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A tool for the interactive 3D visualization of electronic structure in molecules and solids.

This paper presents the Vienna ab initio simulation package (VASP) data viewer, a desktop 3D visualization application for the analysis of valence electronic structure information derived from first-principles quantum-mechanical density functional calculations. This tool allows a scientist to directly view and manipulate the calculated charge density or electron localization function (ELF) from an electronic structure calculation, providing insight into the nature of chemical bonding. Particular attention was given to the design and implementation of the user interface (UI) for the data viewer. It provides for expert and novice usage, and both natural direct manipulation and precise numerical control. The data viewer has proven useful to chemical scientists for understanding the results of electronic structure calculations.

Journal Article↗

Engrailed and retinotectal topography.

We examine the role of the Engrailed homeobox gene in establishment of local tectal topography. In the mesencephalon, a gradient of Engrailed appears early and defines the rostrocaudal axis of the tectum. Various experiments that cause ectopic Engrailed expression cause predictable readjustments of the retinotectal map. The newly discovered 'realisators' of the retinotopic map, such as receptor tyrosine kinase ligands ELF-1 and RAGS could be controlled directly by Engrailed. Indeed, recent results show that Engrailed regulates the expression of these ligands. The Engrailed gradient itself appears to be set up by signals including FGF8 and WNTI, allowing us to begin to trace the molecular cascade that is responsible for the correct wiring of the visual projection back into the early embryo.

Animals↗

A conserved IL-2 responsive enhancer in the IL-2R alpha gene.

IL-2 stimulates expression of the alpha subunit of the high affinity IL-2 receptor (IL-2R alpha) in antigen-activated T lymphocytes, by increasing IL-2R alpha gene transcription. This response is mediated by a 52 nt IL-2 responsive enhancer (IL-2rE) that is conserved between mouse and man. The mouse enhancer is 1.3 kb upstream of the transcription start site and co-localizes with an inducible DNasel hypersensitive site, whereas the human homologue maps to -4 kb. The human IL-2rE is functional in rodent cells. Both enhancers contain two potential STAT binding sites and an Ets consensus motif. One of the STAT motifs overlaps with a binding site for GATA factors. Functional analysis of the mouse and human enhancers indicates that IL-2-activated STAT5 and the constitutively active Ets protein Elf-1 play a predominant role in controlling IL-2rE activity.

Animals↗

Transplant of cultured neuron-like differentiated chromaffin cells in a Parkinson's disease patient. A preliminary report.

BACKGROUND: Treatment of Parkinson's Disease (PD) has been attempted by others by transplanting either the patient's own adrenal medullary tissue or fetal substantia nigra into caudate or putamen areas. However, the difficulties inherent in using the patient's own adrenal gland, or the difficulty in obtaining human fetal tissue, has generated the need to find alternative methods. METHODS: We report here of an alternative to both procedures by using as transplant material cultured human adrenal chromaffin cells differentiated into neuron-like cells by extremely low frequency magnetic fields (ELF MF). RESULTS: The results of this study show that human differentiated chromaffin cells can be grafted into the caudate nucleus of a PD patient, generating substantial clinical improvement, as measured by the Unified Rating Scale for PD, which correlated with glucose metabolism and D2 DA receptor increases as seen in a PET scan, while allowing a 70% decrease in L-Dopa medication. DISCUSSION: This is the first preliminary report showing that transplants of cultured differentiated neuron-like cells can be successfully used to treat a PD patient.

Adrenal Medulla↗

Ion-protein dissociation predicts 'windows' in electric field-induced wound-cell proliferation.

There are many experiments showing that weak, non-thermal electric fields influence living tissues. In many cases, biological effects display 'windows' in biologically effective parameters of electric fields: most dramatic is the fact that relatively intense electric fields sometimes do not cause appreciable effect, while smaller fields do. Linear resonant physical processes do not explain frequency windows in this case. Both frequency and amplitude windows are evident from experiments on human dermal fibroblasts in a collagen matrix. For this in vitro model of skin, exposure to extremely low frequency (ELF) electric fields in the frequency range 10-100 Hz and the amplitude range of 0-130 microA/cm(2) macroscopic current density demonstrates such unusual 'window' behavior. Amplitude window phenomena suggest a non-linear physical mechanism. We consider non-linear quantum-interference effects on protein-bound substrate ions: These ions experience, due to electric fields in the media or biological tissue as small as 1 mV/m, electric gradients produced by polarized binding ligand atomic shells. The electric gradients cause an interference of ion quantum states. This ion-interference mechanism predicts specific electric-field frequency and amplitude windows within which fibroblast proliferation occurs.

Cell Division↗

Cell-to-cell communication in response of E. coli cells at different phases of growth to low-intensity microwaves.

Effects of millimeter waves (MMW) at the frequency of 51.755 GHz were studied in logarithmic and stationary E. coli cells at various cell densities. The changes in the genome conformational state (GCS) were analyzed by the method of anomalous viscosity time dependence (AVTD). Before lysis, the cells were adjusted to the cell density of 4x10(7) cells/ml and all AVTD measurements were run at this cell density. Stationary cells responded to MMW by increase in AVTD, while the same MMW exposure decreased AVTD in logarithmic cells. MMW effects depended on cell density during exposure and were stronger for stationary cells. The observed dependence on cell density suggested a cell-to-cell communication between cells during exposure to microwaves. Decrease in power density (PD) resulted in more striking differences between responses at different cell densities. The data provided evidence that intercellular communication in response to MMW depended on cell status and PD of microwaves. The MMW effects were studied in more detail at low intensity of 10(-17) W/cm(2) in the range of cell densities 4x10(7) to 8x10(8) cells/ml. The obtained sigmoid-like dependence of MMW effect on cell density saturated at approximately 5x10(8) cells/ml. The dependence of MMW effect on cell density was very similar in this study and in previous studies with weak extremely low frequency (ELF) electromagnetic fields (EMF). The data suggested that cell-to-cell communication might be involved in response of cells to weak EMF of various frequency ranges.

Cell Communication↗

A hypothetical mathematical construct explaining the mechanism of biological amplification in an experimental model utilizing picoTesla (PT) electromagnetic fields.

We seek to answer the conundrum: What is the fundamental mechanism by which very weak, low frequency Electromagnetic fields influence biosystems? In considering the hydrophobicity of intramembranous protein (IMP) H-bonds which cross the phospholipid bilayer of plasma membranes, and the necessity for photonic recycling in cell surface interactions after dissipation of energetic states, present models lack structure and thermodynamic properties to maintain (DeltaE) sufficient energy sources necessary for amplifications by factors of 10(12). Even though one accepts that the ligand-receptor association alters the conformation of extracellular, extruding portions of IMP's at the cell surface, and that this change can be transmitted to the cytoplasm by the transmembranous helical segments by nonlinear vibrations of proteins with generation of soliton waves, one is still unable to account for repair and balanced function. Indeed, responses of critical molecules to certain magnetic field signals may include enhanced vibrational amplitudes, increased quanta of thermal energies and order inducing interactions. We may accept that microtrabecular reticulum-receptor is associated with actin filaments and ATP molecules which contribute to the activation of the cyclase enzyme system through piezoelectricity. Magnetic fields will pass through the membrane which sharply attenuates the electric field component of an EM field, due to its high impedance. Furthermore, EM oscillations are converted to mechanical vibrations; i.e., photon-phonon transduction, to induce molecular vibrations of frequencies specifically responsible for bioamplifications of weak triggers at the membrane surface, as well as GAP junctions. The hydrogen bonds of considerable importance are those in proteins (10(12)Hz) and DNA (10(11)Hz) and may be viewed as centers of EM radiation emission in the range from the mm microwaves to the far IR. However, classical electrodynamical theory does not yield a model for biomolecular resonant responses which are integrated over time and account for the connection between the phonon field and photons. Jacobson Resonance does supply an initial physical mechanism, as equivalencies in energy to that of Zeeman Resonance (i.e., zero-order magnetic resonance) and cyclotron resonance may be derived from the DeBroglie wave particle equation. For the first time, we view the introduction of Relativity Theory to biology in the expression, mc(2)=BvLq, where m is the mass of a particle in the 'box' or 'string' (molecule in a biosystem), c is the velocity of electromagnetic field in space, independent of its inertial frame of reference, B is the magnetic flux density,v is the velocity of the carrier or 'string' (a one or two dimensional 'box') in which the particle exists, L is its dimension (length) and q represents a unit charge q=1C, by defining electromotive force as energy per unit charge. Equivalencies suggest that qvBL is one of the fundamental expressions of energy of a charged wave-particle in magnetic fields, just as Zeeman and cyclotron resonance energy expressions, gbetaB and qhB/2pim, and is applicable to all charged particles (molecules in biological systems). There may exist spontaneous, independent and incessant interactions of magnetic vector B and particles in biosystems which exert Lorentz forces. Lorentz forces may be transmitted from EM field to gravitational field as a gravity wave which return to the phonon field as microgravitational fluctuations to therein produce quantum vibrational states that increase quanta of thermal energies integrated over time. This may account for the differential of 10(12) between photonic energy of ELF waves and the Boltzman energy kT. Recent data from in vivo controlled studies are included as empirical support for the various hypotheses presented.

Animals↗

Disturbances of calcium homeostasis within the endoplasmic reticulum may contribute to the development of ischemic-cell damage.

It is widely accepted that disturbances of calcium homeostasis play a key role in the development of cell damage produced by transient cerebral ischemia. It is believed that the sharp increase in cytosolic calcium activity during ischemia activates a cascade of calcium-dependent metabolic processes which ultimately destroy the integrity of the cell. However, it has never been taken into account that ischemic cell damage may, at least in part, be caused by a disturbance of calcium homeostasis within the endoplasmic reticulum after transient cerebral ischemia. In fact, depletion of the endoplasmic reticulum from calcium induces metabolic changes resembling, in many respects, those produced by transient cerebral ischemia: it causes an inhibition of the activity of the eucaryotic initiation factor elF-2 alpha (by phosphorylation), a disaggregation of polyribosomes and thus an inhibition of global protein synthesis, and an increased expression of certain genes such as transcription factors (c-fos and c-jun) and the glucose-related protein grp78. Finally, a depletion of calcium in the endoplasmic reticulum induces tissue damage within the brain and triggers apoptosis in neuronal and non-neuronal cells. It is therefore concluded that cell damage induced by transient ischemia may, at least in part, be caused by a disturbance of calcium homeostasis within the endoplasmic reticulum.

Animals↗

Context-dependent Pax-5 repression of a PU.1/NF-kappaB regulated reporter gene in B lineage cells.

Enhancers located in the 3' end of the locus in part regulate immunoglobulin heavy chain (IgH) gene expression. One of these enhancers, HS 1,2, is developmentally regulated by DNA binding proteins like NF-kappaB, Pax-5 and the protein complex NF-alphaP in B lineage cells. Here we report that NF-alphaP is the ets protein PU.1. A glutathione-S-transferase (GST)-pulldown assay demonstrated that PU.1 can physically interact with NF-kappaB in solution. Experiments in COS cells showed that PU.1 and NF-kappaB (p50/c-Rel) can activate transcription of an enhancer linked reporter gene. The paired domain protein Pax-5 has previously been shown to repress enhancer-dependent transcription. Additional co-transfection experiments revealed that PU.1/NF-kappaB dependent transcription could be repressed in a context dependent manner by Pax-5, but not by the paired domain of Pax-5. When the PU.1 binding site was substituted with a binding site for the ets-protein Elf-1, Pax-5 could no longer repress reporter gene activity. Our data indicate a model where Pax-5 mediated repression of the HS 1,2 enhancer requires the recruitment of a co-factor which is dependent on Pax-5/PU.1 but which cannot be recruited by Pax-5/Elf-1.

Animals↗

Stimulation of protein kinase A activity and induced terminal differentiation of human skin fibroblasts in culture by low-frequency electromagnetic fields.

In the present study experiments are described, which indicate that the exposure of normal human skin fibroblasts (HSFs) to a low-frequency electromagnetic field of 20 Hz and 7-8 mT does induce terminal differentiation within 14 days of daily exposure of 12 h. As demonstrated by the analysis of the expression level of the proto-oncogene c-myc, the induction of terminal differentiation of progenitor fibroblasts to postmitotic fibrocytes does most likely not involve changes in the c-myc protein. As one possible candidate being involved in the ELF-EMF-mediated inhibition of fibroblast growth and the subsequent induction of terminal differentiation the cyclic AMP-dependent protein kinase A (PKA) could be characterised. Thus, the data presented clearly indicate that the specific EMF field of 20 Hz and 7-8 mT significantly interfere with regulatory processes of fibroblast proliferation and differentiation.

Blotting, Northern↗

Responses of the estrous cycle in dairy cows exposed to electric and magnetic fields (60 Hz) during 8-h photoperiods.

To study the effects of exposure to extremely low frequency (ELF) electric and magnetic fields (EMF) on the estrous cycle of dairy cows under short-day photoperiod, 16 non-lactating, non-pregnant Holstein cows were exposed to a vertical electric field of 10 kV/m and a horizontal magnetic field of 30 microT for 16 h per day in a cross-over design consisting of two sequences. Each sequence included three periods, and each period corresponded to the duration of one estrous cycle. All animals were maintained under short photoperiod (8 h light/16 h dark) during the trial. Exposure to EMF had an impact on the duration of a complete estrous cycle (P<0.01) and on the duration of the luteal phase (P<0.01). The mean duration of one cycle was 19.5+/-0.4 for the control and 21.3+/-0.4 days for the exposed animals, respectively. The mean duration of the luteal phase was 15.4+/-0.4 days for the control and 17.2+/-0.4 days for the exposed group. The total area under the progesterone (P(4)) curve, the amplitude of the curve or the slope of the P(4) rise at the onset of the luteal phase were not affected by EMF exposure. Results indicate that exposure to EMF may increase the duration of the estrous cycle.

Animals↗

Differentiation between used motor oils on the basis of their IR spectra with application of the correlation method.

Two brands of motor oils (Elf and Castrol) that had been used for various periods of time were examined. The aim was to differentiate these samples (of varying degree of use) on the basis of their infrared spectra, for criminalistic purposes. The correlation method was used. It was found that the FTIR method is capable of providing sufficiently detailed information if some specific fragments of spectra are examined. Hence, it can be concluded that the investigation procedure proposed is adequate.

Fuel Oils↗

Fluorimetric determination of theophylline in serum by inhibition of bovine alkaline phosphatase in AOT based water/in oil microemulsion.

Theophylline is an effective bronchodilatator used in the treatment of asthma which requires frequent control because of its narrow therapeutic index. Over the past decade much attention has been dedicated to the peculiar properties of the inner water pools of AOT (sodium 2-bishexyl-ethyl sulfosuccinate) microemulsions as enzyme microreactors, yet few analytical applications of the latter have been reported. We developed an original assay based on the uncompetitive inhibition by theophylline of the reaction catalyzed by alkaline phosphatase from bovine liver (E.C. 3.1.3.1) of the ELF-97 fluorogenic substrate in borate buffer 20 mM (pH 8.6)/AOT/iso-octane-ethyl acetate (95:5) at a temperature of 37 degrees C. Optimal activity of endogenous plasmatic alkaline phosphatase isoenzymes approximately pH 10.5, interfering activity of the serum are avoided. The assay is multiple point rate, monitoring the appearance of the photostable fluorescence emission of the reaction product (510-530 nm) out of the water pool. The influence of several parameters such as the amount of buffer (W(o)), the amount of alkaline phosphatase, sample volume (10-30 microl) [corrected], optimal run time (1-7 min) and the use of phosphorylating acceptor (2A2MP) are discussed. The method was compared to HPLC UV and TDx methods.

Alkaline Phosphatase↗

Does exposure to an artificial ULF magnetic field affect blood pressure, heart rate variability and mood?

The aim of this study was to determine whether an artificial magnetic field with an amplitude and frequency equivalent to those of geomagnetic pulsations during geomagnetic storms could affect physiology and psychology. Three healthy volunteers wore anambulatory BP monitor and an ECG recorder around the clock for 12 consecutive weekends in Winnipeg, Manitoba, Canada. In a room shielded against ELF and VLF waves, they were exposed for 8 hours per week to either a 50 nT 0.0016 Hz or a sham magnetic field at one of six circadian stages. Real exposure randomly alternated with sham exposure. They provided saliva and recorded mood and reaction time every 4 hours while awake. Systolic (S) and diastolic (D) blood pressure (BP), and heart rate (HR) were recorded every 30 minutes. Spectral analysis of HR variability (HRV) was performed using the maximum entropy method and a complex demodulation method. For these variables, daily means were compared between real and sham exposure, using paired t-tests. Their circadian MESOR, amplitude, and acrophase were analyzed and summarized using single cosinor and population-mean cosinor. Circadian rhythms were demonstrated for HR, SBP, DBP for sham exposure, salivary flow rate, positive affect, vigor, and subjective alertness (p < 0.001, -0.02). One participant showed higher HR, lower LF, HF, and VLF powers, and a steeper power-law slope (p < 0.005, -0.0001) in an early night exposure to the real magnetic field, but not in other circadian stages. There was no significant difference between circadian responses to real and sham exposure in any variable at any circadian stage.

Adult↗

Basic pharmacodynamics of antibacterials with clinical applications to the use of beta-lactams, glycopeptides, and linezolid.

Time above MIC for free drug concentrations is the important PK-PD parameter correlating with the efficacy of beta-lactam antibiotics. The duration of time plasma concentrations needed to exceed the MIC is relatively similar for most organisms except staphylococci. Neutrophils contribute very little to the overall activity of beta-lactams. The appearance of increasing antimicrobial resistance can challenge the efficacy of these drugs when concentrations do not exceed the MIC for 40% to 50% of the dosing interval. Time above MIC with oral amoxicillin and amoxicillin-clavulanate can be enhanced with high-dose formulations. Time above MIC with parenteral preparations can be enhanced by longer intravenous infusions or even continuous infusion. The 24-hour AUC-MIC is probably the important PK-PD parameter correlating with the efficacy of vancomycin and teicoplanin. It clearly is the important parameter for the efficacy of linezolid. Usual doses of these drugs generally provide adequate plasma concentrations to treat effectively infections in which plasma concentrations are predictive of tissue concentrations. Penetration of these drugs into respiratory secretions, such as ELF, is enhanced for linezolid and reduced for vancomycin. This may give linezolid an advantage over vancomycin in certain respiratory infections.

Acetamides↗

Expression of urokinase plasminogen activator and receptor in conjunction with the ets family and AP-1 complex transcription factors in high grade prostate cancers.

Expression of the urokinase plasminogen activator (uPA) and its receptor (uPAR) correlates with tumour cell invasiveness and helps to determine the prognosis of prostate and other cancers. The purpose of this study was to establish in prostate cancer, the ets family and AP-1 complex transcription factors that might activate the inducible AP-1 and AP-1/PEA3 elements of the uPA enhancer. uPA and uPAR were expressed preferentially in adenocarcinoma cells, but not the stroma of high grade prostate cancers. The ets family paralogues Fli-1 and Elf-1 were also highly expressed in adenocarcinoma cells of the majority of cancers, while Erg 1,2 and Ets-2 were expressed in a minority of cancers and Elk-1, PEA3 and PU.1 were minimally expressed. A minority of cancers expressed high levels of cytoplasmic and/or nuclear c-Jun and c-Fos transcription factors. We speculate as to the molecular basis for such expression.

Humans↗

CPT-11 in gastrointestinal cancer.

Colorectal, gastric and pancreatic cancers are major health problems worldwide. Although surgery is a curative option in 50% of patients with colorectal cancer, it is much less effective in gastric cancer (< 20% of patients) and virtually ineffective in pancreatic cancer. These three cancer types also respond poorly to chemotherapy. CPT-11 (irinotecan), a novel cytotoxic drug, is now available in many countries as a single agent for second-line therapy in metastatic colorectal cancer. The response rate in the pivotal European study of metastatic colorectal cancer patients was 14%, with a median duration of response of 8.5 months. There was also a high rate of disease stabilisation (44%), with a median duration of 4.8 months. Median survival time was 10.4 months. The dose-limiting toxicities (DLT) for CPT-11 are delayed diarrhoea and neutropenia, both of which are schedule dependent and non-cumulative. These encouraging data in second-line therapy support the further study of CPT-11 as first-line therapy for colorectal cancer in combination with other agents. Four Japanese trials of CPT-11 as first- and/or second-line single-agent therapy for advanced gastric cancer report response rates of 18-43%. The median durations for response and survival time in the late phase II trial were 2.3 months and 5.8 months, respectively. These results are in the range of those reported for sequential high-dose methotrexate and 5-fluorouracil (5-FU)/doxorubicin (FAMTX), etoposide/leucovorin/5-FU (ELF) or cisplatin/5-FU therapy in gastric cancer. Data are currently available from five phase II studies of CPT-11 in advanced pancreatic cancer: four Japanese and one European. The response rates ranged from 9 to 19%. The median duration of survival for all treated patients in the European study was 5.2 months. CPT-11 in combination with 5-FU is currently being investigated in Japan, the U.S.A. and Europe in patients with gastrointestinal tumours. CPT-11 is also being evaluated in combination with each of the following agents: oxaliplatin, docetaxel, raltitrexed, etoposide and mitomycin C. Japanese studies of CPT-11 plus cisplatin in patients with gastric cancer have produced response rates of 48-59%. These encouraging data highlight the potential for CPT-11 in combination therapy for gastrointestinal tumours.

Antineoplastic Agents, Phytogenic↗

The helC gene encodes a putative DEAD-box RNA helicase required for development in Dictyostelium discoideum.

DEAD-box RNA helicases, defined by the sequence Asp-Glu-Ala-Asp (DEAD, in single-letter amino-acid code), regulate RNA unwinding and secondary structure in an ATP-dependent manner in vitro [1] and control mRNA stability and protein translation. Both yeast and mammals have large families of DEAD-box proteins, many of unknown function. We have disrupted a Dictyostelium discoideum gene, helC, which encodes helicase C, a member of the DEAD-box family of RNA helicases that shows strong homology to the product of the essential Saccharomyces cerevisiae gene dbp5 [2] and to related helicases in mouse and Schizosaccharomyces pombe. The HelC protein also shows weaker homology to the translation initiation factor elF-4a. Other DEAD-box-containing proteins, which are less closely related to HelC, have been implicated in developmental roles in Drosophila [3] and Xenopus laevis; one example is the Xenopus Vasa-like protein (XVLP) [4-6]. In Drosophila and Xenopus, Vasa and XVLP, respectively, are required for the establishment of tissue polarity during development. In yeast, DEAD-box helicases such as Prp8 [7] are components of the spliceosome and connect pre-mRNA splicing with the cell cycle. Disruption of the helC gene in D. discoideum led to developmental asynchrony, failure to differentiate and aberrant morphogenesis. We postulate that one reason for the existence of large families of homologous DEAD-box proteins in yeast, mammals and Dictyostelium could be that some DEAD-box proteins have developmentally specific roles regulating protein translation or mRNA stability.

Animals↗