Learning rate and attractor size of the single-layer perceptron.

We study the simplest possible order one single-layer perceptron with two inputs, using the delta rule with online learning, in order to derive closed form expressions for the mean convergence rates. We investigate the rate of convergence in weight space of the weight vectors corresponding to each of the 14 out of 16 linearly separable rules. These vectors follow zigzagging lines through the piecewise constant vector field to their respective attractors.

Assessing the impact of animal waste lagoon seepage on the geochemistry of an underlying shallow aquifer.

Evidence of seepage from animal waste holding lagoons at a dairy facility in the San Joaquin Valley of California is assessed in the context of a process geochemical model that addresses reactions associated with the formation of the lagoon water as well as reactions occurring upon the mixture of lagoon water with underlying aquifer material. Comparison of model results with observed concentrations of NH4+, K+, PO4(3-), dissolved inorganic carbon, pH, Ca2+, Mg2+, SO4(2-), Cl-, and dissolved Ar in lagoon water samples and groundwater samples suggests three key geochemical processes: (i) off-gassing of significant quantities of CO2 and CH4 during mineralization of manure in the lagoon water, (ii) ion exchange reactions that remove K+ and NH4+ from seepage water as it migrates into the underlying anaerobic aquifer material, and (iii) mineral precipitation reactions involving phosphate and carbonate minerals in the lagoon water in response to an increase in pH as well as in the underlying aquifer from elevated Ca2+ and Mg2+ levels generated by ion exchange. Substantial off-gassing from the lagoons is further indicated by dissolved argon concentrations in lagoon water samples that are below atmospheric equilibrium.

Control of S-based aggregation: designed synthesis of NiM2 and Ni2M trinuclear complexes.

Modification of the nickel dithiolate metalloligand, Ni(bme-daco) [where bme-daco = bis(mercaptoethyl)diazacyclooctane] or Ni-1, by oxygenation of one thiolate into a sulfinate, Ni(mese-daco) [where mese-daco = (mercaptoethyl)(sulfinatoethyl)diazacyclooctane] or Ni-2, restricts the ligating ability to monodentate and is expected to reduce the donor ability of the remaining thiolate S. Nevertheless, the Ni-2 complex forms a stable thiolate S-bound adduct of W0(CO)5, (Ni-2)W(CO)5, a complex whose upsilon(CO) IR spectrum reports insignificant differences in the donor abilities of Ni-1 and Ni-2 in (eta1-NiN2S2)W(CO)5 complexes. In the presence of the strong sulfophile CuI, a CuNi2 trimetallic, (Ni-2)2CuBr, was isolated.

Communication between subunits within an archaeal clamp-loader complex.

We have investigated the communication between subunits in replication factor C (RFC) from Archaeoglobus fulgidus. Mutation of the proposed arginine finger in the small subunits results in a complex that can still bind ATP but has impaired clamp-loading activity, a process that normally only requires binding of nucleotide. The small subunit alone forms a hexameric ring that is six-fold symmetric in the absence of ATP.

Modulation of CaM kinase II activity is coincident with induction of status epilepticus in the rat pilocarpine model.

Purpose: This study was conducted to characterize the early cellular changes in CaM kinase II activity that occur during the induction of status epilepticus (SE).

Methods: The pilocarpine model of SE was characterized both behaviorally and electrographically. At specific time points after the first discrete seizure, specific brain regions were isolated for biochemical study.

Tracking sources of unsaturated zone and groundwater nitrate contamination using nitrogen and oxygen stable isotopes at the Hanford site, Washington.

The nitrogen and oxygen isotopic compositions of nitrate in pore water extracts from unsaturated zone (UZ) core samples and groundwater samples indicate at least four potential sources of nitrate in groundwaters at the U.S. DOE Hanford Site in south-central Washington.

Age dependence of pilocarpine-induced status epilepticus and inhibition of CaM kinase II activity in the rat.

This study was conducted to characterize the post-pubertal developmental aspects on seizure susceptibility and severity as well as calcium/calmodulin protein kinase type II (CaM kinase II) activity in status epilepticus (SE). Thirty- to ninety-day-old rats, in 10-day increments, were studied. This corresponds to a developmental age group that has not received thorough attention.

Chloroplast-derived vaccine antigens and other therapeutic proteins.

The chloroplast genetic engineering offers a number of unique advantages including high level of transgene expression, multi-gene expression in single transformation event and transgene containment due to maternal inheritance. Hyper-expression of vaccine antigens or therapeutic proteins in transgenic chloroplasts (leaves) or chromoplasts (fruits/roots) facilitates efficient oral delivery. Ability of chloroplasts to correctly fold human blood proteins with proper disulfide bridges (human serum albumin or interferons) or presence of chaperones in chloroplasts to facilitate assembly of complex multi-subunit proteins or their prokaryotic nature to express native bacterial genes (up to 46.

Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks.

RecBCD is a multi-functional enzyme complex that processes DNA ends resulting from a double-strand break. RecBCD is a bipolar helicase that splits the duplex into its component strands and digests them until encountering a recombinational hotspot (Chi site). The nuclease activity is then attenuated and RecBCD loads RecA onto the 3' tail of the DNA.

Conformational changes induced by nucleotide binding in Cdc6/ORC from Aeropyrum pernix.

Archaea contain one or more proteins with homology to eukaryotic ORC/Cdc6 proteins. Sequence analysis suggests the existence of at least two subfamilies of these proteins, for which we propose the nomenclature ORC1 and ORC2. We have determined crystal structures of the ORC2 protein from the archaeon Aeropyrum pernix in complexes with ADP or a non-hydrolysable ATP analogue, ADPNP.

Factors associated with higher levels of injury severity in occupants of motor vehicles that were severely damaged in traffic crashes in Kentucky, 2000-2001.

Objectives: The majority of motor vehicle occupants who were killed or hospitalized in crashes in Kentucky in 2000-2001 occupied vehicles that were severely damaged in the crash. Even so, overall only a small percentage of all severely damaged vehicle occupants were killed or hospitalized. The purpose was to identify occupant, vehicle, crash, and roadway/environmental factors that were associated with increased risk of severe injury in crashes where the occupant's vehicle was severely damaged.

Two-photon imaging of brain pericytes in vivo using dextran-conjugated dyes.

Pericytes in the central nervous system (CNS) are hypothesized to be involved in important circulatory functions, including local blood flow regulation, angiogenesis, immune reaction, and regulation of blood-brain barrier. Despite these putative functions, functional correlates of pericytes in vivo are scarce. We have labeled CNS pericytes using the dextran-conjugated fluorescent calcium indicator Calcium Green I and imaged them in somatosensory cortex of the mouse in vivo.

Multiple roles for ATP hydrolysis in nucleic acid modifying enzymes.

Enzymes that operate on nucleic acid substrates are faced with the unusual situation where the substrate is much larger than themselves. Despite the potential to promote catalysis by utilizing the significant binding energy available through their interaction with substrate, ATP hydrolysis is frequently a part of the mechanism of these enzymes. The reasons for this have become clearer in recent years, and a surprising range of ways that these enzymes utilize the free energy of hydrolysis of ATP has been revealed.

Functional and phylogenetic implications of molar flare variation in Miocene hominoids.

Comparative analyses of molar shape figure prominently in Miocene hominoid evolutionary studies, and incomplete understanding of functional and phylogenetic influences on molar shape variation can have direct consequences for the interpretation of fossil taxa. Molar flare is a shape trait whose polarity, phylogenetic distribution, and functional significance have been sources of contention. To clarify the determinants of molar flare variation in the hominoid radiation, a combination of statistical methods was employed to investigate the effects of diet, phylogeny, and geologic age upon several measures of molar shape, to identify interactions among these factors, and to estimate their relative influence.

Biochemical characterisation of the clamp/clamp loader proteins from the euryarchaeon Archaeoglobus fulgidus.

Replicative polymerases of eukaryotes, prokaryotes and archaea obtain processivity using ring-shaped DNA sliding clamps that are loaded onto DNA by clamp loaders [replication factor C (RFC) in eukaryotes]. In this study, we cloned the two genes for the subunits of the RFC homologue of the euryarchaeon Archaeoglobus fulgidus. The proteins were expressed and purified from Escherichia coli both individually and as a complex.

Structure of the single-strand annealing domain of human RAD52 protein.

In eukaryotic cells, RAD52 protein plays a central role in genetic recombination and DNA repair by (i) promoting the annealing of complementary single-stranded DNA and (ii) stimulation of the RAD51 recombinase. The single-strand annealing domain resides in the N-terminal region of the protein and is highly conserved, whereas the nonconserved RAD51-interaction domain is located in the C-terminal region. An N-terminal fragment of human RAD52 (residues 1-209) has been purified to homogeneity and, similar to the full-size protein (residues 1-418), shown to promote single-strand annealing in vitro.

Patterns of cranial shape variation in the Papionini (Primates: Cercopithecinae).

Traditional classifications of the Old World monkey tribe Papionini (Primates: Cercopithecinae) recognized the mangabey genera Cercocebus and Lophocebus as sister taxa. However, molecular studies have consistently found the mangabeys to be diphyletic, with Cercocebus and Mandrillus forming a clade to the exclusion of all other papionins. Recent studies have identified cranial and postcranial features which distinguish the Cercocebus-Mandrillus clade, however the detailed similarities in cranial shape between the mangabey genera are more difficult to reconcile with the molecular evidence.

Pharmacokinetics of para-aminosalicylic acid granules under four dosing conditions.

Objective: To determine the pharmacokinetics and relative bioavailability of para-aminosalicylic acid (PAS) granules.

Design: Phase I pharmacokinetics study.

Setting: University of Arizona School of Pharmacy.

Crystallization and preliminary X-ray analysis of RecG, a replication-fork reversal helicase from Thermotoga maritima complexed with a three-way DNA junction.

The monomeric 3'-5' helicase RecG from the thermophilic bacterium Thermotoga maritima has been crystallized in complex with a three-way DNA junction, the preferred physiological substrate. The crystals were obtained by hanging-drop vapour diffusion. The crystals belong to space group C2, with unit-cell parameters a = 133.

Structural analysis of DNA replication fork reversal by RecG.

The stalling of DNA replication forks that occurs as a consequence of encountering DNA damage is a critical problem for cells. RecG protein is involved in the processing of stalled replication forks, and acts by reversing the fork past the damage to create a four-way junction that allows template switching and lesion bypass. We have determined the crystal structure of RecG bound to a DNA substrate that mimics a stalled replication fork.