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PubMed2006

Photon echo spectroscopy of porphyrins and heme proteins: effects of quasidegenerate electronic structure on the peak shift decay.

Three pulse photon echo peak shift spectroscopy and transient grating measurements on Zn-substituted cytochrome c, Zn-tetraphenylporphyrin, and Zn-protoporphyrin IX are reported. The effects of protein conformation, axial ligation, and solvent are investigated. Numerical simulations of the peak shift and transient grating experiments are presented. The simulations employed recently derived optical response functions for square-symmetric molecules with doubly degenerate excited states. Simulations exploring the effects of excited-state energy splitting, symmetric and asymmetric fluctuations, and excited-state lifetime show that the time scales of the peak shift decay in the three-level system largely reflect the same dynamics as in the two-level system. However, the asymptotic peak shift, which is a clear indicator of inhomogeneous broadening in a two-level system, must be interpreted more carefully for three-level systems, as it is also influenced by the magnitude of the excited-state splitting. The calculated signals qualitatively reproduce the data.

Animals↗

PubMed2006

A comparative molecular simulation study of the glass former ortho-terphenyl in bulk and freestanding films.

We performed molecular dynamics simulations of the low-molecular weight organic glass former ortho-terphenyl in bulk and freestanding films. The main motivation is to provide molecular insight into the confinement effect without explicit interfaces. Based on earlier models of ortho-terphenyl we developed an atomistic model for bulk simulations. The model reproduces literature data both from simulations and experiments starting from specific volume and diffusivity to mean square displacement and radial distribution functions. After characterizing the bulk model we form freestanding films by the elongation and expansion method. These films give us the opportunity to study the dynamical heterogeneity near the glass transition through in-plane mobility and reorientation dynamics. We finally compare the model in bulk and under confinement. We found qualitatively a lower glass transition temperature for the freestanding film compared to the bulk.

Journal Article↗

PubMed2006

The correlation-consistent composite approach: application to the G3/99 test set.

The correlation-consistent composite approach (ccCA), an ab initio composite technique for computing atomic and molecular energies, recently has been shown to successfully reproduce experimental data for a number of systems. The ccCA is applied to the G3/99 test set, which includes 223 enthalpies of formation, 88 adiabatic ionization potentials, 58 adiabatic electron affinities, and 8 adiabatic proton affinities. Improvements on the original ccCA formalism include replacing the small basis set quadratic configuration interaction computation with a coupled cluster computation, employing a correction for scalar relativistic effects, utilizing the tight-d forms of the second-row correlation-consistent basis sets, and revisiting the basis set chosen for geometry optimization. With two types of complete basis set extrapolation of MP2 energies, ccCA results in an almost zero mean deviation for the G3/99 set (with a best value of -0.10 kcal mol(-1)), and a 0.96 kcal mol(-1) mean absolute deviation, which is equivalent to the accuracy of the G3X model chemistry. There are no optimized or empirical parameters included in the computation of ccCA energies. Except for a few systems to be discussed, ccCA performs as well as or better than Gn methods for most systems containing first-row atoms, while for systems containing second-row atoms, ccCA is an improvement over Gn model chemistries.

Journal Article↗

PubMed2007

Phase diagrams of alkali halides using two interaction models: a molecular dynamics and free energy study.

Phase diagrams for potassium and sodium chlorides are determined by molecular dynamics and free energy calculations. Two rigid-ion interaction models, namely, the Born-Mayer-Huggins (BMH) and Michielsen-Woerlee-Graaf (MWG) effective pair potentials, have been used. The critical and triple point properties are discussed and compared with available experimental and simulation data. The MWG model reproduces the experimental liquid-gas equilibria better than the BMH model, being the accordance very good in the lowest temperature region of the coexistent liquids, particularly for NaCl. However, both models underestimate the critical temperatures of KCl and NaCl. Relatively to the solid-gas equilibria, the models do not reproduce well the experimental data. As for the solid-liquid coexistences either the BMH or the MWG models appear unrealistic.

Journal Article↗

PubMed2001

Barriers to measuring and achieving optimal outcomes in pediatric asthma.

To measure the effectiveness of any therapeutic endeavor, a set of defined outcome measurements must be performed, or the task of determining the effectiveness of any therapeutic step becomes difficult. With asthma, however, in which case it is difficult to establish the initial diagnosis, beginning a program of outcome measurements regarding any therapeutic interaction is nearly impossible. Conventional means are thwarted at the outset. One way of approaching the problem of obtaining reproducible outcomes data is to examine those areas in which measurements can be made and determine the barriers to obtaining the data. Establishing a good medical history is a critical step that, in general, is especially difficult with very young children, and tools that provide objective measurements that are used in the normal evaluation of older children are of little use in the very young child with asthma. Parts of the physical examination are difficult to perform in very young children, and findings associated with asthma can be found in other clinical states. In this age group, diary keeping suffers from the same problems and issues that are related to obtaining an accurate medical history. Barriers also exist to obtaining the best outcomes. The choice of medications for the very young child is limited; there are several typical adherence problems, and information about adverse effects is limited.

Asthma↗

PubMed1998

Gene number in an invertebrate chordate, Ciona intestinalis.

Gene number can be considered a pragmatic measure of biological complexity, but reliable data is scarce. Estimates for vertebrates are 50-100,000 genes per haploid genome, whereas invertebrate estimates fall below 25,000. We wished to test the hypothesis that the origin of vertebrates coincided with extensive gene creation. A prediction is that gene number will differ sharply between invertebrate and vertebrate members of the chordate phylum. A gene number estimation method requiring limited sequence sampling of genomic DNA was developed and validated by using data for Caenorhabditis elegans. Using the method, we estimated that the invertebrate chordate Ciona intestinalis has 15,500 protein-coding genes (+/-3,700). This number is significantly lower than gene numbers of vertebrate chordates, but similar to those of invertebrates in distantly related phyla. The data indicate that evolution of vertebrates was accompanied by a dramatic increase in protein-coding capacity of the genome.

Animals↗

PubMed1998

Investigation of the action patterns of pectinmethylesterase isoforms through kinetic analyses and NMR spectroscopy. Implications In cell wall expansion.

Well characterized pectin samples were incubated with cell wall-bound and -solubilized pure isoforms of pectinmethylesterase from mung bean hypocotyls (Vigna radiata). Both enzyme activity and average product structure were determined at intervals along the deesterification pathway at pH 5.6 and 7.6. The latter analyses were performed by 13C NMR spectroscopy, and the degree of esterification was probed by both 13C NMR and potentiometric measurements. A dichotomy was observed in the behavior of the alpha and gamma isoforms when compared with that of the beta isoenzyme. Ideal blockwise deesterification mechanisms reproduced the experimental average structures (methylester distribution) throughout the course of the reaction. In the case of the alpha and gamma isoforms, a single chain mechanism associated with a free carboxyl group at the second nearest neighbor position could be postulated at pH 5.6, whereas some multiple attack character was required to reproduce the data at pH 7.6. Several mechanisms that differed from the preceding ones were compatible with the data for the beta isoform at the two pH values. Both the nature of the polysaccharides produced in these reactions and the role of pectinmethylesterase in the cell wall-stiffening process along the growth gradient are discussed.

Carboxylic Ester Hydrolases↗

PubMed1987

Cardiopulmonary resuscitation. Historical and future perspectives.

Although cardiopulmonary resuscitation (CPR) has been practiced for over a century, further study into methods for reviving victims of cardiac arrest is obviously needed. We now know that standard external CPR has numerous drawbacks, and modifications must be tested in a careful, randomized fashion. Three alternatives to standard external CPR (simultaneous compression-ventilation, interposed abdominal compression, and open-chest CPR) are currently being investigated. Of these procedures, open-chest CPR appears to show the most promise. Reproducible animal data must demonstrate the advantages of any method before widespread human studies are begun, however. If techniques seem promising in animals, well-controlled multicenter studies will be needed to verify applicability to humans. Major changes in CPR techniques should be made only after careful study, not on the basis of a limited number of reports from a single source. Resuscitation research must also extend beyond the study of techniques of cardiac massage. Although CPR is effective in some cases, clearly a person's chance of survival is directly linked to the speed of definitive care, that is, defibrillation. Research must continue into ways of providing rapid advanced cardiac care, such as home defibrillators or rapid prehospital response to the victims of cardiac arrest by those trained in advanced cardiac life support (ACLS). In addition, to counteract the problem of neurologic demise after prolonged anoxia, study of postresuscitative care must continue. Only through the combination of these measures will survival rates after cardiac arrest improve.

Animals↗

PubMed2004

A feasibility study of interstitial hyperthermia plus external beam radiotherapy in glioblastoma multiforme using the Multi ELectrode Current Source (MECS) system.

PURPOSE: Thermoradiotherapy has been shown in several randomized trials to increase local control compared to radiotherapy alone. The first randomized study of interstitial hyperthermia in glioblastoma multiforme showed a survival benefit for hyperthermia, though small. Improvement of the heating technique could lead to improved results. The purpose of this feasibility study is to present the clinical and thermal data of application of an improved interstitial hyperthermia system. METHODS AND MATERIALS: Six patients with a glioblastoma multiforme were treated with interstitial hyperthermia using the Multi Electrode Current Source Interstitial Hyperthermia (MECS-IHT) system. The MECS-IHT system has the capability of spatial monitoring of temperature and individually steering of heating electrodes. Three sessions were given aiming at a steady state temperature of 42 degrees C for 1 h, with an interval of 3-4 days, during an external irradiation scheme of 60 Gy in 6 weeks. Hyperthermia was delivered with a mean of 10 catheters, 18 heating electrodes and 38 thermal probes per patient. RESULTS: Sub-optimal temperatures were encountered in the first two patients leading to adjustments in technique thereafter with subsequent improvement of thermal data. With a catheter spacing of 11-12 mm, measurements yielded a mean T(90), T(50) and T(10) of 39.9, 43.7 and 45.2 degrees C, respectively, over three sessions in the last patient. The power per electrode to reach this temperature distribution varied from 25-100% of full power in each of the last four patients. Thermal data were reproducible over the three sessions. Acute toxicity was minimal. CONCLUSIONS: Despite the spatial steering capabilities of the MECS-IHT system, a large temperature heterogeneity was encountered. The heterogeneity was the reason to limit the catheter spacing to 11-12 mm, thus making only small tumour volumes feasible for interstitial heating.

Aged↗

PubMed1996

Heavy ion inactivation in Escherichia coli cells: experiment and theory.

Cross sections for inactivation of stationary cells of E. coli strains (B(s-1) and B/r) by heavy ions (Z = 8-92) with energies <15 MeV/u were determined from survival curves and compared with track structure calculations. Whereas for low energies, inactivation cross sections for both strains are similar, and thus do not reflect their difference in X-ray sensitivity, the ratios of cross sections of the two strains approach the ratio of X-rays sensitivities for heavy ions at high energies. The essential features of the experimental data are reproduced well by the track structure calculations, which do not use fitted values for the model parameters but independently determined values for the X-ray sensitivities and the size of the target structure. Quantitatively, the calculations underestimate the cross sections for heavier ions as well as their ratios at higher energies. Some possible reasons for these discrepancies are discussed.

Escherichia coli↗

PubMed2005

The role of potassium, magnesium and calcium in the Enhanced Biological Phosphorus Removal treatment plants.

Cations as potassium and magnesium play an important role in maintaining the stability of Enhanced Biological Phosphorus Removal (EBPR) process. In this paper potassium, magnesium and calcium behaviour in EBPR treatment plants has been studied. An ASM2d model extension which takes into account the role of potassium and magnesium in the EBPR process has been developed. Finally, a simulation of the effect on P removal of a shortage of K and Mg was studied. The experimental results showed that K and Mg play an important role in the EBPR process being cotransported with P into and out of bacterial cells. It has been observed that calcium is not involved in P release and uptake. The values of the molar ratios K/P (0.28 mol K mol P(-1)) and Mg/P (0.36 mol Mg mol P(-1)) were obtained accomplishing the charge balance, with different K/Mg mass ratios and without phosphorus precipitation. Model predictions accurately reproduced experimental data. The simulations carried out showed the important effect of the K and Mg influent concentration for P removal efficiency. The results illustrate that the proposed ASM2d model extension must be considered in order to accurately simulate the phosphorus removal process.

Aerobiosis↗

PubMed2005

Using human microarrays to identify differentially expressed genes associated with increased steroidogenesis in boars.

Human microarrays are readily available, and it would be advantageous if they could be used to study gene expression in other species, such as pigs. The objectives of this research were to validate the use of human microarrays in the analysis of porcine gene expression, to assess the variability of the data generated, and to compare gene expression in boars with different levels of steroidogenesis. Cytochrome b5 (CYB5) expression was used to assess array detection sensitivity. Samples having high or low CYB5 RNA levels were hybridized to microarrays to determine if the known expression difference could be detected. Six hybridizations were conducted using human microarrays containing 3840 total spots representing 1718 characterized human ESTs. To analyze gene expression in boars with different levels of steroidogenesis, testis RNA from four boars with high levels of plasma estrone sulphate was hybridized to testis RNA from four boars with lower levels. Eight microarray hybridizations were conducted including fluor-flips. Self-self hybridizations were also conducted to assess the variability of array experiments. The Cy5 and Cy3 intensity values for each array were normalized using a locally weighted linear regression (LOESS). Statistical significance was assessed using a Student's t-test followed by the Benjamini and Hochberg multiple testing correction procedure. Quantitative real-time PCR (Q-RT-PCR) was used to verify select gene expression differences. The results show that CYB5 was significantly overexpressed in the high CYB5 sample by 1.8 fold (P < 0.05), verifying the known expression difference. The average log2 ratio of the majority of genes (1643) falls within one standard deviation of the mean, indicating the data were reproducible. In the high versus low steroidogenesis experiment, seven genes were significantly overexpressed in the high group (P < 0.05). Quantitative real-time PCR was used to validate five genes with the highest fold change, and the results corroborated those found by the microarray experiments. The results of the self-self hybridizations showed that no genes were significantly differentially expressed following the application of the Benjamini and Hochberg multiple testing correction procedure. The results presented in this report show that human arrays can be used for gene expression analysis in pigs.

Animals↗

PubMedDate not supplied

Health risk of low-dose pesticides mixtures: a review of the 1985-1998 literature on combination toxicology and health risk assessment.

A literature review covering the last 14 yr has been performed in the field of combination toxicology and human risk assessment from exposure to chemical mixtures, with special emphasis on mixtures of pesticides at low doses, that is, at levels likely to occur in human diet and environment. Despite a large body of knowledge in the field of risk assessment methodologies for exposure to chemical and pesticide mixtures, there is no single methodological approach in "combination toxicology" and health risk assessment of chemical mixtures, and therefore professional judgment is still required. Generally, the dose or response additivity approach that may be applied to evaluate potential risk for chemical mixtures in human toxicology overestimates the risk of a combination of chemicals. The recent endocrine disrupter issue demonstrated the difficulty of reproducibility of data when testing environmental toxicants at very low levels, and the need for more basic work in this field. The use of integrated methodological approaches may provide more reliable predictive data in the risk assessment of chemical mixtures in future. Yet data have demonstrated that exposure to a combination of compounds does not cause effects stronger than the ones of their most active component, provided components are present at low concentration levels, like acceptable daily intake (ADI) or reference dose (RfD) levels, well below their respective no-observed-adverse-effect levels (NOAELs). Although it has been demonstrated that a combination of compounds with the same target organ and the same or very similar mechanisms of action may cause additive or synergistic effects, the chance of such effects will most likely diminish with decreasing exposure levels to such combinations. Synergism and antagonism may both occur at the same time at different organs or targets in the same organism. However, and despite some exceptions, it has been demonstrated that interaction between components is not a common event at low levels of human exposure such as those that may occur through pesticides residues in food or drinking water. The introduction of a special safety factor as a standard for mixtures in addition to those normally used for deriving ADIs, RfDs, or minimal risk levels is not supported by data. It can be concluded from our review that, as a general rule, exposure to mixtures of pesticides at low doses of the individual constituents does not represent a potential source of concern to human health.

Environmental Pollutants↗

PubMed1983

Quantitative studies on T cell diversity. IV. Mathematical analysis of multiple limiting populations of effector and suppressor T cells.

Limiting dilution (LD) analyses of polyclonally activated T cells yielded results suggesting the existence of multiple paired populations of effector and suppressor precursors for a number of different T cell functions and specificities analyzed. These populations occur at graded frequencies and suppression occurs within a pair but not between pairs. In this paper, we establish the mathematical basis for the interpretation of these multi-component limiting dilution results. First, we derive equations for a number of mathematical models and identify one model that both makes biological sense and can be used to reproduce experimental data. Second, within this model, we identify parameters such as the frequency of suppressive cells and the number of suppressive cells required for suppression. The results suggest that within each paired population, suppressor precursors are 20 times more frequent that effector precursors. Furthermore, a similar but variable excess of suppressor cells is required for suppression to become effective. Together with the high frequency (1/50-1/500) of most effector T cell precursors previously reported, the results suggest that up to 40% of the T cells can become involved in suppression of an antigen-specific effector T cell population. These studies may provide exact estimates for predictions to be tested in experiments on immune regulation.

Cell Count↗

PubMed1995

Reconstruction of megavoltage photon spectra by attenuation analysis.

A simple analytical model for reconstructing photon spectra from the indirect measurement of transmission or depth-dose curves is presented, based on the Schiff expression for forward-directed bremsstrahlung differential in photon energy with added inherent filtration. Calculated transmission curves for 21 simulated and measured bremsstrahlung spectra with maximum photon energies in the range 4 to 30 MeV covering a broad range of filtration conditions were used to assess the model's ability to represent megavoltage spectra. Input data were reproduced to within 0.1 per cent in all cases, which is the same order of magnitude as the uncertainty involved in its calculation. Inclusion of a fourth parameter in the model is shown to allow the effective maximum photon energy present in the spectrum to be derived to an accuracy of approximately 3 per cent.

Humans↗

PubMed1996

Determination of the relative neutron sensitivity of a C-CO2 ionization chamber.

The neutron sensitivity of a C-CO2 ionization chamber has been experimentally determined in the neutron energy range of 0.1-1.2 MeV. Eleven kU data were obtained which ranged from 0.04 to 0.1 as a function of neutron energy. There were two peaks in the spectrum of the kU factor, and their positions corresponded to the resonance energies of the kerma factors of carbon dioxide, of which the energies are about 0.4 and 1 MeV. The present data agree with the data obtained at the National Institute for Radiological Sciences in Chiba, Japan (NIRS). The energy dependences of the sensitivity were calculated by using the kerma and the W-value ratios of gas to soft tissue for comparison. The experimental data were reproduced well by the calculations.

Biophysical Phenomena↗

PubMed2003

Radiation improves intratumoral gene therapy for induction of cancer vaccine in murine prostate carcinoma.

Our goal was to convert murine RM-9 prostate carcinoma cells in vivo into antigen-presenting cells capable of presenting endogenous tumor antigens and triggering a potent T-helper cell-mediated immune response essential for the generation of a specific antitumor response. We showed that generating the major histocompatibility complex (MHC) class I+/class II+/Ii- phenotype, within an established subcutaneous RM-9 tumor nodule, led to an effective immune response limiting tumor growth. This phenotype was created by intratumoral injection of plasmid cDNAs coding for interferon gamma, MHC class II transactivator, and an antisense reverse gene construct (RGC) for a segment of the gene for Ii protein (-92,97). While this protocol led to significant suppression of tumor growth, there were no disease-free survivors. Nevertheless, irradiation of the tumor nodule on the day preceding initiation of gene therapy yielded 7 of 16 mice that were disease-free in a long-term follow up of 57 days compared to 1 of 7 mice receiving radiotherapy alone. Mice receiving radiotherapy and gene therapy rejected challenge with parental RM-9 cells and demonstrated specific cytotoxic T-cell activity in their splenocytes but not the mouse cured by radiation alone. These data were reproduced in additional experiments and confirmed that tumor irradiation prior to gene therapy resulted in complete tumor regression and specific tumor immunity in more than 50% of the mice. Increasing the number of plasmid injections after tumor irradiation induced tumor regression in 70% of the mice. Administering radiation before this novel gene therapy approach, that creates an in situ tumor vaccine, holds promise for the treatment of human prostate carcinoma.

Adenoviridae↗

PubMed2004

Toward general experimentation and discovery in conditioned laboratory spaces: Part I. Experimental pH change findings at some remote sites.

OBJECTIVES: To fulfill the general scientific method requirement for one of our earlier Minnesota experiments, namely that laboratory spaces operated by other investigators at different sites in the United States can be conditioned to a higher electromagnetic gauge symmetry state than our normal background state and such a space can be specifically tuned so that the pH of purified water in equilibrium with air will be increased by approximately 1.0 pH unit with no chemical additions. DESIGN: Insertion of a specific intention imprinted electrical device (IIED) into the space for a period of at least 3 months while continuously monitoring the pH of purified water wherein the water was replaced and the pH-electrode recalibrated on a 2-week cycle. Control sites were associated with each IIED site. SETTING/LOCATION: Offices in homes and clinics. SUBJECTS: Three IIED sites plus three control sites. INTERVENTIONS: None. OUTCOME MEASURES: Continuously recorded pH and temperature. RESULTS: (1) Linear and exponential pH(t) variations with time at IIED sites, with the Delta pH-values increasing with each 2-week cycle up to a value of approximately 0.8-1.0 pH units, (2) control sites, 2-20 miles distant from the IIED sites exhibited similar behavior but with smaller Delta pH-values, and (3) a new information transfer mechanism in nature has been demonstrated. CONCLUSIONS: Human consciousness, at least under some conditions, can strongly influence well-designed target experiments in physical reality and the primary data are reproducible in other laboratories provided the specific protocol is followed.

Arizona↗