Showing papers by "University of California, Santa Cruz published in 1989"

Learnability and the Vapnik-Chervonenkis dimension

Abstract: Valiant's learnability model is extended to learning classes of concepts defined by regions in Euclidean space En. The methods in this paper lead to a unified treatment of some of Valiant's results, along with previous results on distribution-free convergence of certain pattern recognition algorithms. It is shown that the essential condition for distribution-free learnability is finiteness of the Vapnik-Chervonenkis dimension, a simple combinatorial parameter of the class of concepts to be learned. Using this parameter, the complexity and closure properties of learnable classes are analyzed, and the necessary and sufficient conditions are provided for feasible learnability.

Intermediate states in the movement of transfer RNA in the ribosome

Abstract: Direct chemical 'footprinting' shows that translocation of transfer RNA occurs in two discrete steps. During the first step, which occurs spontaneously after the formation of the peptide bond, the acceptor end of tRNA moves relative to the large ribosomal subunit resulting in 'hybrid states' of binding. During the second step, which is promoted by elongation factor EF-G, the anticodon end of tRNA, along with the messenger RNA, moves relative to the small ribosomal subunit.

Evolution of the Vacuolar H + -ATPase: Implications for the Origin of Eukaryotes

Abstract: Active transport across the vacuolar components of the eukaryotic endomembrane system is energized by a specific vacuolar H+-ATPase. The amino acid sequences of the 70- and 60-kDa subunits of the vacuolar H+-ATPase are approximately equal to 25% identical to the beta and alpha subunits, respectively, of the eubacterial-type F0F1-ATPases. We now report that the same vacuolar H+-ATPase subunits are approximately equal to 50% identical to the alpha and beta subunits, respectively, of the sulfur-metabolizing Sulfolobus acidocaldarius, an archaebacterium (Archaeobacterium). Moreover, the homologue of an 88-amino acid stretch near the amino-terminal end of the 70-kDa subunit is absent from the F0F1-ATPase beta subunit but is present in the alpha subunit of Sulfolobus. Since the two types of subunits (alpha and beta subunits; 60- and 70-kDa subunits) are homologous to each other, they must have arisen by a gene duplication that occurred prior to the last common ancestor of the eubacteria, eukaryotes, and Sulfolobus. Thus, the phylogenetic tree of the subunits can be rooted at the site where the gene duplication occurred. The inferred evolutionary tree contains two main branches: a eubacterial branch and an eocyte branch that gave rise to Sulfolobus and the eukaryotic host cell. The implication is that the vacuolar H+-ATPase of eukaryotes arose by the internalization of the plasma membrane H+-ATPase of an archaebacterial-like ancestral cell.

Latitudinal variations in plankton δ 13 C: implications for CO 2 and productivity in past oceans

Abstract: Low C-13/C-12 in present-day Antarctic plankton has been ascribed to high CO2 availability. It is reported here, however, that this high-latitude C-13 depletion develops at CO2 partial pressures that are often below that of the present atmosphere and usually below that of equatorial upwelling systems. Nevertheless, because of much lower water temperatures and hence greater CO2 solubility at high latitude, the preceding pCO2 measurements translate into Antarctic surface-water CO2 (aq) concentrations that are as much as 2.5 times higher than in equatorial waters. It is calculated that an oceanic pCO2 level greater than 800 micro-atm is a warmer low-latitude Cretaceous ocean would have been required to produce the plankton C-13 depletion preserved in Cretaceous sediments.

The alternating fixpoint of logic programs with negation

Abstract: We introduce and describe the alternating fixpoint of a logic program with negation. The underlying idea is to monotonically build up a set of negative conclusions until the least fixpoint is reached, using a transformation related to the one that defines stable models, developed by Gelfand and Lifschitz. From a fixed set of negative conclusions, we can derive the positive conclusions that follow (without deriving any further negative ones), by traditional Horn clause semantics. The union of positive and negative conclusions is called the alternating fixpoint partial model. The name “alternating” was chosen because the transformation runs in two passes; the first pass transforms an underestimate of the set of negative conclusions into an (intermediate) overestimate; the second pass transforms the overestimates into a new underestimate; the composition of the two passes is monotonic.Our main theorem is that the alternating fixpoint partial model is exactly the well-founded partial model.We also show that a system is fixpoint logic, which permits rule bodies to be first order formulas but requires inductive relations to be positive within them, can be transformed straightforwardly into a normal logic program whose alternating fixpoint partial model corresponds to the least fixpoint of the fixpoint logic system. Thus alternating fixpoint logic is at least as expressive as fixpoint logic. The converse is shown to hold for finite structures.

Complexation of zinc by natural organic ligands in the central North Pacific

Abstract: The complexation of Cd by natural organic ligands in the upper 600 m of the central North Pacific was determined with differential pulse anodic stripping voltametry at a thin mercury film, rotating glassy-carbon disk electrode. About 70% of the dissolved Cd in surface waters was bound in strong complexes (K’,,, ,‘,, c.,2, = 10’2.0 M-‘) by relatively Cd-specific organic ligands existing at low concentrations (0.1 nM). This ligand class is only observed within the surface 175 m and exhibits a concentration maximum at depths between 40 and 100 m. Due to the complexation of dissolved Cd in surface waters by this class of organic ligands, together with the vertical distribution of total dissolved Cd (ranging from 2 to 800 PM), the concentration of inorganic forms of Cd varies from o-O.7 pM in surface waters to 800 pM at 600 m. The concentration of free Cd ion ranges from 20 fM (- lo- 13.7 M) in surface waters to 22 pM at 600 m-a 1 ,OOO-fold variation! Although complexation with inorganic chloride ligands dominates the speciation of Cd in intermediate and deep waters, these results demonstrate that complexation with natural organic ligands is important in influencing Cd speciation in oceanic surface waters.

The Weil-Petersson geometry of the moduli space of SU( n≧3) (Calabi-Yau) manifolds I

Abstract: The Weil-Petersson metric is defined on the moduli space of Calabi-Yau manifolds. The curvature of this Weil-Petersson metrics is computed and its potential is explicitely defined. It is proved that the moduli space of Calabi-Yau manifolds is unobstructed (see Tian).

A general lower bound on the number of examples needed for learning

Abstract: We prove a lower bound of Ω ((1/ɛ)ln(1/δ)+VCdim( C )/ɛ) on the number of random examples required for distribution-free learning of a concept class C , where VCdim( C ) is the Vapnik-Chervonenkis dimension and ɛ and δ are the accuracy and confidence parameters. This improves the previous best lower bound of Ω ((1/ɛ)ln(1/δ)+VCdim( C )) and comes close to the known general upper bound of O ((1/ɛ)ln(1/δ)+(VCdim( C )/ɛ)ln(1/ɛ)) for consistent algorithms. We show that for many interesting concept classes, including k CNF and k DNF, our bound is actually tight to within a constant factor.

Conformational states in .beta.-lactamase: molten-globule states at acidic and alkaline pH with high salt

Abstract: We present evidence that beta-lactamase is close to fully unfolded (i.e., random coil conformation) at low ionic strength at the extremes of pH and that the presence of salt causes a cooperative transition to a conformation with the properties of a molten globule, namely, a compact state with native-like secondary structure but disordered side chains (tertiary structure). The conformation of beta-lactamase I from Bacillus cereus was examined over the pH 1.5-12.5 region by circular dichroism (CD), tryptophan fluorescence, dynamic light scattering, and 1-anilino-8-naphthalenesulfonate (ANS) binding. Under conditions of low ionic strength (I = 0.05) beta-lactamase was unfolded below pH 2.5 and above pH 11.5, on the basis of the far-UV and near-UV CD and tryptophan fluorescence. However, at high ionic strength and low pH an intermediate conformation (state A) was observed, with a secondary structure content similar to that of the native protein but a largely disordered tertiary structure. The transition from the unfolded state (U) to state A induced by KCl was cooperative and had a midpoint at 0.12 M KCl (I = 0.17 M) at pH 1.6. A similar conformation (state B) was observed at high pH and high ionic strength. The transition from the alkaline U state to state B induced by KCl at pH 12.2 was cooperative and had a midpoint at 0.6 M KCl (I = 0.65 M). Light scattering measurements showed that state B was compact although somewhat expanded compared to the N state. The compactness of state A could not be determined due to its strong propensity to aggregate.(ABSTRACT TRUNCATED AT 250 WORDS)

Debugging concurrent programs

Abstract: The main problems associated with debugging concurrent programs are increased complexity, the "probe effect," nonrepeatability, and the lack of a synchronized global clock. The probe effect refers to the fact that any attempt to observe the behavior of a distributed system may change the behavior of that system. For some parallel programs, different executions with the same data will result in different results even without any attempt to observe the behavior. Even when the behavior can be observed, in many systems the lack of a synchronized global clock makes the results of the observation difficult to interpret. This paper discusses these and other problems related to debugging concurrent programs and presents a survey of current techniques used in debugging concurrent programs. Systems using three general techniques are described: traditional or breakpoint style debuggers, event monitoring systems, and static analysis systems. In addition, techniques for limiting, organizing, and displaying a large amount of data produced by the debugging systems are discussed.

Growth layers in teeth from known-age, free-ranging bottlenose dolphins

Abstract: Growth layers were examined in teeth collected from free-ranging bottlenose dolphins, Tursiops truncatus, from Florida that have been part of a long-term study begun in 1970; 26 of the dolphins were of known or approximately known age, and 19 were of minimum known age. A second tooth was extracted from 6 animals for examination of growth that had taken place in the interval following the initial extraction. The teeth were read for age estimates without knowledge of any data pertaining to the animals. Most of the estimated ages were the same as or close to the known and approximately known ages of the animals, ranging from 2 to 16 yr. We conclude that the structures we define as dentinal growth layer groups (GLGs) are annual, we describe sources of error in age estimates, and we provide a description of the GLG pattern that can be used by others to estimate age for dolphins.

Mouse Serum Growth Hormone (GH) Binding Protein has GH Receptor Extracellular and Substituted Transmembrane Domains

Abstract: Predicted amino acid sequences for the mouse GH receptor and the related serum GH binding protein were deducted from cDNAs. Two types of cDNA clones were isolated. Both types coded an identical peptide domain with extensive homology to the extracellular domains of the recently cloned human and rabbit GH receptors. However, while one type of clone also encoded regions with homology to the transmembrane and cytoplasmic domains of the human and rabbit GH receptors, the other encoded a short hydrophilic carboxyl-terminal region in place of the transmembrane domain. It is speculated that these two types of clones encode the high and low molecular weight variants of the mouse GH receptor/serum binding proteins, respectively. The low molecular weight variant has been previously found to constitute the majority of the serum GH binding activity in mice. It is proposed that the substitution of the hydrophilic tail for the transmembrane domain may give the low molecular weight variant its soluble nature and account ...

RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA

Abstract: Chemical probing methods have been used to "footprint" 16S ribosomal RNA (rRNA) at each step during the in vitro assembly of twenty 30S subunit ribosomal proteins. These experiments yield information about the location of each protein relative to the structure of 16S rRNA and provide the basis for derivation of a detailed model for the three-dimensional folding of 16S rRNA. Several lines of evidence suggest that protein-dependent conformational changes in 16S rRNA play an important part in the cooperativity of ribosome assembly and in fine-tuning of the conformation and dynamics of 16S rRNA in the 30S subunit.

Experimental and theoretical equation of state of cubic boron nitride

Abstract: The phase diagram of boron nitride (BN) is similar to that of carbon, incorporating phases at high temperatures and pressures whose structures and physical properties resemble diamond1–9. Cubic zinc-blende-structured BN is especially important because it is extremely hard—second only to diamond. Here we report the first measurement of the 300-K equation of state of this material to ultrahigh pressures (115 GPa), and obtain a zero-pressure bulk modulus of 369 ± 14 GPa. A theoretical equation of state derived from first-principles pseudopotential calculations yields a 300-K isotherm that agrees with our experimental results to better than 2.5% in volume and 2.0% in bulk modulus. The high-pressure Hugoniot (shock-wave equation of state) calculated from our equation of state for BN is in good agreement with existing shock-wave data. Our study illustrates the reliability of current experimental techniques (such as the ruby-fluorescence calibra-tion) and theoretical methods (pseudopotentials) for characterizing the behaviour of superhard, incompressible materials under high pressure.

Learning decision trees from random examples needed for learning

Abstract: We define the rank of a decision tree and show that for any fixed r , the class of all decision trees of rank at most r on n Boolean variables is learnable from random examples in time polynomial in n and linear in 1/ɛ and log(1/δ), where ɛ is the accuracy parameter and δ is the confidence parameter. Using a suitable encoding of variables, Rivest's polynomial learnability result for decision lists can be interpreted as a special case of this result for rank 1. As another corollary, we show that decision trees on n Boolean variables of size polynomial in n are learnable from random examples in time linear in n O (log n ) , 1/ɛ, and log(1/δ). As a third corollary, we show that Boolean functions that have polynomial size DNF expressions for both their positive and their negative instances are learnable from random examples in time linear in n O ((log n ) 2 ) , 1/ɛ, and log(1/δ).

Vibrational spectra of Mg(OH)2 and Ca(OH)2 under pressure

Abstract: The effects of compression on the structure and bonding of Mg(OH)2 brucite and Ca(OH)2 portlandite are documented to pressures of 34 and 24 GPa, respectively, by way of infrared spectroscopy of the O–H stretching vibration at 300 K. The frequency of the infrared‐active (A2u) mode of both hydroxides decreases with pressure, by −0.6 cm−1/GPa for Mg(OH)2 over the pressure range studied, and by −3.5 cm−1/GPa for Ca(OH)2 to 10.6 GPa. An additional mode observed in Mg(OH)2 is due to an optically induced hot band (A2u X A2u overtone): with increasing pressure, its intensity grows and its frequency decreases (−3.7 cm−1/GPa). The negative pressure dependencies of these modes (negative Gruneisen parameters) are explained in terms of compression increasing the hydrogen bond strength within the hydroxide structure. On increasing pressure above 12.8 GPa, the full width at half‐maximum of the O–H vibration in Ca(OH)2 rapidly broadens by a factor of 4. The infrared data suggest that Ca(OH)2 undergoes pressure‐induced am...

The Ecology of Extinctions in Kelp Forest Communities

Abstract: We recognize three levels of extinction–global, local, and ecological – and provide examples of each. The protection and recovery of sea otters (Enhydra lutris) has provided abundant evidence of the consequences of their local extinction from kelp forest communities in the North Pacifc Ocean. These consequences include release of benthic invertebrate populations from limitation by predation; deforestation of kelp beds due to increased grazing by herbivorous sea urchins, one of the otter's main prey; and various cascading effects resulting from the biological and physical importance of kelp in coastal ecosystems. These interactions probably were important agents of selection for certain species. Two other examples are discussed: Steller's sea cow (Hydrodamalis gigas), a case of global extinction, and spiny lobsters, a possible case of ecological extinction. We speculate that grazing by sea cows was an important disturbance to surface-canopy-forming kelps and other algae in the littoral zones, but also point out that any such interactions probably acted in concert with physical disturbances by ocean waves. The ecological and evolutionary importance of sea cow grazing probably will remain a matter of speculation and conjecture because the species is globally extinct. Predation by spiny lobsters limits a variety of littoral and sublittoral invertebrate populations, particularly mollusks In one remarkable example, the reduction or local extinction of spiny lobsters enabled predutory whelks to increase in size and abundance, ultimately resulting in a predutor-prey role reversal. From these and other case studies we can clued that (1) the extinction of consumers may have brad and sometimes unexpected influences on kelp forest ecosystems; (2) direct or indirect interactions with now-extinct species probably exerted important selective influences on many extant forms; (3) such ecological and evolutionary influences are best understood where local or ecological extinctions, followed by recoveries, have provided comparisons in space or time; and (4) because of various ecological and behavioral barriers, local extinctions and their ecological consequences may not be simply reversed by protecting or reintroducing depleted or locally extinct species.

The biota of Antarctic pack ice in the Weddell sea and Antarctic Peninsula regions

Abstract: Pack ice surrounding Antarctica supports rich and varied populations of microbial organisms. As part of the Antarctic Marine Ecosystem Research in the Ice Edge Zone (AMERIEZ) studies, we have examined this community during the late spring, autumn, and winter. Although organisms are found throughout the ice, the richest concentrations often occur in the surface layer. The ice flora consists of diatoms and flagellates. Chrysophyte cysts (archaeomonads) of unknown affinity and dinoflagellate cysts are abundant and may serve as overwintering stages in ice. The ice fauna includes a variety of heterotrophic flagellates, ciliates, and micrometazoa. The abundance of heterotrophs indicates an active food web within the ice community. Ice may serve as a temporary habitat or refuge for many of the microbial forms and some of these appear to provide an inoculum for planktonic populations when ice melts. Larger consumers, such as copepods and the Antarctic krill, Euphausia superba are often found on the underside of ice floes and within weathered floes. The importance of the ice biota as a food resource for these pelagic consumers is unknown.