Showing papers by "University of California, Santa Cruz published in 1991"

Quantum statistical mechanics in a closed system

Abstract: A closed quantum-mechanical system with a large number of degrees of freedom does not necessarily give time averages in agreement with the microcanonical distribution. For systems where the different degrees of freedom are uncoupled, situations are discussed that show a violation of the usual statistical-mechanical rules. By adding a finite but very small perturbation in the form of a random matrix, it is shown that the results of quantum statistical mechanics are recovered. Expectation values in energy eigenstates for this perturbed system are also discussed, and deviations from the microcanonical result are shown to become exponentially small in the number of degrees of freedom.

The well-founded semantics for general logic programs

Abstract: A general logic program (abbreviated to "program" hereafter) is a set of roles that have both positive and negative subgoals. It is common to view a deductive database as a general logic program consisting of rules (IDB) slttmg above elementary relations (EDB, facts). It is desirable to associate one Herbrand model with a program and think of that model as the "meaning of the program, " or Its "declarative semantics. " Ideally, queries directed to the program would be answered in accordance with this model. Recent research indicates that some programs do not have a "satisfactory" total model; for such programs, the question of an appropriate partial model arises. Unfounded sets and well-founded partial models are introduced and the well-founded semantics of a program are defined to be its well-founded partial model. If the well-founded partial model is m fact a total model. it is called the well-founded model. It n shown that the class of programs possessing a total well-founded model properly includes previously studied classes of "stratified" and "locally stratified" programs, The method in this paper is also compared with other proposals in the literature, including Clark's "program completion, " Fitting's and Kunen's 3-vahred interpretations of it, and the "stable models" of Gelfond and Lifschitz.

A Simple Weight Decay Can Improve Generalization

Abstract: It has been observed in numerical simulations that a weight decay can improve generalization in a feed-forward neural network. This paper explains why. It is proven that a weight decay has two effects in a linear network. First, it suppresses any irrelevant components of the weight vector by choosing the smallest vector that solves the learning problem. Second, if the size is chosen right, a weight decay can suppress some of the effects of static noise on the targets, which improves generalization quite a lot. It is then shown how to extend these results to networks with hidden layers and non-linear units. Finally the theory is confirmed by some numerical simulations using the data from NetTalk.

A DNA Transformation–Competent Arabidopsis Genomic Library in Agrobacterium

Abstract: We have constructed a nuclear genomic library from the cruciferous plant Arabidopsis thaliana ecotype Columbia in a cosmid vector, pLZO3, and a host organism, Agrobacterium tumefaciens AGL1, which can directly DNA-transform the parent organism, Arabidopsis. The broad host range cosmid pLZO3 carries a gentamicin acetyltransferase gene as bacterial selective marker and tandem, chimeric neomycin and streptomycin phosphotransferase genes as plant selective markers. Agrobacterium AGL1 carries the hypervirulent, attenuated tumor-inducing plasmid pTiBo542 from which T-region DNA sequences have been precisely deleted, allowing optimal DNA transformation of many dicotyledonous plants. Agrobacterium AGL1 also carries an insertion mutation in its recA general recombination gene, which stabilizes the recombinant plasmids. The Arabidopsis genomic library consists of some 21,600 clones gridded onto 96-well microtiter dishes and, if random, carries at least three genomic equivalents. When probed for the presence of several Arabidopsis low copy-number genes, the genomic library seems representative. As with the unicellular organisms Escherichia coli and Saccharomyces cerevisiae, this DNA transformation competent genomic library should expedite gene isolation, by gene rescue, in multicellular organisms like Arabidopsis.

Dynamical effects of the cosmological constant.

Abstract: The possibility of measuring the density parameter OMEGA-0 and the cosmological constant lambda-0 = LAMBDA/(3H0(2)) using dynamical tests is explored in linear and non-linear theory. In linear theory we find that the rate of growth of the perturbations at the present epoch is approximated by f(z = 0) almost-equal-to-OMEGA-0(0.6) + 1/70 lambda-0(1 + 1/2 OMEGA-0). Therefore, dynamical tests such as infall around clusters and dipoles at the present epoch do not distinguish well between universes with and without a cosmological constant. At higher redshifts, the perturbations also depend mainly on the matter density at a particular epoch, f(z) almost-equal-to OMEGA-0.6(z), which has a strong dependence on lambda-0 at z almost-equal-to 0.5-2.0. Therefore, information on both parameters can be obtained by looking at clustering at different redshifts. In practice, however, the other observables also depend on the cosmology, and in some cases conspire to give a weak dependence on lambda-0. By using the non-linear spherical infall model for a family of Cold Dark Matter (CDM) power-spectra we also find that dynamics at z = 0 does not tell much about lambda-0. At higher redshifts there is unfortunately another conspiracy between conventional observables, which hides information about lambda-0. The final radius of a virialized cluster (relative to the turnaround radius) is approximated by R(f)/R(ta) almost-equal-to (1 - eta/2)/(2 - eta/2), where eta is the ratio of LAMBDA to the density at turn-around. Therefore a repulsive-LAMBDA gives a smaller final radius than a vanishing-LAMBDA.

Interactive influences of bioactive trace metals on biological production in oceanic waters

Abstract: We present an overview of the oceanic chemistries of the bioactive trace metals, Mn, Fe, Co, Ni, Cu, and Zn; we combine field data with results from laboratory phytoplankton culture-trace metal studies and speculate on the potential influences of these trace metals on oceanic plankton production and species composition. Most field studies have focused on the effects of single metals. However, we propose that synergistic and antagonistic interactions between multiple trace metals could be very important in the oceans. Trace metal antagonisms that may prove particularly important are those between Cu and the potential biolimiting metals Fe, Mn, and Zn. These antagonistic interactions could have the greatest influence on biological productivity in areas of the open ocean isolated from terrestrial inputs, such as the remote high nutrient regions of the Pacific and Antarctic Oceans. The emerging picture of trace metal-biota interactions in these oceanic areas is one in which biology strongly influences distribution and chemical speciation of all these bioactive trace metals. It also seems likely that many of these bioactive trace metals and their speciation may influence levels of primary productivity, species composition, and trophic structure. Future investigations should give more complete consideration to the interactive effects of biologically important trace metals.

Multiple forms of dynamin are encoded by shibire, a Drosophila gene involved in endocytosis.

Abstract: DYNAMIN was discovered in bovine brain tissue as a nucleotide-sensitive microtubule-binding protein of relative molecular mass 100,0001. It was found to cross-link microtubules into highly ordered bundles, and appeared to have a role in intermicrotubule sliding in vitro. Cloning and sequencing of rat brain dynamin complementary DNA identified an N-terminal region of about 300 amino acids which contained the three consensus elements characteristic of GTP-binding proteins2. Extensive homology was found between this domain and the mammalian MX proteins which are involved in interferon-induced viral resistance3,4, and with the product of the VPS1 locus in Saccharomyces cerevisiae, which has been implicated both in membrane protein sorting5, and in meiotic spindle pole separation6. Dynamin-containing microtubule bundles were not observed in an immunofluorescence study of cultured mammalian cells7, but a role for a GTP-requiring protein in intermicrotubule sliding during mitosis in plants has been reported8. We report here that Drosophila melanogaster contains multiple tissue-specific and developmentally-regulated forms of dynamin, which are products of the shibire locus previously implicated in endocytic protein sorting9,10.

Ribosomal RNA and Translation

Abstract: BIOCHEMICAL EVIDENCE.. """'''''''' ''''' ''' .... ' " ' ' '' ' Activity of Protein-Depleted RNA . Affinity Labeling and Cross-Linking . . Protection from Chemical and Enzymatic Probes . Binding of IRNA to the A, P, and E Sites . Intermediale States in Translocation: Hybrid Sites . Interactions of Antibiotics with Ribosomal RNA . Elongation Factors and Ribosomal RNA . Initiation Factors and Ribosomal RNA . Subunit Association . RNA-Direcled Biochemical Inactivation .

Wind modification and bed response during saltation of sand in air

Abstract: A model of eolian sediment transport has been constructed, a special case of which is that corresponding to sand-sized mineral grains subjected to moderate winds: saltation. The model consists of four compartments corresponding to (1) aerodynamic entrainment, (2) grain trajectories, (3) grain-bed impacts, and (4) momentum extraction from the wind. Each sub-model encapsulates the physics of the process, and is constrained where necessary by experimental data. When combined, the full model allows simulation of eolian saltation from inception by aerodynamic entrainment to steady state.

Unsupervised learning of distributions on binary vectors using two layer networks

Abstract: We present a distribution model for binary vectors, called the influence combination model and show how this model can be used as the basis for unsupervised learning algorithms for feature selection. The model can be represented by a particular type of Boltzmann machine with a bipartite graph structure that we call the combination machine. This machine is closely related to the Harmonium model defined by Smolensky. In the first part of the paper we analyze properties of this distribution representation scheme. We show that arbitrary distributions of binary vectors can be approximated by the combination model. We show how the weight vectors in the model can be interpreted as high order correlation patterns among the input bits, and how the combination machine can be used as a mechanism for detecting these patterns. We compare the combination model with the mixture model and with principle component analysis. In the second part of the paper we present two algorithms for learning the combination model from examples. The first learning algorithm is the standard gradient ascent heuristic for computing maximum likelihood estimates for the parameters of the model. Here we give a closed form for this gradient that is significantly easier to compute than the corresponding gradient for the general Boltzmann machine. The second learning algorithm is a greedy method that creates the hidden units and computes their weights one at a time. This method is a variant of projection pursuit density estimation. In the third part of the paper we give experimental results for these learning methods on synthetic data and on natural data of handwritten digit images.

Depletion of U3 small nucleolar RNA inhibits cleavage in the 5' external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA

Abstract: Multiple processing events are required to convert a single eukaryotic pre-ribosomal RNA (pre-rRNA) into mature 18S (small subunit), 5.8S and 25-28S (large subunit) rRNAs. We have asked whether U3 small nucleolar RNA is required for pre-rRNA processing in vivo by depleting Saccharomyces cerevisiae of U3 by conditional repression of U3 synthesis. The resulting pattern of accumulation and depletion of specific pre-rRNAs indicates that U3 is required for multiple events leading to the maturation of 18S rRNA. These include an initial cleavage within the 5' external transcribed spacer, resembling the U3 dependent initial processing event of mammalian pre-rRNA. Formation of large subunit rRNAs is unaffected by U3 depletion. The similarity between the effects of U3 depletion and depletion of U14 small nucleolar RNA and the nucleolar protein fibrillarin (NOP1) suggests that these could be components of a single highly conserved processing complex.

Interaction of hsp70 with unfolded proteins: effects of temperature and nucleotides on the kinetics of binding.

Abstract: Circular dichroism and HPLC gel filtration were used to show that cytosolic hsp70 is thermally stable but undergoes a conformational transition (midpoint, 43 degrees C; 57 degrees C in the presence of ATP or ADP) leading to oligomerization. hsp70 binds to unfolded, but not to folded, proteins in a temperature-dependent manner; complex formation is significant only at physiologically relevant temperatures. hsp70 binds ADP more tightly than ATP to form a binary complex, which binds to the unfolded protein more rapidly than free hsp70. ADP also inhibits the ATP-induced dissociation of the hsp70-protein complex. A regulatory role for the hsp70-nucleotide binary complexes is proposed.

Selection of benevolence in a host-parasite system.

Abstract: A paradigm for the evolution of cooperation between parasites and their hosts argues that the mode of parasite transmission is critical to the long-term maintenance of cooperation. Cooperation is not expected to be maintained whenever the chief mode of transmission is hori- zontal: a parasite's progeny infect hosts unrelated to their parent's host. Cooperation is expected to be maintained if the chief mode of transmission is vertical: a parasite's progeny infect only the parent's host or descendants of that host. This paradigm was tested using bacteria and filamentous bacteriophage (fl). When cells harboring different varian&ts of these phage were cultured so that no infectious spread was allowed, ensuring that all parasite transmission was vertical, selection favored the variants that were most benevolent to the host-those that least harmed host growth rate. By changing the culture conditions so that horizontal spread of the phage was allowed, the selective advantage of the benevolent forms was lost. These experiments thus support the theoretical ar- guments that mode of transmission is a major determinant in the evolution of cooperation between a parasite and its host.

Reconstruction and analysis of human Alu genes.

Abstract: The existing classification of human Alu sequences is revised and expanded using a novel methodology and a larger set of sequence data. Our study confirms that there are two major Alu subfamilies, Alu-J and Alu-S. The Alu-S subfamily consists of at least five distinct subfamilies referred to as Alu-Sx, Alu-Sq, Alu-Sp, Alu-Sc, and Alu-Sb. The Alu-Sp and Alu-Sq subfamilies have been revealed by this study. Alu subfamilies differ from one another in a number of positions called diagnostic. In this paper the diagnostic positions are defined in quantitative terms and are used to evaluate statistical significance of the observed subfamilies. Each Alu subfamily most likely represents pseudogenes retroposed from evolving functional source Alu genes. Evidence presented in this paper indicates that Alu-Sp and Alu-Sc pseudogenes were retroposed from different source genes, during overlapping periods of time, and at different rates. Our analysis also indicates that the previously identified Alu-type transcript BC200 comes from an active Alu gene that might have existed even before the origin of dimeric Alu sequences. The source genes for Alu pseudogene families are reconstructed. It is assumed that diagnostic differences between reconstructed source genes reflect mutations that have occurred in true source Alu genes under natural selection. Some of these mutations are compensatory and are used to reconstruct a common secondary structure of Alu RNAs transcribed from the source genes. The biological function of Alu RNA is discussed in the context of its homology to the elongation-arresting domain of 7SL RNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Overcoming denial and increasing the intention to use condoms through the induction of hypocrisy.

Abstract: Feelings of hypocrisy were induced in college students to increase condom use. Hypocrisy was created by making subjects mindful of their past failure to use condoms and then having them persuade others about the importance of condoms for AIDS prevention. The induction of hypocrisy decreased denial and led to greater intent to improve condom use relative to the control conditions. The implications of these findings for AIDS prevention are discussed.

A functional pseudoknot in 16S ribosomal RNA.

Abstract: Several lines of evidence indicate that the universally conserved 530 loop of 16S ribosomal RNA plays a crucial role in translation, related to the binding of tRNA to the ribosomal A site. Based upon limited phylogenetic sequence variation, Woese and Gutell (1989) have proposed that residues 524-526 in the 530 hairpin loop are base paired with residues 505-507 in an adjoining bulge loop, suggesting that this region of 16S rRNA folds into a pseudoknot structure. Here, we demonstrate that Watson-Crick interactions between these nucleotides are essential for ribosomal function. Moreover, we find that certain mild perturbations of the structure, for example, creation of G-U wobble pairs, generate resistance to streptomycin, an antibiotic known to interfere with the decoding process. Chemical probing of mutant ribosomes from streptomycin-resistant cells shows that the mutant ribosomes have a reduced affinity for streptomycin, even though streptomycin is thought to interact with a site on the 30S subunit that is distinct from the 530 region. Data from earlier in vitro assembly studies suggest that the pseudoknot structure is stabilized by ribosomal protein S12, mutations in which have long been known to confer streptomycin resistance and dependence.

A coherent projection approach for direct volume rendering

Abstract: Direct volume rendering offers the opportunity to visualize all of a three-dimensional sample volume in one image. However, processing such images can be very expensive and good quality high-resolution images are far from interactive. Projection approaches to direct volume rendering process the volume region by region as opposed to ray-casting methods that process it ray by ray. Projection approaches have generated interest because they use coherence to provide greater speed than ray casting and generate the image in a layered, informative fashion. This paper discusses two topics: First, it introduces a projection approach for directly rendering rectilinear, parallel-projected sample volumes that takes advantage of coherence across cells and the identical shape of their projection. Second, it considers the repercussions of various methods of integration in depth and interpolation across the scan plane. Some of these methods take advantage of Gouraud-shading hardware, with advantages in speed but potential disadvantages in image quality.

Energy spectra and coherent structures in forced two-dimensional and beta-plane turbulence

Abstract: Results from a wide range of direct numerical simulations of forced-dissipative, differentially rotating two-dimensional turbulence are presented, in order to delineate the broad dependence of flow type on forcing parameters. For most parameter values the energy spectra of simulations forced at low wavenumbers are markedly steeper than the classical k−3 enstrophy inertial-range prediction, and although k−3 spectra can be produced under certain circumstances, the regime is not robust, and the Kolmogorov constant is not universal unless a slight generalization is made in the phenomenology. Long-lived, coherent vortices form in many cases, accompanied by steep energy spectra and a higher than Gaussian vorticity kurtosis. With the addition of differential rotation (the β-effect), a small number of fairly distinct flow regimes are observed. Coherent vortices weaken and finally disappear as the strength of the β-effect increases, concurrent with increased anisotropy and decreased kurtosis. Even in the absence of coherent vortices and with a Gaussian value of the kurtosis, the spectra remain relatively steep, although not usually as steep as for the non-rotating cases. If anisotropy is introduced at low wavenumbers, the anisotropy is transferred to all wavenumbers in the inertial range, where the dynamics are isotropic.For those simulations that are forced at relatively high wavenumbers, a well resolved and very robust k−5/3 energy inertial range is observed, and the Kolmogorov constant appears universal. The low-wavenumber extent of the reverse energy cascade is essentially limited by the β-effect, which produces an effective barrier in wavenumber space at which energy accumulates, and by frictional effects which must be introduced to achieve equilibrium. Anisotropy introduced at large scales remains largely confined to the low wavenumbers, rather than being cascaded to small scales. When there is forcing at both large and small scales (which is of relevance to the Earth's atmosphere), energy and enstrophy inertial ranges coexist, with an upscale energy transfer and downscale enstrophy transfer in the same wavenumber interval, without the need for any dissipation mechanism between forcing scales.

Regulated expression and growth inhibitory effects of transforming growth factor-beta isoforms in mouse mammary gland development.

Abstract: Transforming Growth Factor-beta 1 (TGF-beta 1) was previously shown to inhibit reversibly the growth of mouse mammary ducts when administered in vivo by miniature slow-release plastic implants. We now report a comparative analysis of three TGF-beta isoforms with respect to gene expression and localization of protein products within the mouse mammary gland. Our studies revealed overlapping expression patterns of TGF-beta 1, TGF-beta 2 and TGF-beta 3 within the epithelium of the actively-growing mammary end buds during branching morphogenesis, as well as within the epithelium of growth-quiescent ducts. However, TGF-beta 3 was the only isoform detected in myoepithelial progenitor cells (cap cells) of the growing end buds and myoepithelial cells of the mature ducts. During pregnancy, TGF-beta 2 and TGF-beta 3 transcripts increased to high levels, in contrast to TGF-beta 1 transcripts which were moderately abundant; TGF-beta 2 was significantly transcribed only during pregnancy. Molecular hybridization in situ revealed overlapping patterns of expression for the three TGF-beta isoforms during alveolar morphogenesis, but showed that, in contrast to the patterns of TGF-beta 1 and TGF-beta 2 expression, TGF-beta 3 is expressed more heavily in ducts than in alveoli during pregnancy. Developing alveolar tissue and its associated ducts displayed striking TGF-beta 3 immunoreactivity which was greatly reduced during lactation. All three isoforms showed dramatically reduced expression in lactating tissue. The biological effects of active, exogenous TGF-beta 2 and TGF-beta 3 were tested with slow-release plastic implants. These isoforms, like TGF-beta 1, inhibited mammary ductal elongation in situ by causing the disappearance of the proliferating stem cell layer (cap cells) and rapid involution of ductal end buds. None of the isoforms were active in inhibiting alveolar morphogenesis. We conclude that under the limited conditions of these tests, the three mammalian isoforms are functionally equivalent. However, striking differences in patterns of gene expression and in the distribution of immunoreactive peptides suggest that TGF-beta isoforms may have distinct roles in mammary growth regulation, morphogenesis and functional differentiation.

Influence and Involvement in Children's Discourse: Age, Gender, and Partner Effects

Abstract: Children's discourse with peers was examined in relation to speaker gender, partner gender, and age level. 138 children were matched with either a same- or an other-gender peer at the early childhood and middle childhood age levels (median ages = 5 and 7 years) and asked to play with puppets for 10 min. Speech acts were coded as either collaborative (affiliative involvement and direct influence), controlling (distancing involvement and direct influence), obliging (affiliative involvement and nondirect influence), or withdrawing (distancing involvement and nondirect influence). Girls' and boys' communication patterns were more similar than different. However, gender-related differences with medium to large effect sizes were found. Gender-typed communications were more likely at the middle childhood than the early childhood age level and in same-gender than mixed-gender dyads. The findings are interpreted in terms of developmental and contextual accounts of gender and social behavior. Recommendations for future research are offered.

Steps toward determination of the size and structure of the broad-line region in active galactic nuclei. II - An intensive study of NGC 5548 at optical wavelengths

Abstract: A large, international program of ground-based optical spectroscopy and photometry of the variable Seyfert 1 galaxy NGC 5548 undertaken in support of an IUE monitoring campaign is described. This contribution presents the data base and describes the methods used to correct for systematic differences between spectra from different sources. Optical continuum and H-beta emission-line light curves are derived from the spectra. The behavior of the optical continuum is qualitatively the same as the behavior of the ultraviolet continuum. Cross-correlation of the ultraviolet and optical continuum measurements does not reveal any significant lag between them. The h-beta emission-line variations show the same basic pattern as seen in the continuum and ultraviolet emission lines, with H-beta lagging behind the continuum by about 20 days. This is significantly larger than the about 10 day lag deduced for Ly-alpha.

Mechanisms underlying priming on perceptual tests

Abstract: Four experiments examined perceptual, lexical, and conceptual processing effects in priming on word fragment completion (WFC) and perceptual identification (PID). In Experiment 1, visual words produced more priming than auditory or generated words, and pictures produced the least priming, suggesting that the effects of different encoding processes can be distinguished. In Experiments 2 and 3, Ss studied anagrams (e.g., tripocs), but only Ss instructed to think of the original words by mentally interchanging the vowels exhibited significant priming. Thus, lexical access is more important than surface similarity in priming. In Experiment 4, Ss studied compounds that either preserved the target's meaning (e.g., scotch bottle) or altered its meaning (e.g., scotch tape). Encoded meaning affected priming on WFC but not on PID, suggesting that conceptual processing plays a larger role in WFC. Overall the results suggest that priming must be understood in terms of multiple processes. Language: en

Equivalence of models for polynomial learnability

Abstract: In this paper we consider several variants of Valiant's learnability model that have appeared in the literature. We give conditions under which these models are equivalent in terms of the polynomially learnable concept classes they define. These equivalences allow comparisons of most of the existing theorems in Valiant-style learnability and show that several simplifying assumptions on polynomial learning algorithms can be made without loss of generality. We also give a useful reduction of learning problems to the problem of finding consistent hypotheses, and give comparisons and equivalences between Valiant's model and the prediction learning models of Haussler, Littlestone, and Warmuth ( in “29th Annual IEEE Symposium on Foundations of Computer Science,” 1988).