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PubMed2003

European data format 'plus' (EDF+), an EDF alike standard format for the exchange of physiological data.

The European data format (EDF) is a widely accepted standard for exchange of electroencephalogram and polysomnogram data between different equipment and labs. But it hardly accommodates other investigations. EDF+ is a more flexible but still simple format which is compatible to EDF except that an EDF+ file may contain interrupted recordings. Also, EDF+ supports time-stamped annotations for the storage of events such as text annotations, stimuli, averaged signals, electrocardiogram parameters, apnoeas and so on. When compared to EDF, EDF+ can not only store annotations but also electromyography, evoked potentials, electroneurography, electrocardiography and many more types of investigations. Further improvements over EDF include the use of standard electrode names. EDF+ is so much like EDF that existing EDF viewers still display the signals in EDF+ files. Software development is limited mainly to implementing the annotations. EDF+ offers a format for a wide range of neurophysiological investigations which can become a standard within a few years.

Data Interpretation, Statistical↗
PubMed1995

Incorporation of 2'-deoxy-6-thioguanosine into G-rich oligodeoxyribonucleotides inhibits G-tetrad formation and facilitates triplex formation.

An efficient and expeditious method for the synthesis of S6-(cyanoethyl)-N2-isobutyryl (or trifluoroacetyl)-2'-deoxy-6-thioguanosine (7 and 2) from 2'-deoxyguanosine (G) has been developed. Compound 7 has been incorporated into several G-rich triple-helix-forming oligonucleotides (TFOs) using solid-support, phosphoramidite chemistry. The purified oligonucleotides containing 2'-deoxy-6-thioguanosine (S6-dG) residues in the place of G have been characterized by nucleoside composition analysis. These modified TFOs have been shown to be stable in aqueous, as well as buffered, solutions normally used to assay triple-helix formation. It has also been demonstrated that partial incorporation of S6-dG is effective in inhibiting the formation of G tetrads in G-rich oligodeoxyribonucleotides, thus facilitating triple-helix formation in potassium-containing buffers.

Base Sequence↗
PubMed2001

Modeling the formation of secondary organic aerosol (SOA). 2. The predicted effects of relative humidity on aerosol formation in the alpha-pinene-, beta-pinene-, sabinene-, delta 3-carene-, and cyclohexene-ozone systems.

Atmospheric oxidation of volatile organic compounds can lead to the formation of secondary organic aerosol (SOA) through the gas/particle (G/P) partitioning of the oxidation products. Since water is ubiquitous in the atmosphere, the extent of the partitioning for any individual organic product depends not only on the amounts and properties of the partitioning organic compounds, but also on the amount of water present. Predicting the effects of water on the atmospheric G/P distributions of organic compounds is, therefore, central to understanding SOA formation. The goals of the current work are to gain understanding of how increases in RH affect (1) overall SOA yields, (2) water uptake by SOA, (3) the behaviors of individual oxidation products, and (4) the fundamental physical properties of the SOA phase that govern the G/P distribution of each of the oxidation products. Part 1 of this series considered SOA formation from five parent hydrocarbons in the absence of water. This paper predicts how adding RH to those systems uniformly increases both the amount of condensed organic mass and the amount of liquid water in the SOA phase. The presence of inorganic components is not considered. The effect of increasing RH is predicted to be stronger for SOA produced from cyclohexene as compared to SOA produced from four monoterpenes. This is likely a result of the greater general degree of oxidation (and hydrophilicity) of the cyclohexene products. Good agreement was obtained between predicted SOA yields and laboratory SOA yield data actually obtained in the presence of water. As RH increases, the compounds that play the largest roles in changing both the organic and water masses in the SOA phase are those with vapor pressures that are intermediate between those of essentially nonvolatile and highly volatile species. RH-driven changes in the compound-dependent G/P partitioning coefficient Kp result from changes in both the average molecular weight MWom of the absorbing organic/water phase, and the compound-dependent activity coefficient zeta values. Adding water to the SOA phase by increasing the RH drives down MWom and thereby uniformly favors SOA condensation. The effect of RH on zeta values is compound specific and depends on the hydrophilicity of the specific compound of interest; the more hydrophilic a compound, the more increasing RH will favor its condensation into the SOA phase. The results also indicate that it may be a useful first approximation to assume that zeta = 1 for many compounds making up SOA mixtures.

Aerosols↗
PubMed2002

Kinetics and mechanism of the formation of nitroprusside from aquapentacyanoferrate(III) and NO: complex formation controlled by outer-sphere electron transfer.

The kinetics and mechanism of the reaction between nitric oxide and aquapentacyanoferrate(III) were studied in detail. Pentacyanonitrosylferrate (nitroprusside, NP) was produced quantitatively in a pseudo-first-order process. The complex-formation rate constant was found to be 0.252 +/- 0.004 M(-1) s(-1) at 25.5 degrees C, pH 3.0 (HClO(4)), and I = 0.1 M (NaClO(4)), for which the activation parameters are DeltaH++ = 52 +/- 1 kJ mol(-1), DeltaS++ = -82 +/- 4 J K(-1) mol(-1), and DeltaV++ = -13.9 + 0.5 cm(3) mol(-1). These data disagree with earlier studies on complex-formation reactions of aquapentacyanoferrate(III), for which a dissociative interchange (I(d)) mechanism was suggested. The aquapentacyanoferrate(II) ion was detected as a reactive intermediate in the reaction of aquapentacyanoferrate(III) with NO, by using pyrazine and thiocyanate as scavengers for this intermediate. In addition, the reactions of other [Fe(III)(CN)(5)L](n-) complexes (L = NCS(-), py, NO(2)(-), and CN(-)) with NO were studied. These experiments also pointed to the formation of Fe(II) species as intermediates. It is proposed that aquapentacyanoferrate(III) is reduced by NO to the corresponding Fe(II) complex through a rate-determining outer-sphere electron-transfer reaction controlling the overall processes. The Fe(II) complex rapidly reacts with nitrite producing [Fe(II)(CN)(5)NO(2)](4)(-), followed by the fast and irreversible conversion to NP.

Algorithms↗
PubMed2003

15N CIDNP study of formation and decay of peroxynitric acid: evidence for formation of hydroxyl radicals.

The reaction of nitrous acid with hydrogen peroxide leads to nitric acid as the only stable product. In the course of this reaction, peroxynitrous acid (ONOOH) and, in the presence of CO(2), a peroxynitrite-CO(2) adduct (ONOOCO(2)(-)) are intermediately formed. Both intermediates decompose to yield highly oxidizing radicals, which subsequently react with excess hydrogen peroxide to yield peroxynitric acid (O(2)NOOH) as a further intermediate. During these reactions, (15)N chemically induced dynamic nuclear polarization (CIDNP) effects are observed, the analysis of the pH dependency of which allows the elucidation of mechanistic details. The formation and decay of peroxynitric acid via free radicals NO(2)(*) and HOO(*) is demonstrated by the appearance of (15)N CIDNP leading to emission (E) in the (15)N NMR signal of O(2)NOOH during its formation and to enhanced absorption (A) during its decay reaction. Additionally, the (15)N NMR signal of the nitrate ion (NO(3)(-)) appears in emission at pH approximately 4.5. These observations are explained by proposing the intermediate formation of short-lived radical anions O(2)NOOH(*)(-) probably generated by electron transfer between peroxynitric acid and peroxynitrate anion, followed by decomposition of O(2)NOOH(*)(-) into NO(3)(-) and HO(*) and NO(2)(-) and HOO(*) radicals, respectively. The feasibility of such reactions is supported by quantum-chemical calculations at the CBS-Q level of theory including PCM solvation model corrections for aqueous solution. The release of free HO(*) radicals during decomposition of O(2)NOOH is supported by (13)C and (1)H NMR product studies of the reaction of preformed peroxynitric acid with [(13)C(2)]DMSO (to yield the typical "HO(*) products" methanesulfonic acid, methanol, and nitromethane) and by ESR spectroscopic detection of the HO(*) and CH(3)(*) radical adducts to the spin trap compound POBN in the absence and presence of isotopically labeled DMSO, respectively.

Journal Article↗
PubMed2000

Kinetics and mechanism of complex formation reactions in the Iron(III)-phosphate ion system at large iron(III) excess. Formation of a tetranuclear complex.

The kinetics and mechanism of the iron(III)-phosphate ion reaction were studied at large iron(III) excess using the stopped-flow method at 10.0 degrees C in 1.0 M NaClO4. In the first few hundred milliseconds of the reaction, the formation of a novel tetranuclear complex was confirmed. The following composition is proposed for the new species: Fe4(PO4)(OH)2(H2O)16(7+). According to detailed kinetic studies, the formation of this species is first order with respect to Fe2(OH)2(H2O)8(4+) and H2PO4- and presumably proceeds via a dinuclear intermediate species. At longer reaction times slow dissociation of the tetranuclear complex controls the formation of the thermodynamically favored Fe(PO4)(H2O)5 complex. The overall reaction was interpreted in terms of the following reactions: Fe2(OH)2(H2O)8(4+) [symbol: see text] 2Fe3+ mn; Fe2(OH)2(H2O)8(4+) + P(V) [symbol: see text] Fe2PV; Fe2PV + Fe2(OH)2(H2O)8(4+) [symbol: see text] Fe4PV; Fe3+ mn + P(V) [symbol: see text] Fe(PO4)(H2O)5. (Fe3+ mn = Fe(H2O)6(3+) + Fe(OH)(H2O)5(2+); P(V) = H3PO4 + H2PO4-; Fe2PV = Fe2(HPO4)(OH)(H2O)8(3+); Fe4PV = Fe4(PO4)(OH)2(H2O)16(7+).) The pH dependence and relevant rate and equilibrium constants are reported for the individual reaction steps.

Journal Article↗
PubMed2000

Structure-function relationships in aminoquinolines: effect of amino and chloro groups on quinoline-hematin complex formation, inhibition of beta-hematin formation, and antiplasmodial activity.

Comparison of 19 aminoquinolines supports the hypothesis that chloroquine and related antimalarials act by complexing ferriprotoporphyrin IX (Fe(III)PPIX), inhibiting its conversion to beta-hematin (hemozoin) and hence its detoxification. The study suggests that a basic amino side chain is also essential for antiplasmodial activity. 2- And 4-aminoquinolines are unique in their strong affinity for Fe(III)PPIX, and attachment of side chains to the amino group has relatively little influence on the strength of complex formation. Association with Fe(III)PPIX is necessary, but not sufficient, for inhibiting beta-hematin formation. Presence of a 7-chloro group in the 4-aminoquinoline ring is a requirement for beta-hematin inhibitory activity, and this is also unaffected by side chains attached to the amino group. In turn, beta-hematin inhibitory activity is necessary, but not sufficient, for antiplasmodial activity as the presence of an aminoalkyl group attached to the 4-amino-7-chloroquinoline template is essential for strong activity. We thus propose that the 4-aminoquinoline nucleus of chloroquine and related antimalarials is responsible for complexing Fe(III)PPIX, the 7-chloro group is required for inhibition of beta-hematin formation, and the basic amino side chain is required for drug accumulation in the food vacuole of the parasite.

Aminoquinolines↗
PubMed2003

The formation of cluster elliptical galaxies as revealed by extensive star formation.

The most massive galaxies in the present-day Universe are found to lie in the centres of rich clusters. They have old, coeval stellar populations suggesting that the bulk of their stars must have formed at early epochs in spectacular starbursts, which should be luminous phenomena when observed at submillimetre wavelengths. The most popular model of galaxy formation predicts that these galaxies form in proto-clusters at high-density peaks in the early Universe. Such peaks are indicated by massive high-redshift radio galaxies. Here we report deep submillimetre mapping of seven high-redshift radio galaxies and their environments. These data confirm not only the presence of spatially extended regions of massive star-formation activity in the radio galaxies themselves, but also in companion objects previously undetected at any wavelength. The prevalence, orientation, and inferred masses of these submillimetre companion galaxies suggest that we are witnessing the synchronous formation of the most luminous elliptical galaxies found today at the centres of rich clusters of galaxies.

Journal Article↗
PubMed1997

Color pattern formation on the wing of the butterfly Pieris rapae. 1. Cautery induced alteration of scale color and delay of arrangement formation.

Experimental approaches to color pattern formation of lepidopteran insects have been made exclusively by analyzing pattern alterations in adult wings induced by operations. We microcauterized the presumptive black region of the dorsal forewing of the butterfly Pieris rapae and analyzed not only the resultant color pattern in the adult wing but also the cell behavior in the pupal wing epidermis around the injury. Cautery induced color alterations were as follows: (i) cautery up to 49.5 h after pupation resulted in white regions appearing within the black region while later cauteries induced larger white regions; (ii) cautery between 50 and 59.5 h resulted in the white regions induced by the cauteries being dramatically decreased; (iii) cautery after 60 h resulted in white regions that had almost disappeared. The examination of the cell behavior in the pupal wing epidermis after cauteries showed that the row formation of scale precursor cells was delayed. This delayed area varied with the time of cautery, in the same manner as that in the induced white area in the adult wing ((i)-(iii) above). The relationship between scale color alteration and the developmental delay of the scale row formation is discussed.

Animals↗
PubMed1997

Effect of protein phosphatase inhibitors on cleavage furrow formation in newt eggs: inhibition of normal furrow formation and concomitant induction of furrow-like dents.

The effects of three protein phosphatase inhibitors, okadaic acid, calyculin A and tautomycin, on the formation of cleavage furrows and the induction of furrow-like dents in the egg of the newt, Cynops pyrrhogaster, were examined. Solutions of the individual compound were injected into the animal hemisphere of one of the two presumptive blastomere regions of the embryo during the first cleavage. Injection of a solution containing any of the chemicals often disturbed the formation of a normal furrow in the injected blastomere at second cleavage. Injection with okadaic acid or calyculin A often induced furrow-like dents on the surface of the injected blastomere at the same time as second cleavage in control embryos, while that with tautomycin usually did not induce them. In an injected blastomere, formation of dents started in the animal half and moved towards the vegetal half as the furrow in its counterpart blastomere extended from the animal half towards the vegetal. Dents gradually became slightly deeper and formed cytoplasmic projections that later degenerated, leaving a surface scar. Cytological observations on blastomeres injected with calyculin A revealed that nuclear division occurred normally.

Animals↗
PubMed2005

Fluorescence quenching by excimer formation: quenching constant approximations for excimer formation-dissociation by classical potential models.

Fluorescence quenching by excimer formation is studied on the assumption that the excimer formation and dissociation can be modeled as overdamped motion in an attractive potential (classical potential models). An approach to the zeroth-order, concentration-independent quenching constants is proposed which starts from a mean reaction-time ansatz and reduces the calculation essentially to the solution of the eigenvalue problem for the Smoluchowski operator which describes the excimer equilibration. For a square-well potential model it is shown that a quenching constant expansion in terms of relaxation modes, truncated at the kinetic level, gives a satisfactory approximation of the recently obtained exact zeroth-order result under defined conditions. It is demonstrated how this two-mode approach can be applied for a quenching constant estimation if the excimer formation and dissociation are modeled by more realistic interaction potentials, as for instance, Morse- or Gaussian-type ones.

Journal Article↗
PubMed1999

Targeted down-regulation of caveolin-3 is sufficient to inhibit myotube formation in differentiating C2C12 myoblasts. Transient activation of p38 mitogen-activated protein kinase is required for induction of caveolin-3 expression and subsequent myotube formation.

Caveolin-3 is the principal structural protein of caveolae membrane domains in striated muscle cells. Caveolin-3 mRNA and protein expression are dramatically induced during the differentiation of C2C12 skeletal myoblasts, coincident with myoblast fusion. In these myotubes, caveolin-3 localizes to the sarcolemma (muscle cell plasma membrane), where it associates with the dystrophin-glycoprotein complex. However, it remains unknown what role caveolin-3 plays in myoblast differentiation and myotube formation. Here, we employ an antisense approach to derive stable C2C12 myoblasts that fail to express the caveolin-3 protein. We show that C2C12 cells harboring caveolin-3 antisense undergo differentiation and express normal amounts of four muscle-specific marker proteins. However, C2C12 cells harboring caveolin-3 antisense fail to undergo myoblast fusion and, therefore, do not form myotubes. Interestingly, treatment with specific p38 mitogen-activated protein kinase inhibitors blocks both myotube formation and caveolin-3 expression, but does not affect the expression of other muscle-specific proteins. In addition, we find that three human rhabdomyosarcoma cell lines do not express caveolin-3 and fail to undergo myoblast fusion. Taken together, these results support the idea that caveolin-3 expression is required for myoblast fusion and myotube formation, and suggest that p38 is an upstream regulator of caveolin-3 expression.

Caveolin 3↗
PubMed1985

Elevated levels of petite formation in strains of Saccharomyces cerevisiae restored to respiratory competence. II. Organization of mitochondrial genomes in strains having high and moderate frequencies of petite mutant formation.

Restriction enzyme analysis of aberrant mtDNA molecules in restored strains of Saccharomyces cerevisiae that displays an elevated level of petite formation has shown the occurrence of novel junction fragments and nonstoichiometric amounts for some unaltered bands. Five aberrant mitochondrial genomes from high-frequency petite-forming (hfp) strains (greater than 60% petites per generation) contain like-oriented duplications and single copy regions. High-frequency petite formation is postulated to arise from increased intramolecular recombination between duplicated segments. Mitochondrial DNA structures in two other hfp strains cannot be easily interpreted and might arise from intramolecular recombination. Mitochondria DNA from moderate-frequency petite-forming (mfp) strains (5-16% petites per generation) contains inverted duplications in two cases. The elevated petite formation is postulated to arise from homologous recombination between directly repeated sequences. In mtDNA from one mfp strain, deletion end-points have been shown to overlap. Such deletion endpoint overlap is postulated to be required for the maintenance of the tandem duplication in hfp strains. Two regions of the wild-type mtDNA (between cyb and oli2 and between SrRNA and oxi2) appear to be dispensable for mitochondrial function.

Chromosome Deletion↗
PubMed2005

Calpain inhibitor MDL28170 modulates Abeta formation by inhibiting the formation of intermediate Abeta46 and protecting Abeta from degradation.

The observations that three major cleavages within the transmembrane domain of APP, namely, the gamma-cleavage, -cleavage, and the newly identified zeta-cleavage, are involved in the generation of secreted Abeta40 and Abeta42 prompted us to determine how the calpain inhibitor III MDL 28170 influences these three cleavages and Abeta formation. With the use of a cell culture system, our data demonstrate that 1) at either high concentrations, or at a low range of concentrations, at early time points, MDL 28170 inhibits the formation of secreted Abeta40 and Abeta42. However, this effect is due to inhibition of the intermediate Abeta46 generation by zeta-cleavage and not due to direct inhibition of the gamma-cleavage that produces Abeta40/42 from Abeta46; 2) at low range of concentrations and at late time points, MDL 28170 causes an increase in secreted Abeta40/42 that likely results from inhibition of degradation of both the initial substrate, CTFbeta, and the final product, Abeta40/42, of gamma-secretase. These data strongly suggest that formation of Abeta46 is a key step in the gamma-secretase mediated generation of Abeta40/42 and provide a new target for the development of Abeta inhibitors. These data also suggest that calpain and related proteases, which are sensitive to MDL 28170, play an important role in the accumulation of secreted Abeta.

Amyloid Precursor Protein Secretases↗
PubMedDate not supplied

Evolution of the medical record format during two years' use of an open-format microcomputer charting system.

In 1988, the authors implemented a microcomputer charting system (SmartChart) within a busy dialysis unit and an outpatient dialysis practice, to be used as the primary recording instrument for physicians and nurses. The program defined the organization of the medical record as three types of titles: problems, therapies, and numerics. Each title had a variety of associated data, such as comments, dosages, values and normals. Predefined care plans were created, and keyboard entry was in a completely open format. Over the next two years, the overall format of this medical record proved to be highly effective, and strict problem orientation allowed both nurses and physicians to use the same problem list. A more specific organization of the title lists in the medical record was needed, however. Separate symbols were placed in front of: problem titles related to prior therapies; problems recorded during current therapies; History and Physical (H&P) data; Plans/Orders; and inactive problems. PRN therapies, those therapies related to patient treatments, vital signs, and numeric data recorded during treatments were identified. The basic format of the medical record that evolved has proven suitable for outpatient, inpatient, and specialized treatment centers.

Attitude to Computers↗
PubMed2003

TNP-470 inhibits 7,12-dimethylbenz[a]anthracene-induced mammary tumor formation when administered before the formation of carcinoma in situ but is not additive with tamoxifen.

In many women pathologic lesions, such as hyperplasia and carcinoma in situ, precede invasive breast cancer. We have shown that tissue vascularity increases with histologic progression to invasive disease. Similarly, in the well-characterized 7,12-dimethylbenz[a]anthracene (DMBA) model of mammary tumorigenesis, preinvasive lesions exhibit increased vascularity with progression. Using this model we asked whether inhibition of angiogenesis would block progression and if so, at which stage. We treated rats with DMBA followed by the potent angiogenic inhibitor, TNP-470, and/or tamoxifen starting 1 day or 6 weeks later. Histopathology and in vitro angiogenic potential of mammary organoids were evaluated 3 months after DMBA. All statistical tests were two-sided. Early TNP-470 and tamoxifen treatment inhibited the formation of carcinoma in situ (p < 0.001) and invasive disease (p < 0.001). However, their effects were not additive, despite their unique mechanisms of action. TNP-470 administration begun at the time of microscopic carcinoma in situ formation was unable to prevent the further development of carcinoma in situ or invasive breast cancer, whereas tamoxifen was highly effective (p = 0.001). There was no added benefit of combining TNP-470 and tamoxifen. TNP-470 therapy, unlike tamoxifen, did not inhibit the angiogenic potential of DMBA-treated normal mammary organoids, supporting its lack of a direct effect on the epithelium. These data provide proof-in-principle that inhibition of angiogenesis early in mammary tumorigenesis prevents mammary tumor formation in a hormone-sensitive model, indicating that angiogenesis is a potential target for cancer chemoprevention. Interactions with other chemopreventive strategies and the timing of administration must be thoroughly examined in vivo.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1994

Rhizobium nod factors reactivate the cell cycle during infection and nodule primordium formation, but the cycle is only completed in primordium formation.

Rhizobia induce the formation of root nodules on the roots of leguminous plants. In temperate legumes, nodule organogenesis starts with the induction of cell divisions in regions of the root inner cortex opposite protoxylem poles, resulting in the formation of nodule primordia. It has been postulated that the susceptibility of these inner cortical cells to Rhizobium nodulation (Nod) factors is conferred by an arrest at a specific stage of the cell cycle. Concomitantly with the formation of nodule primordia, cytoplasmic rearrangement occurs in the outer cortex. Radially aligned cytoplasmic strands form bridges, and these have been called preinfection threads. It has been proposed that the cytoplasmic bridges are related to phragmosomes. By studying the in situ expression of the cell cycle genes cyc2, H4, and cdc2 in pea and alfalfa root cortical cells after inoculation with Rhizobium or purified Nod factors, we show that the susceptibility of inner cortical cells to Rhizobium is not conferred by an arrest at the G2 phase and that the majority of the dividing cells are arrested at the G0/G1 phase. Furthermore, the outer cortical cells forming a preinfection thread enter the cell cycle although they do not divide.

Amino Acid Sequence↗
PubMed1990

Ectopic head and foot formation in Hydra: diacylglycerol-induced increase in positional value and assistance of the head in foot formation.

In wild type Hydra magnipapillata, daily application of the protein kinase C activator diacylglycerol (DAG) evokes sprouting of periodically spaced ectopic heads along the body column and leads to loss of the ability to regenerate proximal structures including the foot. The present transplantation studies show that the appearance of ectopic heads is preceded by an early increase in the 'positional value' (P-value) or 'head activation potential' of the gastric column. Long before ectopic head structures emerge, pieces of DAG-treated tissue transplanted into the corresponding positional level of untreated hosts induce head formation instead of being integrated, whereas pieces implanted from untreated donors into DAG-treated hosts form feet. Foot formation implies a decrease in the P-value. This down-regulation is promoted through long-range assistance by the head. Thus, after termination of the DAG treatment ectopic feet are intercalated midway between the periodically spaced heads; moreover, untreated polyps onto which additional distal heads have been grafted regenerate feet faster than do one-headed polyps and may form supernumerary feet. Multiheaded animals can also be produced using two substances (K-252a and xanthate D609) that interfere with signal transduction, but the mode by which secondary heads arise is different from DAG-induced ectopic head formation. Presumably because the assistance by the parental head is impaired, buds fail to form a foot and detach and instead give rise to stable secondary body axes. It is assumed that the P-value along the body varies according to the number of cellular receptors for factors serving as intercellular signals.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗