Showing papers by "University of California, Davis published in 1997"

Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology

Abstract: Part I. Exact String Matching: The Fundamental String Problem: 1. Exact matching: fundamental preprocessing and first algorithms 2. Exact matching: classical comparison-based methods 3. Exact matching: a deeper look at classical methods 4. Semi-numerical string matching Part II. Suffix Trees and their Uses: 5. Introduction to suffix trees 6. Linear time construction of suffix trees 7. First applications of suffix trees 8. Constant time lowest common ancestor retrieval 9. More applications of suffix trees Part III. Inexact Matching, Sequence Alignment and Dynamic Programming: 10. The importance of (sub)sequence comparison in molecular biology 11. Core string edits, alignments and dynamic programming 12. Refining core string edits and alignments 13. Extending the core problems 14. Multiple string comparison: the Holy Grail 15. Sequence database and their uses: the motherlode Part IV. Currents, Cousins and Cameos: 16. Maps, mapping, sequencing and superstrings 17. Strings and evolutionary trees 18. Three short topics 19. Models of genome-level mutations.

SINGLE-PARTICLE TRACKING: Applications to Membrane Dynamics

Abstract: Measurements of trajectories of individual proteins or lipids in the plasma membrane of cells show a variety of types of motion. Brownian motion is observed, but many of the particles undergo non-Brownian motion, including directed motion, confined motion, and anomalous diffusion. The variety of motion leads to significant effects on the kinetics of reactions among membrane-bound species and requires a revision of existing views of membrane structure and dynamics.

Uncoupling protein-2: a novel gene linked to obesity and hyperinsulinemia

Abstract: A mitochondrial protein called uncoupling protein (UCP1) plays an important role in generating heat and burning calories by creating a pathway that allows dissipation of the proton electrochemical gradient across the inner mitochondrial membrane in brown adipose tissue, without coupling to any other energy-consuming process. This pathway has been implicated in the regulation of body temperature, body composition and glucose metabolism. However, UCP1-containing brown adipose tissue is unlikely to be involved in weight regulation in adult large-size animals and humans living in a thermoneutral environment (one where an animal does not have to increase oxygen consumption or energy expenditure to lose or gain heat to maintain body temperature), as there is little brown adipose tissue present. We now report the discovery of a gene that codes for a novel uncoupling protein, designated UCP2, which has 59% amino-acid identity to UCP1, and describe properties consistent with a role in diabetes and obesity. In comparison with UCP1, UCP2 has a greater effect on mitochondrial membrane potential when expressed in yeast. Compared to UCP1, the gene is widely expressed in adult human tissues, including tissues rich in macrophages, and it is upregulated in white fat in response to fat feeding. Finally, UCP2 maps to regions of human chromosome 11 and mouse chromosome 7 that have been linked to hyperinsulinaemia and obesity. Our findings suggest that UCP2 has a unique role in energy balance, body weight regulation and thermoregulation and their responses to inflammatory stimuli.

Measuring accessibility: an exploration of issues and alternatives

Abstract: Accessibility is an important characteristic of metropolitan areas and is often reflected in transportation and land-use planning goals. But the concept of accessibility has rarely been translated into performance measures by which policies are evaluated, despite a substantial literature on the concept. This paper is an attempt to bridge the gap between the academic literature and the practical application of such measures and provide a framework for the development of accessibility measures. Issues that planners must address in developing an accessibility measure are outlined, and two case studies suggestive of the range of possible approaches are presented.

A Catalog of 1.4 GHz Radio Sources from the FIRST Survey

Abstract: We present a catalog of 138,665 radio sources derived from the initial 1550 deg2 of the FIRST survey. The survey parameters are reviewed, and a map depicting the coverage for the first two observing sessions is presented. We then describe in detail our algorithm for radio source detection and parameterization, as well as our procedures for constructing the final catalog. The results of extensive tests for astrometric and photometric accuracy, as well as for uncertainties in source extent and morphological characterization, are presented. Source positions are all good to better than 1'', and the flux density scale is accurate to 5%; our elliptical Gaussian fitting procedure is shown both to provide a high-fidelity representation of source morphology for most objects and to characterize correctly bright sources extended on scales down to ~ the synthesized beam size of 54. We use the catalog to construct a log N-log S relation for 20 cm radio sources over four decades of flux density, finding excellent agreement with previous determinations from smaller surveys. As one example of the catalog's utility, we present comparisons with the Guide Star Catalog, the IRAS Faint Source catalog, and the ROSAT WGA catalog, identifying radio counterparts to thousands of the objects. Complete instructions for access to this FIRST catalog and subsequent updates thereto are provided.

A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy

Abstract: A new method for estimating divergence times when evolutionary rates are variable across lineages is proposed. The method, called nonparametric rate smoothing (NPRS), relies on minimization of ancestor-descendant local rate changes and is motivated by the likelihood that evolutionary rates are autocorrelated in time. Fossil information pertaining to minimum and/or maximum ages of nodes in a phylogeny is incorporated into the algorithms by constrained optimization techniques. The accuracy of NPRS was examined by comparison to a clock-based maximum-likelihood method in computer simulations. NPRS provides more accurate estimates of divergence times when (1) sequence lengths are sufficiently long, (2) rates are truly nonclocklike, and (3) rates are moderately to highly autocorrelated in time. The algorithms were applied to estimate divergence times in seed plants based on data from the chloroplast rbcL gene. Both constrained and unconstrained NPRS methods tended to produce divergence time estimates more consistent with paleobotanical evidence than did clock-based estimates.

Techniques in insect nematology

Abstract: Publisher Summary This chapter focuses on the techniques used for identifying, isolating, propagating, assaying, and preserving nematodes that are parasitic in or pathogenic to insects. Nematodes are nonsegmented animals with excretory, nervous, digestive, reproductive, and muscular systems but lacking circulatory and respiratory systems. The stage of entomogenous and entomopathogenic nematodes that is infective varies depending on the group. A good stereomicroscope is essential for nematode identification and should have a range of magnification between 10 and 100X, a fairly fiat field, and good resolution. The gonads and other structures of fixed nematodes may be obscured by the granular appearance of the intestine. Specimens can be cleared by processing to lactophenol or glycerin. The cephalic structures and the number of longitudinal chords are diagnostic characters for genetic or specific determination of certain groups of nematodes. Extraction methods for insect nematodes are derived from techniques developed with plant-parasitic nematodes. It is found that the most common methods are the Baermann funnel, sieving, elutriation, and centrifugal flotation.

The Sleep Heart Health Study: design, rationale, and methods.

Abstract: The Sleep Heart Health Study (SHHS) is a prospective cohort study designed to investigate obstructive sleep apnea (OSA) and other sleep-disordered breathing (SDB) as risk factors for the development of cardiovascular disease. The study is designed to enroll 6,600 adult participants aged 40 years and older who will undergo a home polysomnogram to assess the presence of OSA and other SDB. Participants in SHHS have been recruited from cohort studies in progress. Therefore, SHHS adds the assessment of OSA to the protocols of these studies and will use already collected data on the principal risk factors for cardiovascular disease as well as follow-up and outcome information pertaining to cardiovascular disease. Parent cohort studies and recruitment targets for these cohorts are the following: Atherosclerosis Risk in Communities Study (1,750 participants), Cardiovascular Health Study (1,350 participants), Framingham Heart Study (1,000 participants), Strong Heart Study (600 participants), New York Hypertension Cohorts (1,000 participants), and Tucson Epidemiologic Study of Airways Obstructive Diseases and the Health and Environment Study (900 participants). As part of the parent study follow-up procedures, participants will be surveyed at periodic intervals for the incidence and recurrence of cardiovascular disease events. The study provides sufficient statistical power for assessing OSA and other SDB as risk factors for major cardiovascular events, including myocardial infarction and stroke.

A Micro-Analysis of Land Use and Travel in Five Neighborhoods in the San Francisco Bay Area

Abstract: This study examined the effects of land use and attitudinal characteristics on travel behavior for five diverse San Francisco Bay Area neighborhoods. First, socio-economic and neighborhood characteristics were regressed against number and proportion of trips by various modes. The best models for each measure of travel behavior confirmed that neighborhood characteristics add significant explanatory power when socio-economic differences are controlled for. Specifically, measures of residential density, public transit accessibility, mixed land use, and the presence of sidewalks are significantly associated with trip generation by mode and modal split. Second, 39 attitude statements relating to urban life were factor analyzed into eight factors: pro-environment, pro-transit, suburbanite, automotive mobility, time pressure, urban villager, TCM, and workaholic. Scores on these factors were introduced into the six best models discussed above. The relative contributions of the socio-economic, neighborhood, and attitudinal blocks of variables were assessed. While each block of variables offers some significant explanatory power to the models, the attitudinal variables explained the highest proportion of the variation in the data. The finding that attitudes are more strongly associated with travel than are land use characteristics suggests that land use policies promoting higher densities and mixtures may not alter travel demand materially unless residents' attitudes are also changed.

A micro-analysis of land use and travel in five neighborhoods in the San Francisco Bay Area

Abstract: This study examined the effects of land use and attitudinal characteristics on travel behavior for five diverse San Francisco Bay Area neighborhoods. First, socio-economic and neighborhood characteristics were regressed against number and proportion of trips by various modes. The best models for each measure of travel behavior confirmed that neighborhood characteristics add significant explanatory power when socio-economic differences are controlled for. Specifically, measures of residential density, public transit accessibility, mixed land use, and the presence of sidewalks are significantly associated with trip generation by mode and modal split. Second, 39 attitude statements relating to urban life were factor analyzed into eight factors: pro-environment, pro-transit, suburbanite, automotive mobility, time pressure, urban villager, TCM, and workaholic. Scores on these factors were introduced into the six best models discussed above. The relative contributions of the socio-economic, neighborhood, and attitudinal blocks of variables were assessed. While each block of variables offers some significant explanatory power to the models, the attitudinal variables explained the highest proportion of the variation in the data. The finding that attitudes are more strongly associated with travel than are land use characteristics suggests that land use policies promoting higher densities and mixtures may not alter travel demand materially unless residents' attitudes are also changed.

The role of highly unsaturated fatty acids in aquatic foodweb processes

Abstract: 1. Polyunsaturated fatty acids (PUFA) are almost exclusively synthesized by plants. Animals can convert from one form of PUFA to another through elongation and desaturation, but very few can synthesize PUFA de novo. PUFA play an important role in regulating cell membrane properties, serve as precursors for important animal hormones and are essential for animals. 2. In aquaculture studies, highly unsaturated fatty acids (HUFA), a subset of PUFA, have been found to be critical for maintaining high growth, survival and reproductive rates and high food conversion efficiencies for a wide variety of marine and freshwater organisms. 3. The plankton literature suggests high food-quality algae species are rich in HUFA and low food-quality algae are poor in HUFA. Adding semi-pure emulsions of HUFA to algae monocultures can markedly increase the growth rates of zooplankton feeding on these mixtures. 4. A study measuring zooplankton biomass accrual when feeding on natural phytoplankton found a strong correlation between phytoplankton HUFA (specifically eicosapentaenoic acid) content and herbivorous zooplankton production. 5. The aquatic ecology literature suggests that planktonic foodwebs with high HUFA content phytoplankton have high zooplankton to phytoplankton biomass ratios, while systems with low HUFA phytoplankton have low zooplankton biomass. Also, the seasonal succession of plankton in many temperate lakes follows patterns tied to phytoplankton HUFA content, with intense zooplankton grazing and ‘clear-water-phases’ characteristic of periods when the phytoplankton is dominated by HUFA-rich species. 6. Herbivorous zooplankton production is constrained by the zooplankton’s ability to ingest and digest phytoplankton. It is becoming increasingly clear, however, that much of the phytoplankton which is assimilated may be nutritionally inadequate. HUFA may be key nutritional constituents of zooplankton diets, and may determine energetic efficiency across the plant–animal interface, secondary production and the strength of trophic coupling in aquatic pelagic foodwebs.

Do Gasoline Prices Respond Asymmetrically to Crude Oil Price Changes

Abstract: The authors test and confirm that retail gasoline prices respond more quickly to increases than to decreases in crude oil prices. Among the possible sources of this asymmetry are production/inventory adjustment lags and market power of some sellers. By analyzing price transmission at different points in the distribution chain, the authors attempt to shed light on these theories. Spot prices for generic gasoline show asymmetry in responding to crude oil price changes, which may reflect inventory adjustment effects. Asymmetry also appears in the response of retail prices to wholesale price changes, possibly indicating short-run market power among retailers.

Optical Communication Networks

Abstract: A comprehensive explanation of the newest developments in optical networks in the MCGRAW-HILL COMPUTER COMMUNICATIONS series. Case studies and research projects at AT&T, Fujitsu, and NTT are considered in order to provide the reader with hands-on information which can be applied in practice.

Effect of seawater carbonate concentration on foraminiferal carbon and oxygen isotopes

Abstract: Stable oxygen and carbon isotope measurements on biogenic calcite and aragonite have become standard tools for reconstructing past oceanographic and climatic change. In aquatic organisms, 18O/16O ratios in the shell carbonate are a function of the ratio in the sea water and the calcification temperature1. In contrast, 13C/12C ratios are controlled by the ratio of dissolved inorganic carbon in sea water and physiological processes such as respiration and symbiont photosynthesis2. These geochemical proxies have been used with analyses of foraminifera shells to reconstruct global ice volumes3, surface and deep ocean temperatures4,5, ocean circulation changes6 and glacial–interglacial exchange between the terrestrial and oceanic carbon pools7. Here, we report experimental measurements on living symbiotic and non-symbiotic plankton foraminifera (Orbulina universa and Globigerina bulloides respectively) showing that the 13C/12C and 18O/16O ratios of the calcite shells decrease with increasing seawater [CO32−]. Because glacial-period oceans had higher pH and [CO32−] than today8, these new relationships confound the standard interpretation of glacial foraminiferal stable-isotope data. In particular, the hypothesis that the glacial–interglacial shift in the 13C/12C ratio was due to a transfer of terrestrial carbon into the ocean7 can be explained alternatively by an increase in ocean alkalinity25. A carbonate-concentration effect could also help explain some of the extreme stable-isotope variations during the Proterozoic and Phanerozoic aeons9.

Evaluation of the Rate of Evolution in Natural Populations of Guppies (Poecilia reticulata)

Abstract: Natural populations of guppies were subjected to an episode of directional selection that mimicked natural processes. The resulting rate of evolution of age and size at maturity was similar to rates typically obtained for traits subjected to artificial selection in laboratory settings and up to seven orders of magnitude greater than rates inferred from the paleontological record. Male traits evolved more rapidly than female traits largely because males had more genetic variation upon which natural selection could act. These results are considered in light of the ongoing debate about the importance of natural selection versus other processes in the paleontological record of evolution.

The Geometry of the Master Equation and Topological Quantum Field Theory

Abstract: In Batalin–Vilkovisky formalism, a classical mechanical system is specified by means of a solution to the classical master equation. Geometrically, such a solution can be considered as a QP-manifold, i.e. a supermanifold equipped with an odd vector field Q obeying {Q, Q} = 0 and with Q-invariant odd symplectic structure. We study geometry of QP-manifolds. In particular, we describe some construction of QP-manifolds and prove a classification theorem (under certain conditions). We apply these geometric constructions to obtain in a natural way the action functionals of two-dimensional topological sigma-models and to show that the Chern–Simons theory in BV-formalism arises as a sigma-model with target space $\Pi\mathcal{G}$. (Here $\mathcal{G}$ stands for a Lie algebra and Π denotes parity inversion.)

Prospective study of blunt aortic injury: Multicenter trial of the American Association for the Surgery of Trauma

Abstract: Background: Blunt aortic injury is a major cause of death from blunt trauma. Evolution of diagnostic techniques and methods of operative repair have altered the management and posed new questions in recent years. Methods: This study was a prospectively conducted multicenter trial involving 50 trauma centers in North America under the direction of the Multi-institutional Trial Committee of the American Association for the Surgery of Trauma. Results: There were 274 blunt aortic injury cases studied over 2.5 years, of which 81% were caused by automobile crashes. Chest computed tomography and transesophageal echocardiography were applied in 88 and 30 cases, respectively, and were 75 and 80% diagnostic, respectively. Two hundred seven stable patients underwent planned thoracotomy and repair. Clamp and sew technique was used in 73 (35%) and bypass techniques in 134 (65%). Overall mortality was 31%, with 63% of deaths being attributable to aortic rupture; mortality was not affected by method of repair. Paraplegia occurred postoperatively in 8.7%. Logistic regression analysis demonstrated clamp and sew (p = 0.002) and aortic cross clamp time of 30 minutes (p = 0.01) to be associated with development of postoperative paraplegia. Conclusions: Rupture after hospital admission remains a major problem. Although newer diagnostic techniques are being applied, at this time aortography remains the diagnostic standard. Aortic cross clamp time beyond 30 minutes was associated with paraplegia; bypass techniques, which provide distal aortic perfusion, produced significantly lower paraplegia rates than the clamp and sew approach.

Adult Attachment in a Nationally Representative Sample

Abstract: The explosion of adult attachment research in the last decade has been limited by its reliance on college student and distressed samples. Using a large nationally representative sample of American adults, the authors examined the relation of sociodemographics, childhood adversity, parental representations, adult psychopathology, and personality traits to adult attachment in an effort to replicate previous findings and extend the theory. Distribution of adult attachment styles was similar to that in prior studies: 59% secure, 25% avoidant, and 11% anxious. Adult attachment was associated with several sociodemographic variables (e.g., income, age, race) not previously studied. Childhood adversities of an interpersonal nature were strongly related to insecure adult attachment. Various types of adult psychopathologies and personality traits were also strongly related to adult attachment. Implications for adult attachment theory and future research are discussed.

Attachment formation and transfer in young adults’close friendships and romantic relationships

Abstract: Two hundred thirty-seven young adults from an American university completed a questionnaire designed to test several normative implications of attachment theory. As predicted, the majority of participants (60%) used their parents as primary attachment figures but were in the process of transferring attachment-related functions from parents to peers (best friends and romantic partners). The transfer of these functions the parents to peers was found to be a function of the duration of the peer relationship. Furthermore, factors that generally promote the development of attachment formation in infancy (such as caregiving, trust, and intimate contact) were found to be positively associated with the development of attachment in adult relationships. Additional variables were identified that may facilitate peer attachment formation: secure working models of attachment and the perceived security of the peer. It is argued that future investigations into the role of attachment formation and transfer are critical for a comprehensive description of attachment dynamics in adult relationships.

An accurate method for computer-generating tungsten anode x-ray spectra from 30 to 140 kV.

Abstract: A tungsten anode spectral model using interpolating polynomials (TASMIP) was used to compute x-ray spectra at 1 keV intervals over the range from 30 kV to 140 kV. The TASMIP is not semi-empirical and uses no physical assumptions regarding x-ray production, but rather interpolates measured constant potential x-ray spectra published by Fewell et al. [Handbook of Computed Tomography X-ray Spectra (U.S. Government Printing Office, Washington, D.C., 1981)]. X-ray output measurements (mR/mAs measured at 1 m) were made on a calibrated constant potential generator in our laboratory from 50 kV to 124 kV, and with 0-5 mm added aluminum filtration. The Fewell spectra were slightly modified (numerically hardened) and normalized based on the attenuation and output characteristics of a constant potential generator and metal-insert x-ray tube in our laboratory. Then, using the modified Fewell spectra of different kVs, the photon fluence phi at each 1 keV energy bin (E) over energies from 10 keV to 140 keV was characterized using polynomial functions of the form phi (E) = a0[E] + a1[E] kV + a2[E] kV2 + ... + a(n)[E] kVn. A total of 131 polynomial functions were used to calculate accurate x-ray spectra, each function requiring between two and four terms. The resulting TASMIP algorithm produced x-ray spectra that match both the quality and quantity characteristics of the x-ray system in our laboratory. For photon fluences above 10% of the peak fluence in the spectrum, the average percent difference (and standard deviation) between the modified Fewell spectra and the TASMIP photon fluence was -1.43% (3.8%) for the 50 kV spectrum, -0.89% (1.37%) for the 70 kV spectrum, and for the 80, 90, 100, 110, 120, 130 and 140 kV spectra, the mean differences between spectra were all less than 0.20% and the standard deviations were less than approximately 1.1%. The model was also extended to include the effects of generator-induced kV ripple. Finally, the x-ray photon fluence in the units of photons/mm2 per mR was calculated as a function of HVL, kV, and ripple factor, for various (water-equivalent) patient thicknesses (0, 10, 20, and 30 cm). These values may be useful for computing the detective quantum efficiency, DQE(f), of x-ray detector systems. The TASMIP algorithm and ancillary data are made available on line at http:/(/)www.aip.org/epaps/epaps.html.

Bone Microdamage and Skeletal Fragility in Osteoporotic and Stress Fractures

Abstract: The accumulation of bone microdamage has been proposed as one factor that contributes to increased skeletal fragility with age and that may increase the risk for fracture in older women. This paper reviews the current status and understanding of microdamage physiology and its importance to skeletal fragility. Several questions are addressed: Does microdamage exist in vivo in bone? If it does, does it impair bone quality? Does microdamage accumulate with age, and is the accumulation of damage with age sufficient to cause a fracture? The nature of the damage repair mechanism is reviewed, and it is proposed that osteoporotic fracture may be a consequence of a positive feedback between damage accumulation and the increased remodeling space associated with repair.

Oxygen and aroma barrier properties of edible films: A review

Abstract: Interest in maintaining food quality while reducing packaging waste has encouraged the exploration of the oxygen and aroma transport properties of edible films. This review article introduces the theoretical basis for oxygen and aroma barrier property determination and presents a brief historical per- spective of the development of barrier polymers. The effects of structure and composition on mass transport in edible films are examined and compared with those of the more thoroughly investigated synthetic polymers. A survey of edible film oxygen and aroma barrier research is presented; areas re- quiring additional investigation are suggested, for applications as well as basic research. The potential of edible films and coatings to provide excellent aroma retention and superior oxygen barrier properties makes this quite a promising area of research for both food and packaging scientists.

Local food systems and sustainable communities

Abstract: The long-term health of a community's food system is an important indicator of its vitality and sustainability. A logical and appropriate way to revitalize a community is by the development of a local food economy. People throughout the United States are designing and implementing sustainable, local food systems that are rooted in particular places, aim to be economically viable for farmers and consumers, use ecologically sound production and distribution practices, and enhance social equity and democracy for all members of the community. This paper reviews the existing literature on local food systems, examines a variety of strategies and initiatives that are currently underway, and identifies steps that community kaders and citizens can use to develop their own local food systems. Finally, I suggest what research is needed to support these community efforts.