Showing papers by "University of California, Davis published in 1994"

Level spacing distributions and the Airy kernel

Abstract: Scaling level-spacing distribution functions in the “bulk of the spectrum” in random matrix models ofN×N hermitian matrices and then going to the limitN→∞ leads to the Fredholm determinant of thesine kernel sinπ(x−y)/π(x−y). Similarly a scaling limit at the “edge of the spectrum” leads to theAiry kernel [Ai(x)Ai(y)−Ai′(x)Ai(y)]/(x−y). In this paper we derive analogues for this Airy kernel of the following properties of the sine kernel: the completely integrable system of P.D.E.'s found by Jimbo, Miwa, Mori, and Sato; the expression, in the case of a single interval, of the Fredholm determinant in terms of a Painleve transcendent; the existence of a commuting differential operator; and the fact that this operator can be used in the derivation of asymptotics, for generaln, of the probability that an interval contains preciselyn eigenvalues.

The anomaly of silicon in plant biology.

Abstract: Silicon is the second most abundant element in soils, the mineral substrate for most of the world's plant life. The soil water, or the "soil solution," contains silicon, mainly as silicic acid, H4SiO4, at 0.1-0.6 mM--concentrations on the order of those of potassium, calcium, and other major plant nutrients, and well in excess of those of phosphate. Silicon is readily absorbed so that terrestrial plants contain it in appreciable concentrations, ranging from a fraction of 1% of the dry matter to several percent, and in some plants to 10% or even higher. In spite of this prominence of silicon as a mineral constituent of plants, it is not counted among the elements defined as "essential," or nutrients, for any terrestrial higher plants except members of the Equisitaceae. For that reason it is not included in the formulation of any of the commonly used nutrient solutions. The plant physiologist's solution-cultured plants are thus anomalous, containing only what silicon is derived as a contaminant of their environment. Ample evidence is presented that silicon, when readily available to plants, plays a large role in their growth, mineral nutrition, mechanical strength, and resistance to fungal diseases, herbivory, and adverse chemical conditions of the medium. Plants grown in conventional nutrient solutions are thus to an extent experimental artifacts. Omission of silicon from solution cultures may lead to distorted results in experiments on inorganic plant nutrition, growth and development, and responses to environmental stress.

Optimal asymmetric encryption

Abstract: Given an arbitrary k-bit to k-bit trapdoor permutation f and a hash function, we exhibit an encryption scheme for which (i) any string x of length slightly less than k bits can be encrypted as f(rx), where r x is a simple probabilistic encoding of x depending on the hash function; and (ii) the scheme can be proven semantically secure assuming the hash function is “ideal.” Moreover, a slightly enhanced scheme is shown to have the property that the adversary can create ciphertexts only of strings for which she “knows” the corresponding plaintexts—such a scheme is not only semantically secure but also non-malleable and secure against chosen-ciphertext attack.

Mammary Hyperplasia and Carcinoma in MMTV-cyclin D1 Transgenic Mice

Abstract: PHYSICAL associations between cyclins, viral oncogenes and tumour suppressor genes imply a central role for cyclins in growth control1, 2. Cyclin D1 was identified as a candidate oncogene (PRAD1) in tumour-specific DNA rearrangements3, 4. and is suspected to be a contributor to several types of neoplasms including breast cancer5, 6. Cyclin D1 also rescues G1 cyclin-defective Saccharomyces cerevisiae7, and is a growth-regulated gene8. Despite evidence suggesting that cyclin D1 is an oncogene, its ability to transform cells directly in culture remains controversial9–16. To evaluate its potential to deregulate growth in vivo in a physiologically relevant tissue we overexpressed cyclin Dl in mammary cells in transgenic mice. We report here that overexpression of cyclin Dl resulted in abnormal mammary cell proliferation including the development of mammary adenocarcinomas. We conclude that overexpression of cyclin Dl deregulates cell proliferation and can induce tumorigenic changes in mammary tissues, suggesting that cyclin Dl indeed plays an important oncogenic role in breast cancer.

Shifting visual attention between objects and locations: evidence from normal and parietal lesion subjects.

Abstract: Space- and object-based attention components were examined in neurologically normal and parietal-lesion subjects, who detected a luminance change at 1 of 4 ends of 2 outline rectangles. One rectangle end was precued (75% valid); on invalid-cue trials, the target appeared at the other end of the cued rectangle or at 1 end of the uncued rectangle. For normals, the cost for invalid cues was greater for targets in the uncued rectangle, indicating an object-based component. Both right- and left-hemisphere patients showed costs that were greater for contralesional targets. For right-hemisphere patients, the object cost was equivalent for contralesional and ipsilesional targets, indicating a spatial deficit, whereas the object cost for left-hemisphere patients was larger for contralesional targets, indicating an object deficit.

Network intrusion detection

Abstract: Intrusion detection is a new, retrofit approach for providing a sense of security in existing computers and data networks, while allowing them to operate in their current "open" mode. The goal of intrusion detection is to identify unauthorized use, misuse, and abuse of computer systems by both system insiders and external penetrators. The intrusion detection problem is becoming a challenging task due to the proliferation of heterogeneous computer networks since the increased connectivity of computer systems gives greater access to outsiders and makes it easier for intruders to avoid identification. Intrusion detection systems (IDSs) are based on the beliefs that an intruder's behavior will be noticeably different from that of a legitimate user and that many unauthorized actions are detectable. Typically, IDSs employ statistical anomaly and rulebased misuse models in order to detect intrusions. A number of prototype IDSs have been developed at several institutions, and some of them have also been deployed on an experimental basis in operational systems. In the present paper, several host-based and network-based IDSs are surveyed, and the characteristics of the corresponding systems are identified. The host-based systems employ the host operating system's audit trails as the main source of input to detect intrusive activity, while most of the network-based IDSs build their detection mechanism on monitored network traffic, and some employ host audit trails as well. An outline of a statistical anomaly detection algorithm employed in a typical IDS is also included. >

Matched subspace detectors

Abstract: We formulate a general class of problems for detecting subspace signals in subspace interference and broadband noise. We derive the generalized likelihood ratio (GLR) for each problem in the class. We then establish the invariances for the GLR and argue that these are the natural invariances for the problem. In each case, the GLR is a maximal invariant statistic, and the distribution of the maximal invariant statistic is monotone. This means that the GLR test (GLRT) is the uniformly most powerful invariant detector. We illustrate the utility of this finding by solving a number of problems for detecting subspace signals in subspace interference and broadband noise. In each case we give the distribution for the detector and compute performance curves. >

Domestic Saving and International Capital Flows Reconsidered

Abstract: A long literature since Feldstein and Horioka's seminal contribution documents the strong correlation of domestic saving and investment rates since the 1960s. According to conventional wisdom, the result provides evidence of international capital market imperfections. The macroeconomic theory of small open economies prescribes a relationship between the composition of aggregate demand and its relative price structure, a linkage hitherto ignored in the saving-investment literature. Theory and evidence also suggest a role for growth and demographic effects, well known in previous studies. If one controls for these effects, the standard correlation of saving and investment disappears. International capital markets may be better integrated than once thought, and the former correlations may have been spurious. The pattern of domestic investment rates is better explained by domestic price distortions and other variables than by domestic saving constraints.

Combined spatial and temporal imaging of brain activity during visual selective attention in humans.

Abstract: VISUAL–SPATIAL attention is an essential brain function that enables us to select and preferentially process high priority information in the visual fields1,2. Several brain areas have been shown to participate in the control of spatial attention in humans3–5, but little is known about the underlying selection mechanisms. Non-invasive scalp recordings of event-related potentials (e.r.ps) in humans have shown that attended visual stimuli are preferentially selected as early as 80–90 ms after stimulus onset6,7, but current e.r.p. methods do not permit a precise localization of the participating cortical areas. In this study we combined neuroimaging (positron emission tomography) with e.r.p. recording in order to describe both the cortical anatomy and time course of attentional selection processes. Together these methods showed that visual inputs from attended locations receive enhanced processing in the extrastriate cortex (fusiform gyrus) at 80–130 ms after stimulus onset. These findings reinforce early selection models of attention8–10.

Synchronous oscillations in neuronal systems: mechanisms and functions.

Abstract: How are the functions performed by one part of the nervous system integrated with those of another? This fundamental issue pervades virtually every aspect of brain function from sensory and cognitive processing to motor control. Yet from a physiological perspective we know very little about the neural mechanisms underlying the integration of distributed processes in the nervous system. Even the simplest of sensori-motor acts engages vast numbers of cells in many different parts of the brain. Such actions require coordination between a host of neural systems, each of which must carry out parallel computations involving large populations of interconnected neurons. It seems reasonable to assume that a mechanism or class of mechanisms has evolved to temporally coordinate the activity within and between subsystems of the central nervous system. For several reasons, neuronal rhythms have long been thought to play an important role in such coordination. Since the discovery of the Electroencephalogram (EEG) over 60 years ago it has been known that a number of structures in the mammalian brain engage in rhythmic activities. These patterned neuronal oscillations take many forms. They occur over a broad range of frequencies, and are present in a multitude of different systems in the b~ain, during a variety of different behavioral states. They are often the most salient aspect of observable electrical activity in the brain and typically encompass widespread regions of cerebral tissue. With the advent of new techniques of multielectrode recording and neural imaging, it is now within the realm of possibility 'to record from 100 single neurons simultaneously (Wilson and McNaughton, 1993), to optically measure the activity in a cortical area (Blasdel and Salama, 1986; T'so et al., 1990), or to noninvasively image the pattern of electric current flow in an alert human being performing a task (Pantev et al., 1991). These new techniques have revealed that spatially and temporally organized activity among distributed populations of cells often takes the form of synchronous rhythms. When combined with cellular neurophysiological and anatomical studies these findings provide new insights into the behavior and mechanisms controUing the coordination of activity in neuronal populations.

Nocardia species: host-parasite relationships.

Abstract: The nocardiae are bacteria belonging to the aerobic actinomycetes. They are an important part of the normal soil microflora worldwide. The type species, Nocardia asteroides, and N. brasiliensis, N. farcinica, N. otitidiscaviarum, N. nova, and N. transvalensis cause a variety of diseases in both normal and immunocompromised humans and animals. The mechanisms of pathogenesis are complex, not fully understood, and include the capacity to evade or neutralize the myriad microbicidal activities of the host. The relative virulence of N. asteroides correlates with the ability to inhibit phagosome-lysosome fusion in phagocytes; to neutralize phagosomal acidification; to detoxify the microbicidal products of oxidative metabolism; to modify phagocyte function; to grow within phagocytic cells; and to attach to, penetrate, and grow within host cells. Both activated macrophages and immunologically specific T lymphocytes constitute the major mechanisms for host resistance to nocardial infection, whereas B lymphocytes and humoral immunity do not appear to be as important in protecting the host. Thus, the nocardiae are facultative intracellular pathogens that can persist within the host, probably in a cryptic form (L-form), for life. Silent invasion of brain cells by some Nocardia strains can induce neurodegeneration in experimental animals; however, the role of nocardiae in neurodegenerative diseases in humans needs to be investigated.

Interfacial Phenomena in the Evaluation of Antioxidants: Bulk Oils vs Emulsions

Abstract: Antioxidants have been difficult to evaluate in oils and food emulsions due in part to the complex interfacial phenomena involved. Lipophilic and hydrophilic antioxidants were evaluated with corn oil stripped of natural tocopherols in bulk and in emulsion systems. Oridation was followed by determining formation of hydroperoxides and hexanal. The lipophilic antioxidants α-tocopherol and ascorbyl palmitate were more effective in an oil-in-water emulsion system than in bulk oil, while the opposite trend was found for the hydrophilic antioxidants Trolox and ascorbic acid. The oil-insoluble ascorbic acid was a particularly efficient antioxidant in suspension in the bulk oil system

Definitions and Guidelines for Assessment of Wounds and Evaluation of Healing

Abstract: Background: Chronic wounds represent a worldwide problem. For laboratory and clinical research to adequately address this problem, a common language needs to exist. Observation: This language should include a system of wound classification, a lexicon of wound descriptors, and a description of the processes that are likely to affect wound healing and wound healing end points. Conclusions: The report that follows defines wound, acute wound, chronic wound, healing and forms of healing, wound assessment, wound extent, wound burden, and wound severity. The utility of these definitions is demonstrated as they relate to the healing of a skin wound, but these definitions are broadly applicable to all wounds. (Arch Dermatol. 1994;130:489-493)

Oxygen-derived species: their relation to human disease and environmental stress.

Abstract: Free radicals and other reactive oxygen species (ROS) are constantly formed in the human body, often for useful metabolic purposes. Antioxidant defenses protect against them, but these defenses are not completely adequate, and systems that repair damage by ROS are also necessary. Mild oxidative stress often induces antioxidant defense enzymes, but severe stress can cause oxidative damage to lipids, proteins, and DNA within cells, leading to such events as DNA strand breakage and disruption of calcium ion metabolism. Oxidative stress can result from exposure to toxic agents, and by the process of tissue injury itself. Ozone, oxides of nitrogen, and cigarette smoke can cause oxidative damage; but the molecular targets that they damage may not be the same.

Premature p34cdc2 activation required for apoptosis

Abstract: Activation of the serine-threonine kinase p34cdc2 at an inappropriate time during the cell cycle leads to cell death that resembles apoptosis. Premature activation of p34cdc2 was shown to be required for apoptosis induced by a lymphocyte granule protease. The kinase was rapidly activated and tyrosine dephosphorylated at the initiation of apoptosis. DNA fragmentation and nuclear collapse could be prevented by blocking p34cdc2 activity with excess peptide substrate, or by inactivating p34cdc2 in a temperature-sensitive mutant. Premature p34cdc2 activation may be a general mechanism by which cells induced to undergo apoptosis initiate the disruption of the nucleus.

Definitions and guidelines for assessment of wounds and evaluation of healing.

Abstract: Chronic wounds represent a worldwide problem. For laboratory and clinical research to adequately address this problem, a common language needs to exist. This language should include a system of wound classification, a lexicon of wound descriptors, and a description of the processes that are likely to affect wound healing and would healing end points. The report that follows defines wound, acute wound, chronic wound, healing and forms of healing, wound assessment, wound extent, wound burden, and wound severity. The utility of these definitions is demonstrated as they relate to the healing of a skin wound, but these definitions are broadly applicable to all wounds.

Chapter 1 – A Practical Guide to the Preparation of Ca2+ Buffers

Abstract: Calcium (Ca2+) is a critical regulator of an immense array of biological processes, and the intracellular [Ca2+] that regulates these processes is ~ 10,000 lower than the extracellular [Ca2+]. To study and understand these myriad Ca2+-dependent functions requires control and measurement of [Ca2+] in the nano- to micromolar range (where contaminating Ca2+ is a significant problem). As with pH, it is often essential to use Ca2+ buffers to control free [Ca2+] at the desired biologically relevant concentrations. Fortunately, there are numerous available Ca2+ buffers with different affinities that make this practical. However, there are numerous caveats with respect to making these solutions appropriately with known Ca2+ buffers. These include pH dependence, selectivity for Ca2+ (e.g., vs. Mg2+), ionic strength and temperature dependence, and complex multiple equilibria that occur in physiologically relevant solutions. Here we discuss some basic principles of Ca2+ buffering with respect to some of these caveats and provide practical tools (including freely downloadable computer programs) to help in the making and calibration of Ca2+-buffered solutions for a wide array of biological applications.

Survey of plant short tandem DNA repeats

Abstract: Length variations in simple sequence tandem repeats are being given increased attention in plant genetics. Some short tandem repeats (STRs) from a few plant species, mainly those at the dinucleotide level, have been demonstrated to show polymorphisms and Mendelian inheritance. In the study reported here a search for all of the possible STRs ranging from mononucleotide up to tetranucleotide repeats was carried out on EMBL and GenBank DNA sequence databases of 3026 kb nuclear DNA and 1268 kb organelle DNA in 54 and 28 plant species (plus algae), respectively. An extreme rareness of STRs (4 STRs in 1268 kb DNA) was detected in organelle compared with nuclear DNA sequences. In nuclear DNA sequences, (AT)n sequences were the most abundant followed by (A)n · (T)n, (AG)n · (CT)n, (AAT)n · (ATT)n, (AAC)n · (GTT), (AGC)n · (GCT)n, (AAG)n · (CTT)n, (AATT)n · (TTAA)n, (AAAT)n · (ATTT)n and (AC)n · (GT)n sequences. A total of 130 STRs were found, including 49 (AT)n sequences in 31 species, giving an average of 1 STR every 23.3 kb and 1 (AT)n STR every 62 kb. An abundance comparable to that for the dinucleotide repeat was observed for the tri- and tetranucleotide repeats together. On average, there was 1 STR every 64.6 kb DNA in monocotyledons versus 1 every 21.2 kb DNA in dicotyledons. The fraction of STRs that contained G-C basepairs increased as the G+C contents went up from dicotyledons, monocotyledons to algae. While STRs of mono-, di- and tetranucleotide repeats were all located in non coding regions, 57% of the trinucleotide STRs containing G-C basepairs resided in coding regions.

Natural antioxidants in grapes and wines

Abstract: The concentrations of phenolics of three grape varieties and two red wines were determined. The red grape variety and the red wines contain phenolics at concentrations of 920 mg/kg and 1800 and 3200 mg/L, respectively. The antioxidative effects of wine phenolics on the catalysis of lipid peroxidation by biological catalysts such as myoglobin, cytochrome c, iron ascorbate, and copper ions were estimated. Lipid peroxidation catalyzed by myoglobin, cytochrome c, and iron ascorbate was inhibited (I 50 ) by wine phenolics at concentrations of 0.2, 0.35, and 0.9 μg of phenolics/mL

A Clinical Grading Scale to Predict Malignant Hyperthermia Susceptibility

Abstract: Background:The diagnosis of an acute malignant hyperthermia reaction by clinical criteria can be difficult because of the nonspecific nature and variable incidence of many of the clinical signs and laboratory findings. Development of a standardized means for estimating the qualitative likelihood of

The Security of Cipher Block Chaining

Abstract: The Cipher Block Chaining - Message Authentication Code (CBC MAC) specifies that a, message x = x1 ... xm be authenticated among parties who share a secret key a by tagging x with a prefix of fa(m)(x) def = fa(fa(... fa(fa(x1)?x2)?...?xm-1)?xm), where f is some underlying block cipher (eg. f = DES). This method is a pervasively used international and U.S. standard. We provide its first formal justification, showing the following general lemma: that cipher block chaining a pseudorandom function gives a pseudorandom function. Underlying our results is a technical lemma of independent interest, bounding the success probability of a computationally unbounded adversary in distinguishing between a random ml-bit to l-bit function and the CBC MAC of a random l-bit to l-bit function.

Sexual conflict and the evolutionary ecology of mating patterns: water striders as a model system

Abstract: Two core ideas in the study of mating systems and sexual selection are (1) the existence of a conflict between the sexes over mating decisions, and (2) that variation in ecological conditions drives the evolution of adaptive mating strategies and the diversification of mating systems. A recent burst of experimental studies of mating behavior and sexual selection in water striders has focused on the interaction of these ideas and led to new insights into the evolutionary ecology of mating systems and sexual selection.

Level spacing distributions and the Bessel kernel

Abstract: Scaling models of randomN×N hermitian matrices and passing to the limitN→∞ leads to integral operators whose Fredholm determinants describe the statistics of the spacing of the eigenvalues of hermitian matrices of large order. For the Gaussian Unitary Ensemble, and for many others'as well, the kernel one obtains by scaling in the “bulk” of the spectrum is the “sine kernel”\(\frac{{\sin \pi (x - y)}}{{\pi (x - y)}}\). Rescaling the GUE at the “edge” of the spectrum leads to the kernel\(\frac{{Ai(x)Ai'(y) - Ai'(x)Ai(y)}}{{x - y}}\), where Ai is the Airy function. In previous work we found several analogies between properties of this “Airy kernel” and known properties of the sine kernel: a system of partial differential equations associated with the logarithmic differential of the Fredholm determinant when the underlying domain is a union of intervals; a representation of the Fredholm determinant in terms of a Painleve transcendent in the case of a single interval; and, also in this case, asymptotic expansions for these determinants and related quantities, achieved with the help of a differential operator which commutes with the integral operator. In this paper we show that there are completely analogous properties for a class of kernels which arise when one rescales the Laguerre or Jacobi ensembles at the edge of the spectrum, namely $$\frac{{J_\alpha (\sqrt x )\sqrt y J'_\alpha (\sqrt y ) - \sqrt x J'_\alpha (\sqrt x )J_\alpha (\sqrt y )}}{{2(x - y)}},$$ , whereJα(z) is the Bessel function of order α. In the cases α=∓1/2 these become, after a variable change, the kernels which arise when taking scaling limits in the bulk of the spectrum for the Gaussian orthogonal and symplectic ensembles. In particular, an asymptotic expansion we derive will generalize ones found by Dyson for the Fredholm determinants of these kernels.

Structural factors in the economic reforms of China, Eastern Europe, and the Former Soviet Union

Abstract: Reform in China and Russia Jeffrey Sachs and Wing Thye Woo China's experience does not show that gradual reform is superior to the shock therapy undertaken in Eastern Europe and the Former Soviet Union (EEFSU). Differing performance primarily reflects different economic structures prior to reform: China was a peasant agricultural society, EEFSU was urban and overindustrialized. In both, jobs in state enterprises were so heavily subsidized that workers refused to move to new industries elsewhere, even when productivity in the latter was much higher. In EEFSU the large state sector impeded structural adjustment. Curtailing subsidies would have produced many losers who used their power to resist this outcome; failure to curtail subsidies then cut off the potential supply of labour and other factors to new emerging firms. China's state enterprises have not performed as well as the rest of the Chinese economy and do not explain its success; rapid growth was possible because the large agricultural sector contained vast surplus labour, and did not enjoy subsidies and soft budget constraints. Once constraints on migration across regions and jobs were removed, this labour was available to fuel expansion in new industries. Unlike the distributional conflict in EEFSU, in China reallocation of labour allowed all groups to gain. In both, partial liberalization also unleashed macroeconomic pressures, manageable in China because of rapid growth and adequate monetary policy, but explosive in much of EEFSU because of deeper structural problems and gross monetary mismanagement.

Fredholm Determinants, Differential Equations and Matrix Models

Abstract: Orthogonal polynomial random matrix models ofN×N hermitian matrices lead to Fredholm determinants of integral operators with kernel of the form (ϕ(x)ψ(y)−ψ(x)ϕ(y))/x−y. This paper is concerned with the Fredholm determinants of integral operators having kernel of this form and where the underlying set is the union of intervals\(J = \cup _{j = 1}^m (a_{2j - 1 ,{\text{ }}} a_{2j} )\). The emphasis is on the determinants thought of as functions of the end-pointsak.

Evolution of incompatibility-inducing microbes and their hosts.

Abstract: In many insect species, males infected with microbes related to Wolbachia pipientis are "incompatible" with uninfected females. Crosses between infected males and uninfected females produce significantly fewer adult progeny than the other three possible crosses. The incompatibility-inducing microbes are usually maternally transmitted. Thus, incompatibility tends to confer a reproductive advantage on infected females in polymorphic populations, allowing these infections to spread. This paper analyzes selection on parasite and host genes that affect such incompatibility systems. Selection among parasite variants does not act directly on the level of incompatibility with uninfected females. In fact, selection favors rare parasite variants that increase the production of infected progeny by infected mothers, even if these variants reduce incompatibility with uninfected females. However, productivity-reducing parasites that cause partial incompatibility with hosts harboring alternative variants can be favored once they become sufficiently abundant locally. Thus, they may spread spatially by a process analogous to the spread of underdominant chromosome rearrangements. The dynamics of modifier alleles in the host are more difficult to predict, because such alleles will occur in both infected and uninfected individuals. Nevertheless, the relative fecundity of infected females compared to uninfected females, the efficiency of maternal transmission and the mutual compatibility of infected individuals all tend to increase under within-population selection on both host and parasite genes. In addition, selection on host genes favors increased compatibility between infected males and uninfected females. Although vertical transmission tends to harmonize host and parasite evolution, competition among parasite variants will tend to maintain incompatibility.