Showing papers by "ETH Zurich published in 1992"

Amphibole composition in tonalite as a function of pressure: an experimental calibration of the Al-in-hornblende barometer

Abstract: The Al-in-hornblende barometer, which correlates Altot content of magmatic hornblende linearly with crystallization pressure of intrusion (Hammarstrom and Zen 1986), has been calibrated experimentally under water-saturated conditions at pressures of 2.5–13 kbar and temperatures of 700–655°C. Equilibration of the assemblage hornlende-biotite-plagioclase-orthoclasequartz-sphene-Fe-Ti-oxide-melt-vapor from a natural tonalite 15–20° above its wet solidus results in hornblende compositions which can be fit by the equation: P(±0.6 kbar) = −3.01 + 4.76 Al hbl tot r 2=0.99, where Altot is the total Al content of hornblende in atoms per formula unit (apfu). Altot increase with pressure can be ascribed mainly to a tschermak-exchange ( $$t\vec k,{\text{ Mg}}_{{\text{ - 1 }}} {\text{Al}}^{{\text{VI}}} {\text{Si}}_{{\text{ - 1}}} {\text{ Al}}^{{\text{IV}}}$$ ) accompanied by minor plagioclase-substitution ( $$\vec pl,{\text{ Ca}}_{{\text{ - 1 }}} {\text{Na}}^{{\text{M(4)}}} {\text{ Al}}_{{\text{ - 1}}}^{{\text{IV}}} {\text{ Si}}$$ ). This experimental calibration agrees well with empirical field calibrations, wherein pressures are estimated by contact-aureole barometry, confirming that contact-aureole pressures and pressures calculated by the Al-in-hornblende barometer are essentially identical. This calibration is also consistent with the previous experimental calibration by Johnson and Rutherford (1989b) which was accomplished at higher temperatures, stabilizing the required buffer assemblage by use of mixed H2O-CO2 fluids. The latter calibration yields higher Altot content in hornblendes at corresponding pressures, this can be ascribed to increased edenite-exchange ( $$\vec ed,{\text{ }}\square _{{\text{ }} - {\text{ }}1}^{ A} {\text{ Na}}^{\text{A}} {\text{Si }}_{ - {\text{ }}1} {\text{Al}}^{{\text{IV}}}$$ ) at elevated temperatures. The comparison of both experimental calibrations shows the important influence of the fluid composition, which affects the solidus temperature, on equilibration of hornblende in the buffering phase assemblage.

Exhaustive matching of the entire protein sequence database

Abstract: The entire protein sequence database has been exhaustively matched. Definitive mutation matrices and models for scoring gaps were obtained from the matching and used to organize the sequence database as sets of evolutionarily connected components. The methods developed are general and can be used to manage sequence data generated by major genome sequencing projects. The alignments made possible by the exhaustive matching are the starting point for successful de novo prediction of the folded structures of proteins, for reconstructing sequences of ancient proteins and metabolisms in ancient organisms, and for obtaining new perspectives in structural biochemistry.

Water in the Earth's upper mantle

Abstract: Experiments on the stability of hydrous minerals likely to be present in the Earth's mantle provide constraints on the distribution of water in the mantle, and the form in which it is stored. In regions of elevated mantle temperature, water may be stored not in minerals but in melts: such hydrous melts are important metasomatizing agents, and can induce volcanism beneath thick cratonic lithosphere.

NMR determination of residual structure in a urea-denatured protein, the 434-repressor.

Abstract: A nuclear magnetic resonance (NMR) structure determination is reported for the polypeptide chain of a globular protein in strongly denaturing solution. Nuclear Overhauser effect (NOE) measurements with a 7 molar urea solution of the amino-terminal 63-residue domain of the 434-repressor and distance geometry calculations showed that the polypeptide segment 54 to 59 forms a hydrophobic cluster containing the side chains of Val54, Val56, Trp58, and Leu59. This residual structure in the urea-unfolded protein is related to the corresponding region of the native, folded protein by simple rearrangements of the residues 58 to 60. Based on these observations a model for the early phase of refolding of the 434-repressor(1-63) is proposed.

Energy absorption mechanism by biological bodies in the near field of dipole antennas above 300 MHz

Abstract: The energy absorption mechanism in the close near field of dipole antennas is studied by numerical simulations. All computations are performed and validated applying the three-dimensional multiple multipole software package. The numerical model of the plane phantom is additionally checked by accurate as possible experimental measurements. For the plane phantom, the interaction mechanism can be described well by H-field induced surface currents. The spatial peak specific absorption rate can be approximated within 3 dB by a formula given here based on the incident H-field or antenna current and on the conductivity and permittivity of the tissue. These findings can be generalized to heterogeneous tissues and larger biological bodies of arbitrary shape for frequencies above 300 MHz. The specific absorption rate is mainly proportional to the square of the incident H-field, which implies that in the close near field, the spatial peak specific absorption rate is related to the antenna current and not to the input power. >

Conditionally-perfect secrecy and a provably-secure randomized cipher

Abstract: Shannon's pessimistic theorem, which states that a cipher can be perfect only when the entropy of the secret key is at least as great as that of the plaintext, is relativized by the demonstration of a randomized cipher in which the secret key is short but the plaintext can be very long. This cipher is shown to be “perfect with high probability.” More precisely, the eavesdropper is unable to obtain any information about the plaintext when a certain security event occurs, and the probability of this event is shown to be arbitrarily close to one unless the eavesdropper performs an infeasible computation. This cipher exploits the assumed existence of a publicly-accessible string of random bits whose length is much greater than that of all the plaintext to be encrypted; this is a feature that our cipher has in common with the previously considered “book ciphers”. Two modifications of this cipher are discussed that may lead to practical provably-secure ciphers based on either of two assumptions that appear to be novel in cryptography, viz., the (sole) assumption that the enemy's memory capacity (but not his computing power) is restricted and the assumption that an explicit function is, in a specified sense, controllably-difficult to compute, but not necessarily one-way.

Hash functions based on block ciphers

Abstract: Iterated hash functions based on block ciphers are treated. Five attacks on an iterated hash function and on its round function are formulated. The wisdom of strengthening such hash functions by constraining the last block of the message to be hashed is stressed. Schemes for constructing m-bit and 2m-bit hash round functions from m-bit block ciphers are studied. A principle is formalized for evaluating the strength of hash round functions, viz., that applying computationally simple (in both directions) invertible transformations to the input and output of a hash round function yields a new hash round function with the same security. By applying this principle, four attacks on three previously proposed 2m-bit hash round functions are formulated. Finally, three new hash round functions based on an m-bit block cipher with a 2m-bit key are proposed.

A universal statistical test for random bit generators

Abstract: A new statistical test for random bit generators is presented which, in contrast to presently used statistical tests, is universal in the sense that it can detect any significant deviation of a device's output statistics from the statistics of a truly random bit source when the device can be modeled as an ergodic stationary source with finite memory but arbitrary (unknown) state transition probabilities. The test parameter is closely related to the device's per-bit entropy which is shown to be the correct quality measure for a secret-key source in a cryptographic application. The test hence measures the cryptographic badness of a device's possible defect. The test is easy to implement and very fast and thus well suited for practical applications. A sample program listing is provided.

Extremal functions for the trudinger-moser inequality in 2 dimensions

Abstract: We prove that theTrudinger-Moser constant $$\sup \left\{ {\int_\Omega {\exp (4\pi u^2 )dx:u \in H_0^{1,2} (\Omega )\int_\Omega {\left| { abla u} \right|^2 dx \leqslant 1} } } \right\}$$ is attained on every 2-dimensional domain. For disks this result, is due to Carleson-Chang. For other domains we derived an isoperimetric inequality which relates the ratio of the supremum of, the functional and its maximal limit on concentrating sequences to the corresponding quantity for disks. A conformal rearrangement is introduced to prove this inequality. I would like to thank Jurgen Moser and Michael Struwe for helpful advice and criticism.

Expression of tenascin in the developing and adult cerebellar cortex.

Abstract: Since tenascin may influence neuronal cell development, we studied its expression pattern using immunocytochemistry, in situ hybridization, Northern blot analysis, and immunochemistry in the developing and adult mouse cerebellar cortex. Tenascin immunoreactivity was detectable in all layers of the developing cerebellar cortex. In the external granular layer, only the radially oriented processes of Golgi epithelial cells were immunoreactive, whereas the densely packed cell bodies were immunonegative. Tenascin was hardly detectable at contact sites between migrating granule cells and processes of Golgi epithelial cells. Axons of granule cells in the molecular layer were immunoreactive, whereas their cell bodies in the internal granular layer lacked detectable levels of tenascin. By in situ hybridization, only Golgi epithelial cells and astrocytes of the internal granular layer and prospective white matter, but not nerve cells, could be shown to synthesize detectable levels of tenascin mRNA in the developing mouse cerebellar cortex. Thus, tenascin in the cerebellar cortex seems to be a glia-derived molecule that becomes adsorbed to neuronal surfaces in a topographically restricted pattern in situ. Levels of tenascin protein and mRNA decreased significantly with increasing age. In the adult, tenascin immunoreactivity was weak and mainly restricted to the molecular layer and tenascin mRNA was confined to Golgi epithelial cells, indicative for a functional heterogeneity in differentiated cerebellar astrocytes. Quantitative immunoblot analysis revealed that the 225 and 240 kDa components of tenascin were developmentally downregulated at a faster rate than the 190 and 200 kDa components, corresponding to the faster downregulation of the 8 kilobase (kb) mRNA species compared to the 6 kb mRNA species as revealed by Northern blot analysis. These observations indicate a differentially regulated expression of the tenascin components. We hypothesize that glia-derived tenascin modifies the functional properties of nerve cell surfaces and that tenascin is involved in such different morphogenetic events as neurite growth and oligodendrocyte distribution.

Routine quantitative analysis of brain and cerebrospinal fluid spaces with MR imaging

Abstract: A computerized system for processing spin-echo magnetic resonance (MR) imaging data was implemented to estimate whole brain (gray and white matter) and cerebrospinal fluid volumes and to display three-dimensional surface reconstructions of specified tissue classes. The techniques were evaluated by assessing the radiometric variability of MR volume data and by comparing automated and manual procedures for measuring tissue volumes. Results showed (a) the homogeneity of the MR data and (b) that automated techniques were consistently superior to manual techniques. Both techniques, however, were affected by the complexity of the structure, with simpler structures (eg, the intracranial cavity) showing less variability and better spatial correlation of segmentation results between raters. Moreover, the automated techniques were completed for whole brain in a fraction of the time required to complete the equivalent segmentation manually. Additional evaluations included interrater reliability and an evaluation that included longitudinal measurement, in which one subject was imaged sequentially 24 times, with reliability computed from data collected by three raters over 1 year. Results showed good reliability for the automated segmentation procedures.

Voronoi skeletons: theory and applications

Abstract: A novel method of robust skeletonization based on the Voronoi diagram of boundary points, which is characterized by correct Euclidean metries and inherent preservation of connectivity, is presented. The regularization of the Voronoi medial axis (VMA) in the sense of H. Blum's (1967) prairie fire analogy is done by attributing to each component of the VMA a measure of prominence and stability. The resulting Voronoi skeletons appear largely invariant with respect to typical noise conditions in the image and geometric transformations. Hierarchical clustering of the skeleton branches, the so-called skeleton pyramid, leads to further simplification of the skeleton. Several applications demonstrate the suitability of the Voronoi skeleton to higher-order tasks such as object recognition. >

The distribution of some fungal and bacterial endophytes in maize (Zea mays L.)

Abstract: Endophytic bacteria and fungi were isolated from healthy maize plants collected in a field in Devon. The average bacterial counts in the stem core tissues showed that the plant parts closer to the soil were more heavily colonized by bacteria than those near the top of the plants, and that the lower and middle part of the stems hosted the most frequently isolated bacterial species. Of the fungal species isolated, 12 had a relative importance of more than 10% in the core, 15 in the epidermis, and only 5 in the leaves. In general the distribution patterns were different among the three tissue types studied, with core and epidermis of the stems showing almost equal colonization frequencies and the leaves being most heavily colonized. More fungal species were recovered from the core and epidermis of the stem than from the leaves. The fungi most frequently isolated showed some patterns of tissue specificity, with Alternaria alternata almost exclusively associated with the leaves and Aureobasidium pullulans var. melanigerum most often present in the epidermal tissues. Assays showed low fungal colonization of seeds taken from freshly matured cobs and of seeds dried for 8 wk before testing, in contrast to higher colonization frequencies observed for the seeds used for planting. The mean values for fungal isolations in the stem pieces mostly in contact with the soil flora or close to the ground were lower than those of the more centrally placed sections. These areas of low fungal infection yielded the highest bacterial counts. The potential role of bacterial endophytes in biological control is briefly discussed.

Comparison of the NMR solution structure and the x-ray crystal structure of rat metallothionein-2

Abstract: Metallothioneins are small cysteine-rich proteins capable of binding heavy metal ions such as Zn2+ and Cd2+. They are ubiquitous tissue components in higher organisms, which tentatively have been attributed both unspecific protective functions against toxic metal ions and highly specific roles in fundamental zinc-regulated cellular processes. In this paper a detailed comparison of the NMR solution structure [Schultze, P., Worgotter, E., Braun, W., Wagner, G., Vasak, M., Kagi, J. H. R. & Wuthrich, K. (1988) J. Mol. Biol. 203, 251-268] and a recent x-ray crystal structure [Robbins, A. H., McRee, D. E., Williamson, M., Collett, S. A., Xoung, N. H., Furey, W. F., Wang, B. C. & Stout, C. D. (1991) J. Mol. Biol. 221, 1269-1293] of rat metallothionein-2 shows that the metallothionein structures in crystals and in solution have identical molecular architectures. The structures obtained with both techniques now present a reliable basis for discussions on structure-function correlations in this class of metalloproteins.

Chemistry of potentially prebiological natural products

Abstract: A relationship between what might be called a kinetic version of Le Chatelier's principle and chemical self-organization is considered. Some aspects of the search for a pre-RNA genetic system are discussed. Results of an experimental investigation on the pairing properties of alternative nucleic acid systems — including those of pyranosyl-RNA (‘p-RNA’), a constitutional isomer of RNA — are summarized.

Herbicide-resistant Indica rice plants from IRRI breeding line IR72 after PEG-mediated transformation of protoplasts

Abstract: The commercially important Indica rice cultivar Oryza sativa cv. IR72 has been transformed using direct gene transfer to protoplasts. PEG-mediated transformation was done with two plasmid constructs containing either a CaMV 35S promoter/HPH chimaeric gene conferring resistance to hygromycin (Hg) or a CaMV 35S promoter/BAR chimaeric gene conferring resistance to a commercial herbicide (Basta) containing phosphinothricin (PPT). We have obtained so far 92 Hgr and 170 PPTr IR72 plants from protoplasts through selection. 31 Hgr and 70 PPTr plants are being grown in the greenhouse to maturity. Data from Southern analysis and enzyme assays proved that the transgene was stably integrated into the host genome and expressed. Transgenic plants showed complete resistance to high doses of the commercial formulations of PPT.

Protein hydration in aqueous solution.

Abstract: Proton nuclear magnetic resonance was used to study individual molecules of hydration water bound to the protein basic pancreatic trypsin inhibitor (BPTI) and to the nonapeptide oxytocin in aqueous solution. The experimental observations are nuclear Overhauser effects (NOE) between protons of individual amino acid residues of the protein and those of hydration water. These NOEs were recorded by two-dimensional (2D) and three dimensional (3D) NOE spectroscopy (NOESY) in the laboratory frame, and by the corresponding experiments in the rotating frame (ROESY). The studies show that there are two qualitatively different types of hydration sites. Four water molecules in the interior of the BPTI molecule are in identical locations in the crystal structure and in solution. Their NOEs with the protein protons are characterized by large negative cross-relaxation rates sigma NOE, which indicates that the residence times of the water molecules in these hydration sites are longer than ca. 10 ns. Additional experiments with extrinsic shift reagents established an upper limit of 20 ms at 4 degrees C for these residence times. Surface hydration of both the globular protein BPTI and the flexibly disordered polypeptide oxytocin is by water molecules with residence times in the subnanosecond range, as evidenced by small positive sigma NOE values observed for their NOEs with nearby polypeptide protons. Short residence times prevail for all surface hydration sites, independent of whether or not they are occupied by well ordered, X-ray observable water in the protein single crystals.

NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution

Abstract: The residence times of individual hydration water molecules in the major and minor grooves of DNA were measured by nuclear magnetic resonance (NMR) spectroscopy in aqueous solutions of d-(CGCGAATTCGCG)2 and d-(AAAAATTTTT)2. The experimental observations were nuclear Overhauser effects (NOE) between water protons and the protons of the DNA. The positive sign of NOEs with the thymine methyl groups shows that the residence times of the hydration water molecules near these protons in the major groove of the DNA must be shorter than about 500 ps, which coincides with the behavior of surface hydration water in peptides and proteins. Negative NOEs were observed with the hydrogen atoms in position 2 of adenine in both duplexes studied. This indicates that a 'spine of hydration' in the minor groove, as observed by X-ray diffraction in DNA crystals, is present also in solution, with residence times significantly longer than 1 ns. Such residence times are reminiscent of 'interior' hydration water molecules in globular proteins, which are an integral part of the molecular architecture both in solution and in crystals.

Constructions of binary constant-weight cyclic codes and cyclically permutable codes

Abstract: A general theorem is proved showing how to obtain a constant-weight binary cyclic code from a p-ary linear cyclic code, where p is a prime, by using a representation of GF(p) as cyclic shifts of a binary p-tuple. Based on this theorem, constructions are given for four classes of binary constant-weight codes. The first two classes are shown to achieve the Johnson upper bound on minimum distance asymptotically for long block lengths. The other two classes are shown similarly to meet asymptotically the low-rate Plotkin upper bound on minimum distance. A simple method is given for selecting virtually the maximum number of cyclically distinct codewords with full cyclic order from Reed-Solomon codes and from Berlekamp-Justesen maximum-distance-separable codes. Two correspondingly optimum classes of constant-weight cyclically permutable codes are constructed. It is shown that cyclically permutable codes provide a natural solution to the problem of constructing protocol-sequence sets for the M-active-out-of-T-users collision channel without feedback. >

The respiratory system as an exercise limiting factor in normal trained subjects

Abstract: The present study was undertaken to investigate the respiratory system as an exercise limiting factor. Breathing and cycle endurance (i.e. the time until exhaustion at a given performance level) as well as physical working capacity 170 (i.e. the exercise intensity corresponding to a heart rate of 170 beats -min−1 on a cycle ergometer) were determined in four healthy sedentary subjects. Subsequently, the subjects trained their respiratory system for 4 weeks by breathing daily about 901 · min−1 for 30 min. Otherwise they continued their sedentary lifestyle. Immediately after the respiratory training and 18 months later, all performance tests carried out at the beginning of the study were repeated. The respiratory training increased breathing endurance from 4.2 (SD 1.9) min to 15.3 (SD 3.8) min. Cycle endurance was improved from 26.8 (SD 5.9) min to 40.2 (SD 9.2) min whereas physical working capacity 170 remained essentially the same. During the endurance cycling test in the respiratory untrained state, the subjects continuously increased their ventilation up to hyperventilation [ventilation at exhaustion = 96.9 (SD 23.6) 1 · min−1] while after the respiratory training they reached a respiratory steady-state without hyperventilation [ventilation at exhaustion = 63.3 (SD 14.5) 1 · min−1]. The absence of this marked hyperventilation was the cause of the impressive increase of cycle endurance in normal sedentary subjects after respiratory training. The effects gained by the respiratory training were completely lost after 18 months. Our results indicated that the respiratory system was an exercise limiting factor during an endurance test in normal sedentary subjects.

Calculation of jet cross sections in hadron collisions at order alpha s3.

Abstract: We describe an algorithm for calculating any infrared-safe quantity for hadron-hadron collisions at order {alpha}{sub {ital s}}{sup 3} in QCD. Typical quantities that can be calculated are the inclusive cross sections to make one or two high-{ital P}{sub {ital T}} jets.

The L2/HNK‐1 Carbohydrate Epitope is Involved in the Preferential Outgrowth of Motor Neurons on Ventral Roots and Motor Nerves

Abstract: Based on the observation that in adult mice the carbohydrate epitope L2/HNK-1 is detectable on Schwann cells in ventral spinal roots, but only scarcely in dorsal roots (Martini et al., Dev. Biol., 129, 330 - 338, 1988), the possibility was investigated that the carbohydrate is involved in the outgrowth of regenerating motor neuron axons on peripheral nerve substrates expressing the epitope. To monitor whether the L2 carbohydrate remains present during the time periods in which regenerating axons penetrate the denervated distal nerve stumps, the expression of L2 in motor and sensory branches of the femoral nerve was investigated in normal animals and after a crush lesion. During the first two postoperative weeks, L2 immunoreactivity remained high in the myelinating Schwann cells of the motor branch, whereas L2 immunoreactivity was virtually absent in the sensory branch. In a first experimental approach, cryosections of ventral and dorsal spinal roots and of motor and sensory nerves of adult rats and mice were used as substrates for neurite outgrowth. Neurites of motor neurons from chicken embryos were approximately 35% longer after 30 h of maintenance on ventral roots than on dorsal roots. Neurites from sensory neurons had the same length on dorsal as on ventral motors and were as long as neurites from motor neurons grown on dorsal roots. L2 antibodies reduced neurite outgrowth of motor neurons on ventral roots but not on dorsal roots. Neurite outgrowth of sensory neurons on both roots was not altered by the antibodies. Neurite outgrowth of motor neurons on a mixture of the extracellular matrix glycoprotein laminin and the L2 carbohydrate-carrying glycolipid was significantly higher than on the laminin substrate mixture with GD1b ganglioside or sulphatide. L2 antibodies reduced neurite outgrowth of motor neurons by 50% on the L2 glycolipid, but not on GD1b or sulphatide. These observations indicate that the L2 carbohydrate promotes neurite outgrowth of motor neurons in vitro and may thus contribute to the preferential reinnervation of motor nerves by regenerating motor axons in vivo.

Fungal saprobes and pathogens as endophytes of rice (Oryza sativa L.)

Abstract: summary Fungal endophytes have been isolated from inside the leaf blades, leaf sheaths, and roots of six-week-old plants as well as from seeds and ten-day-old seedlings of Oryza sativa (L.). The fungi isolated can be grouped in two categories; one containing organisms known mainly to be saprotrophic and the other comprising potential pathogens. Of the former Alternaria alternata (Fr.) Keissler and Epicoccum purpurascens Ehrenb. ex. Schlecht preferentially colonize the leaf blades of their host, whereas Cladosporium tenuissimum Cooke seems more generally distributed between leaf blades and leaf sheaths. Fusarium equiseti (Cords) Sacc., F. oxysporum Schecht and Phoma sorghina (Sacc. Boerema) are latent in their hosts without causing disease symptoms. A. alternata, E. purpurascens, F, equiseti. and Nigraspora oryzae have also been frequently isolated from seeds and young seedlings and can be considered seed-borne. Principal components analysis has shown a marked tissue specificity among rice endophytes. Leaf sheaths of the rice varieties grown under dry conditions are colonized by endophyte communities different from those of the wet cultivars.

Error bound for the hartree-fock energy of atoms and molecules

Abstract: We estimate the error of the Hartree-Fock energy of atoms and molecules in terms of the one-particle density matrix corresponding to the exact ground state. As an application we show this error to be of orderO(Z5/3−δ) for any δ<2/21 as the total nuclear chargeZ becomes large.