) are more flexible and free from parametric model assumptions. But, the statistical instability of these classifiers may lead to poor performance when we have small numbers of training sample observations. Nonparametric methods, however, do not use any parametric structure of population densities. Therefore, even when one has some additional information about population densities, that important information is not used to modify the nonparametric classification rule. This paper makes an attempt to overcome these limitations of parametric and nonparametric approaches and combines their strengths to develop some hybrid classification methods. We use some simulated examples and benchmark data sets to examine the performance of these hybrid discriminant analysis tools. Asymptotic results on their misclassification rates have been derived under appropriate regularity conditions.     

On the pH dependence of protein stability

This paper treats the free energy contribution of ionizable groups to protein stability. A method is presented for the calculation of the pH dependence of the denaturation free energy of a protein, which yields results that can be compared directly to experiment. The first step in the treatment is the determination of the average charges of all the ionizable groups in both the folded and unfolded protein. An expression due to Tanford then relates the pH dependence of the unfolding free energy to the difference in net charge between the two states. In order to determine absolute rather than relative unfolding free energies, it is necessary to calculate the total contribution of ionizable groups to protein stability at some reference pH. This is accomplished through a statistical mechanical treatment similar to the one used previously in the calculation of pKas. The treatment itself is rigorous but it suffers from uncertainties in the pKa calculations. Nevertheless, the overall shape of experimentally observed plots of denaturation free energy as a function of pH are reasonably well reproduced by the calculations. A number of general conclusions that arise from the analysis are: (1) knowledge of titration curves and/or effective pKa values of ionizable groups in proteins is sufficient to calculate the pH dependence of the denaturation free energy with respect to some reference pH value. However, in order to calculate the absolute contribution of ionizable groups to protein stability, it is necessary to also know the intrinsic pKa of each group. This is defined as the pKa of a group in a hypothetical state of the protein where all other groups are neutral. (2) Due to desolvation effects, ionizable groups destabilize proteins, although the effect is strongly dependent on pH. There are however, strongly stabilizing pairwise Coulombic interactions on the surface of proteins. (3) Plots of stability versus pH should not be interpreted in terms of a group whose pKa corresponds to the titration midpoint, but rather to a group with different pKas (that correspond approximately to the titration end points) in each state. (4) Any residual structure in the GuHCl-denatured state of proteins appears to have little effect on the pH dependence of stability. (5) pH-dependent unfolding, for example to the "molten globule" state, appears due to individual groups with anomalous pKas whose locations on the protein surface may determine the nature of the unfolded state.     

Quadratic nonnegative matrix factorization

In Nonnegative Matrix Factorization (NMF), a nonnegative matrix is approximated by a product of lower-rank factorizing matrices. Most NMF methods assume that each factorizing matrix appears only once in the approximation, thus the approximation is linear in the factorizing matrices. We present a new class of approximative NMF methods, called Quadratic Nonnegative Matrix Factorization (QNMF), where some factorizing matrices occur twice in the approximation. We demonstrate QNMF solutions to four potential pattern recognition problems in graph partitioning, two-way clustering, estimating hidden Markov chains, and graph matching. We derive multiplicative algorithms that monotonically decrease the approximation error under a variety of measures. We also present extensions in which one of the factorizing matrices is constrained to be orthogonal or stochastic. Empirical studies show that for certain application scenarios, QNMF is more advantageous than other existing nonnegative matrix factorization methods.     

Seasonality in Estonian Traditional Landscape: The Example of Large Village Swings

Like every nation, Estonians have their own indigenous customs and habits. Village swings and the place of these swings in the landscape are focused upon as an example of such Estonian customs, and changes in landscape as related to seasonality and liminality are discussed. The word ‘swing’ is used to denote a large construction (traditionally made of wood) that is able to carry and swing at least two people. Village swings (for public use) are usually located in the middle of a village and the site is commonly used by young people as a place to meet and have a good time. Swinging takes place mostly in the spring and summer, forming one of the many seasonal activities that make up the Estonian traditional calendar. The seasonal break in swinging activity contributes to the eagerness with which swinging is resumed when spring returns, so seasonality creates frames, with the most valued time being the spring. With swinging, the spring has been celebrated as a very valuable and long-awaited season. Although the religious background for swinging has been forgotten, the place is still special and is visited mostly on certain festive occasions. As there is no comparable alternative to swing sites as a socializing place in the village, they have persisted through the centuries. The importance of preserving such unique seasonal places in Estonia's social landscape is demonstrated.     

Stable SOI micromachined electrostatic AC voltage reference

We have designed and manufactured a micromachined moving plate capacitor to be used as an AC voltage reference in electrical metrology. The reference is based on the characteristic AC current–voltage curve of the component having a maximum, the value of which ideally depends only on the geometry of the component and material properties of single crystalline silicon. The electrode surface stability is essential in this application and hence a new fabrication process has been developed to metallize both surfaces of an electrostatically actuated micromachined structure. The stability of the AC reference voltage at a frequency of 100 kHz and an RMS voltage value 6.4 V was measured to be ±60 ppm over 14 h.     

Characterization of diffraction gratings in a rigorous domain with optical scatterometry: hierarchical neural-network model

Characterization of microstructures with features from submicrometers to hundreds of micrometers requires versatile methods. Profilometry and optical microscopy cannot cope with submicrometer features, and atomic-force microscopy, scanning-electron microscopy, and near-field microscopy are inherently slow, off-line methods. In optical scatterometry, the laser light scattered from a sample is measured and the sample profile is subsequently characterized. We propose the use of a two-stage model based on neural networks: rough categorization followed by refinement, thus reducing the need for prior information on the sample. We simulate the method for a submicrometer diffraction grating characterized by five parameters. It is shown that intensity measurements of few diffraction orders by use only of one wavelength are enough to yield rms errors of less than 2 nm for the parameters (approximately 2-3% of the optimal values of the parameters).     

Isolation and characterization of the Saccharomyces cerevisiae DPP1 gene encoding diacylglycerol pyrophosphate phosphatase

Diacylglycerol pyrophosphate (DGPP) is involved in a putative novel lipid signaling pathway. DGPP phosphatase (DGPP phosphohydrolase) is a membrane-associated 34-kDa enzyme from Saccharomyces cerevisiae which catalyzes the dephosphorylation of DGPP to yield phosphatidate (PA) and then catalyzes the dephosphorylation of PA to yield diacylglycerol. Amino acid sequence information derived from DGPP phosphatase was used to identify and isolate the DPP1 (diacylglycerol pyrophosphate phosphatase) gene encoding the enzyme. Multicopy plasmids containing the DPP1 gene directed a 10-fold overexpression of DGPP phosphatase activity in S. cerevisiae. The heterologous expression of the S. cerevisiae DPP1 gene in Sf-9 insect cells resulted in a 500-fold overexpression of DGPP phosphatase activity over that expressed in wild-type S. cerevisiae. DGPP phosphatase possesses a Mg2+-independent PA phosphatase activity, and its expression correlated with the overexpression of DGPP phosphatase activity in S. cerevisiae and in insect cells. DGPP phosphatase was predicted to be an integral membrane protein with six transmembrane-spanning domains. The enzyme contains a novel phosphatase sequence motif found in a superfamily of phosphatases. A dpp1Delta mutant was constructed by deletion of the chromosomal copy of the DPP1 gene. The dpp1Delta mutant was viable and did not exhibit any obvious growth defects. The mutant was devoid of DGPP phosphatase activity and accumulated (4-fold) DGPP. Analysis of the mutant showed that the DPP1 gene was not responsible for all of the Mg2+-independent PA phosphatase activity in S. cerevisiae.