Showing papers by "University of California published in 2008"

Allergic rhinitis and its impact on asthma (ARIA) 2008 update (in collaboration with the World Health Organization, GA(2)LEN and AllerGen)

Abstract: Allergic rhinitis is a symptomatic disorder of the nose induced after allergen exposure by an IgE-mediated inflammation of the membranes lining the nose. It is a global health problem that causes major illness and disability worldwide. Over 600 million patients from all countries, all ethnic groups and of all ages suffer from allergic rhinitis. It affects social life, sleep, school and work and its economic impact is substantial. Risk factors for allergic rhinitis are well identified. Indoor and outdoor allergens as well as occupational agents cause rhinitis and other allergic diseases. The role of indoor and outdoor pollution is probably very important, but has yet to be fully understood both for the occurrence of the disease and its manifestations. In 1999, during the Allergic Rhinitis and its Impact on Asthma (ARIA) WHO workshop, the expert panel proposed a new classification for allergic rhinitis which was subdivided into 'intermittent' or 'persistent' disease. This classification is now validated. The diagnosis of allergic rhinitis is often quite easy, but in some cases it may cause problems and many patients are still under-diagnosed, often because they do not perceive the symptoms of rhinitis as a disease impairing their social life, school and work. The management of allergic rhinitis is well established and the ARIA expert panel based its recommendations on evidence using an extensive review of the literature available up to December 1999. The statements of evidence for the development of these guidelines followed WHO rules and were based on those of Shekelle et al. A large number of papers have been published since 2000 and are extensively reviewed in the 2008 Update using the same evidence-based system. Recommendations for the management of allergic rhinitis are similar in both the ARIA workshop report and the 2008 Update. In the future, the GRADE approach will be used, but is not yet available. Another important aspect of the ARIA guidelines was to consider co-morbidities. Both allergic rhinitis and asthma are systemic inflammatory conditions and often co-exist in the same patients. In the 2008 Update, these links have been confirmed. The ARIA document is not intended to be a standard-of-care document for individual countries. It is provided as a basis for physicians, health care professionals and organizations involved in the treatment of allergic rhinitis and asthma in various countries to facilitate the development of relevant local standard-of-care documents for patients.

Plasmonic photothermal therapy (PPTT) using gold nanoparticles

Abstract: The use of lasers, over the past few decades, has emerged to be highly promising for cancer therapy modalities, most commonly the photothermal therapy method, which employs light absorbing dyes for achieving the photothermal damage of tumors, and the photodynamic therapy, which employs chemical photosensitizers that generate singlet oxygen that is capable of tumor destruction. However, recent advances in the field of nanoscience have seen the emergence of noble metal nanostructures with unique photophysical properties, well suited for applications in cancer phototherapy. Noble metal nanoparticles, on account of the phenomenon of surface plasmon resonance, possess strongly enhanced visible and near-infrared light absorption, several orders of magnitude more intense compared to conventional laser phototherapy agents. The use of plasmonic nanoparticles as highly enhanced photoabsorbing agents has thus introduced a much more selective and efficient cancer therapy strategy, viz. plasmonic photothermal therapy (PPTT). The synthetic tunability of the optothermal properties and the bio-targeting abilities of the plasmonic gold nanostructures make the PPTT method furthermore promising. In this review, we discuss the development of the PPTT method with special emphasis on the recent in vitro and in vivo success using gold nanospheres coupled with visible lasers and gold nanorods and silica-gold nanoshells coupled with near-infrared lasers.

Protein structure modeling with MODELLER.

Abstract: Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. This chapter presents an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of similar protocols (correction of protcols) has resulted in models of useful accuracy for domains in more than half of all known protein sequences.

An overview of limited feedback in wireless communication systems

Abstract: It is now well known that employing channel adaptive signaling in wireless communication systems can yield large improvements in almost any performance metric. Unfortunately, many kinds of channel adaptive techniques have been deemed impractical in the past because of the problem of obtaining channel knowledge at the transmitter. The transmitter in many systems (such as those using frequency division duplexing) can not leverage techniques such as training to obtain channel state information. Over the last few years, research has repeatedly shown that allowing the receiver to send a small number of information bits about the channel conditions to the transmitter can allow near optimal channel adaptation. These practical systems, which are commonly referred to as limited or finite-rate feedback systems, supply benefits nearly identical to unrealizable perfect transmitter channel knowledge systems when they are judiciously designed. In this tutorial, we provide a broad look at the field of limited feedback wireless communications. We review work in systems using various combinations of single antenna, multiple antenna, narrowband, broadband, single-user, and multiuser technology. We also provide a synopsis of the role of limited feedback in the standardization of next generation wireless systems.

Introduction to Bayesian Networks

Abstract: Reasoning with incomplete and unreliable information is a central characteristic of decision making, for example in industry, medicine and finance. Bayesian networks provide a theoretical framework for dealing with this uncertainty using an underlying graphical structure and the probability calculus. Bayesian networks have been successfully implemented in areas as diverse as medical diagnosis and finance. We present a brief introduction to Bayesian networks for those readers new to them and give some pointers to the literature.

The THEMIS ESA Plasma Instrument and In-flight Calibration

Abstract: The THEMIS plasma instrument is designed to measure the ion and electron distribution functions over the energy range from a few eV up to 30 keV for electrons and 25 keV for ions. The instrument consists of a pair of “top hat” electrostatic analyzers with common 180°×6° fields-of-view that sweep out 4π steradians each 3 s spin period. Particles are detected by microchannel plate detectors and binned into six distributions whose energy, angle, and time resolution depend upon instrument mode. On-board moments are calculated, and processing includes corrections for spacecraft potential. This paper focuses on the ground and in-flight calibrations of the 10 sensors on five spacecraft. Cross-calibrations were facilitated by having all the plasma measurements available with the same resolution and format, along with spacecraft potential and magnetic field measurements in the same data set. Lessons learned from this effort should be useful for future multi-satellite missions.

Citizenship Norms and the Expansion of Political Participation

Abstract: A growing chorus of scholars laments the apparent decline of political participation in America, and the negative implications of this trend for American democracy. This article questions this position – arguing that previous studies misdiagnosed the sources of political change and the consequences of changing norms of citizenship for Americans' political engagement. Citizenship norms are shifting from a pattern of duty-based citizenship to engaged citizenship. Using data from the 2005 ‘Citizenship, Involvement, Democracy’ survey of the Center for Democracy and Civil Society (CDACS) I describe these two faces of citizenship, and trace their impact on political participation. Rather than the erosion of participation, this norm shift is altering and expanding the patterns of political participation in America.

Isogeometric fluid-structure interaction: theory, algorithms, and computations

Abstract: We present a fully-coupled monolithic formulation of the fluid-structure interaction of an incompressible fluid on a moving domain with a nonlinear hyperelastic solid. The arbitrary Lagrangian–Eulerian description is utilized for the fluid subdomain and the Lagrangian description is utilized for the solid subdomain. Particular attention is paid to the derivation of various forms of the conservation equations; the conservation properties of the semi-discrete and fully discretized systems; a unified presentation of the generalized-α time integration method for fluid-structure interaction; and the derivation of the tangent matrix, including the calculation of shape derivatives. A NURBS-based isogeometric analysis methodology is used for the spatial discretization and three numerical examples are presented which demonstrate the good behavior of the methodology.

Epidemiology of basal-like breast cancer

Abstract: Risk factors for the newly identified “intrinsic” breast cancer subtypes (luminal A, luminal B, basal-like and human epidermal growth factor receptor 2-positive/estrogen receptor-negative) were determined in the Carolina Breast Cancer Study, a population-based, case–control study of African-American and white women. Immunohistochemical markers were used to subtype 1,424 cases of invasive and in situ breast cancer, and case subtypes were compared to 2,022 controls. Luminal A, the most common subtype, exhibited risk factors typically reported for breast cancer in previous studies, including inverse associations for increased parity and younger age at first full-term pregnancy. Basal-like cases exhibited several associations that were opposite to those observed for luminal A, including increased risk for parity and younger age at first term full-term pregnancy. Longer duration breastfeeding, increasing number of children breastfed, and increasing number of months breastfeeding per child were each associated with reduced risk of basal-like breast cancer, but not luminal A. Women with multiple live births who did not breastfeed and women who used medications to suppress lactation were at increased risk of basal-like, but not luminal A, breast cancer. Elevated waist-hip ratio was associated with increased risk of luminal A in postmenopausal women, and increased risk of basal-like breast cancer in pre- and postmenopausal women. The prevalence of basal-like breast cancer was highest among premenopausal African-American women, who also showed the highest prevalence of basal-like risk factors. Among younger African-American women, we estimate that up to 68% of basal-like breast cancer could be prevented by promoting breastfeeding and reducing abdominal adiposity.

Towards responsible use of cognitive-enhancing drugs by the healthy

Abstract: Society must respond to the growing demand for cognitive enhancement. That response must start by rejecting the idea that 'enhancement' is a dirty word, argue Henry Greely and colleagues.

Comparing the input, output, and validation maps for several models of land change

Abstract: This paper applies methods of multiple resolution map comparison to quantify characteristics for 13 applications of 9 different popular peer-reviewed land change models. Each modeling application simulates change of land categories in raster maps from an initial time to a subsequent time. For each modeling application, the statistical methods compare: (1) a reference map of the initial time, (2) a reference map of the subsequent time, and (3) a prediction map of the subsequent time. The three possible two-map comparisons for each application characterize: (1) the dynamics of the landscape, (2) the behavior of the model, and (3) the accuracy of the prediction. The three-map comparison for each application specifies the amount of the prediction’s accuracy that is attributable to land persistence versus land change. Results show that the amount of error is larger than the amount of correctly predicted change for 12 of the 13 applications at the resolution of the raw data. The applications are summarized and compared using two statistics: the null resolution and the figure of merit. According to the figure of merit, the more accurate applications are the ones where the amount of observed net change in the reference maps is larger. This paper facilitates communication among land change modelers, because it illustrates the range of results for a variety of models using scientifically rigorous, generally applicable, and intellectually accessible statistical techniques.

Vote Buying or Turnout Buying? Machine Politics and the Secret Ballot

Abstract: Scholars typically understand vote buying as offering particularistic benefits in exchange for vote choices. This depiction of vote buying presents a puzzle: with the secret ballot, what prevents individuals from accepting rewards and then voting as they wish? An alternative explanation, which I term “turnout buying,” suggests why parties might offer rewards even if they cannot monitor vote choices. By rewarding unmobilized supporters for showing up at the polls, parties can activate their passive constituencies. Because turnout buying targets supporters, it only requires monitoring whether individuals vote. Much of what scholars interpret as vote buying may actually be turnout buying. Reward targeting helps to distinguish between these strategies. Whereas Stokes's vote-buying model predicts that parties target moderate opposers, a model of turnout buying predicts that they target strong supporters. Although the two strategies coexist, empirical tests suggest that Argentine survey data in Stokes 2005 are more consistent with turnout buying.

Bile Acids: Chemistry, Pathochemistry, Biology, Pathobiology, and Therapeutics

Abstract: Bile acids and bile alcohols in the form of their conjugates are amphipathic end products of cholesterol metabolism with multiple physiological functions. The great variety of bile acids and bile alcohols that are present in vertebrates are tabulated. Bile salts have an enterohepatic circulation resulting from efficient vectorial transport of bile salts through the hepatocyte and the ileal enterocyte; such transport leads to the accumulation of a pool of bile salts that cycles between the liver and intestine. Bile salt anions promote lipid absorption, enhance tryptic cleavage of dietary proteins, and have antimicrobial effects. Bile salts are signaling molecules, activating nuclear receptors in the hepatocyte and ileal enterocyte, as well as an increasing number of G-protein coupled receptors. Bile acids are used therapeutically to correct deficiency states, to decrease the cholesterol saturation of bile, or to decrease the cytotoxicity of retained bile acids in cholestatic liver disease.

Coagulation monitoring: current techniques and clinical use of viscoelastic point-of-care coagulation devices

Abstract: Perioperative monitoring of blood coagulation is critical to better understand causes of hemorrhage, to guide hemostatic therapies, and to predict the risk of bleeding during the consecutive anesthetic or surgical procedures. Point-of-care (POC) coagulation monitoring devices assessing the viscoelastic properties of whole blood, i.e., thrombelastography, rotation thrombelastometry, and Sonoclot analysis, may overcome several limitations of routine coagulation tests in the perioperative setting. The advantage of these techniques is that they have the potential to measure the clotting process, starting with fibrin formation and continue through to clot retraction and fibrinolysis at the bedside, with minimal delays. Furthermore, the coagulation status of patients is assessed in whole blood, allowing the plasmatic coagulation system to interact with platelets and red cells, and thereby providing useful additional information on platelet function. Viscoelastic POC coagulation devices are increasingly being used in clinical practice, especially in the management of patients undergoing cardiac and liver surgery. Furthermore, they provide useful information in a large variety of clinical scenarios, e.g., massive hemorrhage, assessment of hypo- and hypercoagulable states, guiding pro- and anticoagulant therapies, and in diagnosing of a surgical bleeding. A surgical etiology of bleeding has to be considered when viscoelastic test results are normal. In summary, viscoelastic POC coagulation devices may help identify the cause of bleeding and guide pro- and anticoagulant therapies. To ensure optimal accuracy and performance, standardized procedures for blood sampling and handling, strict quality controls and trained personnel are required.

Mesocellular oxide foams as hemostatic compositions and methods of use

Abstract: The present invention relates to hemostatic compositions comprising a mesocellular oxide foam and, optionally, a biologically active agent such as a procoagulant, as well as devices and methods of use to promote blood clotting.

Herbal Medicine in the United States: Review of Efficacy, Safety, and Regulation: Grand Rounds at University of California, San Francisco Medical Center

Abstract: Introduction Herbal products have gained increasing popularity in the last decade, and are now used by approximately 20% of the population. Herbal products are complex mixtures of organic chemicals that may come from any raw or processed part of a plant, including leaves, stems, flowers, roots, and seeds. Under the current law, herbs are defined as dietary supplements, and manufacturers can therefore produce, sell, and market herbs without first demonstrating safety and efficacy, as is required for pharmaceutical drugs. Although herbs are often perceived as “natural” and therefore safe, many different side effects have been reported owing to active ingredients, contaminants, or interactions with drugs.

A simple, fast, and accurate method of phylogenomic inference.

Abstract: The explosive growth of genomic data provides an opportunity to make increased use of protein markers for phylogenetic inference. We have developed an automated pipeline for phylogenomic analysis (AMPHORA) that overcomes the existing bottlenecks limiting large-scale protein phylogenetic inference. We demonstrated its high throughput capabilities and high quality results by constructing a genome tree of 578 bacterial species and by assigning phylotypes to 18,607 protein markers identified in metagenomic data collected from the Sargasso Sea.

Automated Structure Solution with the PHENIX Suite

Abstract: Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution, and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template- and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix. refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

Parent-rated anxiety symptoms in children with pervasive developmental disorders: frequency and association with core autism symptoms and cognitive functioning.

Abstract: In addition to the core symptoms, children with Pervasive Developmental Disorders (PDD) often exhibit other problem behaviors such as aggression, hyperactivity, and anxiety, which can contribute to overall impairment and, therefore, become the focus of clinical attention. Limited data are available on the prevalence of anxiety in these children. We examined frequency and correlates of parent-rated anxiety symptoms in a large sample of children with PDD. The goals of this study were to examine the frequency and correlates of parent-rated anxiety symptoms in a sample of 171 medication-free children with PDD who participated in two NIH-funded medication trials. Twenty items of the Child and Adolescent Symptom Inventory (CASI) were used to measure anxiety. Forty three percent of the total sample met screening cut-off criteria for at least one anxiety disorder. Higher levels of anxiety on the 20-item CASI scale were associated with higher IQ, the presence of functional language use, and with higher levels of stereotyped behaviors. In children with higher IQ, anxiety was also associated with greater impairment in social reciprocity. Anxiety is common in PDD and warrants consideration in clinical evaluation and treatment planning. This study suggests that parent ratings could be a useful source of information about anxiety symptoms in this population. Some anxiety symptoms such as phobic and social anxiety may be closer to core symptoms of PDD. Further efforts to validate tools to ascertain anxiety are needed, as are studies to empirically test approaches to treat anxiety in PDD.

Understanding the Experience of Being Taught by Peers: The Value of Social and Cognitive Congruence.

Abstract: Background Medical schools use supplemental peer-teaching programs even though there is little research on students’ actual experiences with this form of instruction.

The Electric Field Instrument (EFI) for THEMIS

Abstract: The design, performance, and on-orbit operation of the three-axis electric field instrument (EFI) for the NASA THEMIS mission is described. The 20 radial wire boom and 10 axial stacer boom antenna systems making up the EFI sensors on the five THEMIS spacecraft, along with their supporting electronics have been deployed and are operating successfully on-orbit without any mechanical or electrical failures since early 2007. The EFI provides for waveform and spectral three-axis measurements of the ambient electric field from DC up to 8 kHz, with a single, integral broadband channel extending up to 400 kHz. Individual sensor potentials are also measured, providing for on-board and ground-based estimation of spacecraft floating potential and high-resolution plasma density measurements. Individual antenna baselines are 50- and 40-m in the spin plane, and 6.9-m along the spin axis.

Tug-of-war and the infinity Laplacian

Abstract: We consider a class of zero-sum two-player stochastic games called tug-of-war and use them to prove that every bounded real-valued Lipschitz function F on a subset Y of a length space X admits a unique absolutely minimal (AM) extension to X, i.e., a unique Lipschitz extension u : X → ℝ for which Lip U u = Lip ∂u u for all open U ⊂ X \ Y.

A conceptual model of medical student well-being: promoting resilience and preventing burnout.

Abstract: This article proposes and illustrates a conceptual model of medical student well-being. The authors reviewed the literature on medical student stress, coping, and well-beingand developed a model of medical student coping termed the “coping reservoir.” The reservoir can be replenished or drained by various aspects of medical students’ experiences. The reservoir itself has an internal structure, conceptualized as consisting of the individual’s personal traits temperament and coping style. The coping reservoir metaphor is used to highlight the dynamic nature of students’ experiences, with potential outcomes including enhanced resilience and mental health versus distress and burnout. Medical student well-being is affected by multiple stressors as well as positive aspects of medical training. Attention to individual students’ coping reservoirs can help promote well-being and minimize burnout; formal and informal offerings within medical schools can help fill the reservoir. Helping students cultivate the skills to sustain their well-being throughout their careers has important payoffs for the overall medical education enterprise, for promotion of physician resilience and personal fulfillment, and for enhancement of professionalism and patient care. This and other models of coping should be empirically validated.

Discrete-dipole approximation for periodic targets: theory and tests

Abstract: The discrete-dipole approximation (DDA) is a powerful method for calculating absorption and scattering by targets that have sizes smaller than or comparable to the wavelength of the incident radiation. The DDA can be extended to targets that are singly or doubly periodic. We generalize the scattering amplitude matrix and the 4 x 4 Mueller matrix to describe scattering by singly and doubly periodic targets and show how these matrices can be calculated using the DDA. The accuracy of DDA calculations using the open-source code DDSCAT is demonstrated by comparison with exact results for infinite cylinders and infinite slabs. A method for using the DDA solution to obtain fields within and near the target is presented, with results shown for infinite slabs.

Flavor physics of leptons and dipole moments

Abstract: This chapter of the report of the “Flavor in the era of the LHC” Workshop discusses the theoretical, phenomenological and experimental issues related to flavor phenomena in the charged lepton sector and in flavor conserving CP-violating processes. We review the current experimental limits and the main theoretical models for the flavor structure of fundamental particles. We analyze the phenomenological consequences of the available data, setting constraints on explicit models beyond the standard model, presenting benchmarks for the discovery potential of forthcoming measurements both at the LHC and at low energy, and exploring options for possible future experiments.

Aquaporins and cell migration.

Abstract: Aquaporin (AQP) water channels are expressed primarily in cell plasma membranes. In this paper, we review recent evidence that AQPs facilitate cell migration. AQP-dependent cell migration has been found in a variety of cell types in vitro and in mice in vivo. AQP1 deletion reduces endothelial cell migration, limiting tumor angiogenesis and growth. AQP4 deletion slows the migration of reactive astrocytes, impairing glial scarring after brain stab injury. AQP1-expressing tumor cells have enhanced metastatic potential and local infiltration. Impaired cell migration has also been seen in AQP1-deficient proximal tubule epithelial cells, and AQP3-deficient corneal epithelial cells, enterocytes, and skin keratinocytes. The mechanisms by which AQPs enhance cell migration are under investigation. We propose that, as a consequence of actin polymerization/depolymerization and transmembrane ionic fluxes, the cytoplasm adjacent to the leading edge of migrating cells undergoes rapid changes in osmolality. AQPs could thus facilitate osmotic water flow across the plasma membrane in cell protrusions that form during migration. AQP-dependent cell migration has potentially broad implications in angiogenesis, tumor metastasis, wound healing, glial scarring, and other events requiring rapid, directed cell movement. AQP inhibitors may thus have therapeutic potential in modulating these events, such as slowing tumor growth and spread, and reducing glial scarring after injury to allow neuronal regeneration.

Effects of Non-Farm Employment on Rural Income Inequality in Developing Countries: an Investment Perspective

Abstract: This paper makes several points based on a review of household survey evidence from Africa, Asia and Latin America. (i) In contrast to conventional wisdom, the evidence is very mixed as to the effect of non-farm employment on rural income inequality. The non-farm employment and microenterprise programmes now in vogue will not necessarily resolve rural income inequality problems and attendant social tensions nor automatically benefit the poor. (ii) Policymakers should be worried by substantial evidence of poor people's inability to overcome important entry barriers to many non-farm activities. (iii) The main determinants of unequal access to non-farm activities are the distribution of capacity to make investments in non-farm assets and the relative scarcity of low capital entry barrier activities. Therefore, it is crucial for public investments and policy to favour an increase in the access of the poor to assets that allow them to overcome non-farm employment entry barriers, (iv) It would be an error to assume that one can address asset-poverty and inequality in the non-farm sector without addressing farm-side problems and vice versa.

S/WAVES: The radio and plasma wave investigation on the STEREO Mission

Abstract: This paper introduces and describes the radio and plasma wave investigation on the STEREO Mission: STEREO/WAVES or S/WAVES. The S/WAVES instrument includes a suite of state-of-the-art experiments that provide comprehensive measurements of the three components of the fluctuating electric field from a fraction of a hertz up to 16 MHz, plus a single frequency channel near 30 MHz. The instrument has a direction finding or goniopolarimetry capability to perform 3D localization and tracking of radio emissions associated with streams of energetic electrons and shock waves associated with Coronal Mass Ejections (CMEs). The scientific objectives include: (i) remote observation and measurement of radio waves excited by energetic particles throughout the 3D heliosphere that are associated with the CMEs and with solar flare phenomena, and (ii) in-situ measurement of the properties of CMEs and interplanetary shocks, such as their electron density and temperature and the associated plasma waves near 1 Astronomical Unit (AU). Two companion papers provide details on specific aspects of the S/WAVES instrument, namely the electric antenna system (Bale et al., Space Sci. Rev., 2007) and the direction finding technique (Cecconi et al., Space Sci. Rev., 2007).