Showing papers by "University of Washington published in 1999"

Atherosclerosis — An Inflammatory Disease

Abstract: Atherosclerosis is an inflammatory disease. Because high plasma concentrations of cholesterol, in particular those of low-density lipoprotein (LDL) cholesterol, are one of the principal risk factors for atherosclerosis,1 the process of atherogenesis has been considered by many to consist largely of the accumulation of lipids within the artery wall; however, it is much more than that. Despite changes in lifestyle and the use of new pharmacologic approaches to lower plasma cholesterol concentrations,2,3 cardiovascular disease continues to be the principal cause of death in the United States, Europe, and much of Asia.4,5 In fact, the lesions of atherosclerosis represent . . .

Surface plasmon resonance sensors: review

Abstract: Since the first application of the surface plasmon resonance (SPR) phenomenon for sensing almost two decades ago, this method has made great strides both in terms of instrumentation development and applications. SPR sensor technology has been commercialized and SPR biosensors have become a central tool for characterizing and quantifying biomolecular interactions. This paper attempts to review the major developments in SPR technology. Main application areas are outlined and examples of applications of SPR sensor technology are presented. Future prospects of SPR sensor technology are discussed.

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

Abstract: We describe an approach for the accurate quantification and concurrent sequence identification of the individual proteins within complex mixtures. The method is based on a class of new chemical reagents termed isotope-coded affinity tags (ICATs) and tandem mass spectrometry. Using this strategy, we com- pared protein expression in the yeast Saccharomyces cerevisiae, using either ethanol or galactose as a carbon source. The measured differences in protein expression correlated with known yeast metabolic function under glucose-repressed conditions. The method is redundant if multiple cysteinyl residues are present, and the relative quantification is highly accurate because it is based on stable isotope dilution techniques. The ICAT approach should provide a widely applicable means to compare quantitatively glob- al protein expression in cells and tissues.

Molecular characterization of mitochondrial apoptosis-inducing factor

Abstract: Mitochondria play a key part in the regulation of apoptosis (cell death). Their intermembrane space contains several proteins that are liberated through the outer membrane in order to participate in the degradation phase of apoptosis. Here we report the identification and cloning of an apoptosis-inducing factor, AIF, which is sufficient to induce apoptosis of isolated nuclei. AIF is a flavoprotein of relative molecular mass 57,000 which shares homology with the bacterial oxidoreductases; it is normally confined to mitochondria but translocates to the nucleus when apoptosis is induced. Recombinant AIF causes chromatin condensation in isolated nuclei and large-scale fragmentation of DNA. It induces purified mitochondria to release the apoptogenic proteins cytochrome c and caspase-9. Microinjection of AIF into the cytoplasm of intact cells induces condensation of chromatin, dissipation of the mitochondrial transmembrane potential, and exposure of phosphatidylserine in the plasma membrane. None of these effects is prevented by the wide-ranging caspase inhibitor known as Z-VAD.fmk. Overexpression of Bcl-2, which controls the opening of mitochondrial permeability transition pores, prevents the release of AIF from the mitochondrion but does not affect its apoptogenic activity. These results indicate that AIF is a mitochondrial effector of apoptotic cell death.

Correlation between Protein and mRNA Abundance in Yeast

Abstract: The description of the state of a biological system by the quantitative measurement of the system constituents is an essential but largely unexplored area of biology. With recent technical advances including the development of differential display-PCR (21), of cDNA microarray and DNA chip technology (20, 27), and of serial analysis of gene expression (SAGE) (34, 35), it is now feasible to establish global and quantitative mRNA expression profiles of cells and tissues in species for which the sequence of all the genes is known. However, there is emerging evidence which suggests that mRNA expression patterns are necessary but are by themselves insufficient for the quantitative description of biological systems. This evidence includes discoveries of posttranscriptional mechanisms controlling the protein translation rate (15), the half-lives of specific proteins or mRNAs (33), and the intracellular location and molecular association of the protein products of expressed genes (32). Proteome analysis, defined as the analysis of the protein complement expressed by a genome (26), has been suggested as an approach to the quantitative description of the state of a biological system by the quantitative analysis of protein expression profiles (36). Proteome analysis is conceptually attractive because of its potential to determine properties of biological systems that are not apparent by DNA or mRNA sequence analysis alone. Such properties include the quantity of protein expression, the subcellular location, the state of modification, and the association with ligands, as well as the rate of change with time of such properties. In contrast to the genomes of a number of microorganisms (for a review, see reference 11) and the transcriptome of Saccharomyces cerevisiae (35), which have been entirely determined, no proteome map has been completed to date. The most common implementation of proteome analysis is the combination of two-dimensional gel electrophoresis (2DE) (isoelectric focusing-sodium dodecyl sulfate [SDS]-polyacrylamide gel electrophoresis) for the separation and quantitation of proteins with analytical methods for their identification. 2DE permits the separation, visualization, and quantitation of thousands of proteins reproducibly on a single gel (18, 24). By itself, 2DE is strictly a descriptive technique. The combination of 2DE with protein analytical techniques has added the possibility of establishing the identities of separated proteins (1, 2) and thus, in combination with quantitative mRNA analysis, of correlating quantitative protein and mRNA expression measurements of selected genes. The recent introduction of mass spectrometric protein analysis techniques has dramatically enhanced the throughput and sensitivity of protein identification to a level which now permits the large-scale analysis of proteins separated by 2DE. The techniques have reached a level of sensitivity that permits the identification of essentially any protein that is detectable in the gels by conventional protein staining (9, 29). Current protein analytical technology is based on the mass spectrometric generation of peptide fragment patterns that are idiotypic for the sequence of a protein. Protein identity is established by correlating such fragment patterns with sequence databases (10, 22, 37). Sophisticated computer software (8) has automated the entire process such that proteins are routinely identified with no human interpretation of peptide fragment patterns. In this study, we have analyzed the mRNA and protein levels of a group of genes expressed in exponentially growing cells of the yeast S. cerevisiae. Protein expression levels were quantified by metabolic labeling of the yeast proteins to a steady state, followed by 2DE and liquid scintillation counting of the selected, separated protein species. Separated proteins were identified by in-gel tryptic digestion of spots with subsequent analysis by microspray liquid chromatography-tandem mass spectrometry (LC-MS/MS) and sequence database searching. The corresponding mRNA transcript levels were calculated from SAGE frequency tables (35). This study, for the first time, explores a quantitative comparison of mRNA transcript and protein expression levels for a relatively large number of genes expressed in the same metabolic state. The resultant correlation is insufficient for prediction of protein levels from mRNA transcript levels. We have also compared the relative amounts of protein and mRNA with the respective codon bias values for the corresponding genes. This comparison indicates that codon bias by itself is insufficient to accurately predict either the mRNA or the protein expression levels of a gene. In addition, the results demonstrate that only highly expressed proteins are detectable by 2DE separation of total cell lysates and that therefore the construction of complete proteome maps with current technology will be very challenging, irrespective of the type of organism.

Dark Matter Substructure within Galactic Halos

Abstract: We use numerical simulations to examine the substructure within galactic and cluster mass halos that form within a hierarchical universe. Clusters are easily reproduced with a steep mass spectrum of thousands of substructure clumps that closely matches the observations. However, the survival of dark matter substructure also occurs on galactic scales, leading to the remarkable result that galaxy halos appear as scaled versions of galaxy clusters. The model predicts that the virialized extent of the Milky Way's halo should contain about 500 satellites with circular velocities larger than the Draco and Ursa Minor systems, i.e., bound masses 108 M☉ and tidally limited sizes 1 kpc. The substructure clumps are on orbits that take a large fraction of them through the stellar disk, leading to significant resonant and impulsive heating. Their abundance and singular density profiles have important implications for the existence of old thin disks, cold stellar streams, gravitational lensing, and indirect/direct detection experiments.

Mechanisms of phagocytosis in macrophages

Abstract: Phagocytosis of pathogens by macrophages initiates the innate immune response, which in turn orchestrates the adaptive response. In order to discriminate between infectious agents and self, macrophages have evolved a restricted number of phagocytic receptors, like the mannose receptor, that recognize conserved motifs on pathogens. Pathogens are also phagocytosed by complement receptors after relatively nonspecific opsonization with complement and by Fc receptors after specific opsonization with antibodies. All these receptors induce rearrangements in the actin cytoskeleton that lead to the internalization of the particle. However, important differences in the molecular mechanisms underlying phagocytosis by different receptors are now being appreciated. These include differences in the cytoskeletal elements that mediate ingestion, differences in vacuole maturation, and differences in inflammatory responses. Infectious agents, such as M. tuberculosis, Legionella pneumophila, and Salmonella typhimurium, enter macrophages via heterogeneous pathways and modify vacuolar maturation in a manner that favors their survival. Macrophages also play an important role in the recognition and clearance of apoptotic cells; a notable feature of this process is the absence of an inflammatory response.

Estimation of failure probabilities in the presence of competing risks: new representations of old estimators

Abstract: A topic that has received attention in both the statistical and medical literature is the estimation of the probability of failure for endpoints that are subject to competing risks. Despite this, it is not uncommon to see the complement of the Kaplan-Meier estimate used in this setting and interpreted as the probability of failure. If one desires an estimate that can be interpreted in this way, however, the cumulative incidence estimate is the appropriate tool to use in such situations. We believe the more commonly seen representations of the Kaplan-Meier estimate and the cumulative incidence estimate do not lend themselves to easy explanation and understanding of this interpretation. We present, therefore, a representation of each estimate in a manner not ordinarily seen, each representation utilizing the concept of censored observations being 'redistributed to the right.' We feel these allow a more intuitive understanding of each estimate and therefore an appreciation of why the Kaplan-Meier method is inappropriate for estimation purposes in the presence of competing risks, while the cumulative incidence estimate is appropriate.

Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit.

Abstract: In an effort to establish a suitable alternative to the widely used 18S rRNA system for molecular systematics of fungi, we examined the nuclear gene RPB2, encoding the second largest subunit of RNA polymerase II. Because RPB2 is a single-copy gene of large size with a modest rate of evolutionary change, it provides good phylogenetic resolution of Ascomycota. While the RPB2 and 18S rDNA phylogenies were highly congruent, the RPB2 phylogeny did result in much higher bootstrap support for all the deeper branches within the orders and for several branches between orders of the Ascomycota. There are several strongly supported phylogenetic conclusions. The Ascomycota is composed of three major lineages: Archiascomycetes, Saccharomycetales, and Euascomycetes. Within the Euascomycetes, plectomycetes, and pyrenomycetes are monophyletic groups, and the Pleosporales and Dothideales are distinct sister groups within the Loculoascomycetes. We confirm the placement of Neolecta within the Archiascomycetes, suggesting that fruiting body formation and forcible discharge of ascospores were characters gained early in the evolution of the Ascomycota. These findings show that a slowly evolving protein-coding gene such as RPB2 is useful for diagnosing phylogenetic relationships among fungi.

Marker tracking and HMD calibration for a video-based augmented reality conferencing system

Abstract: We describe an augmented reality conferencing system which uses the overlay of virtual images on the real world. Remote collaborators are represented on virtual monitors which can be freely positioned about a user in space. Users can collaboratively view and interact with virtual objects using a shared virtual whiteboard. This is possible through precise virtual image registration using fast and accurate computer vision techniques and head mounted display (HMD) calibration. We propose a method for tracking fiducial markers and a calibration method for optical see-through HMD based on the marker tracking.

Impact of formal continuing medical education: do conferences, workshops, rounds, and other traditional continuing education activities change physician behavior or health care outcomes?

Abstract: ContextAlthough physicians report spending a considerable amount of time in continuing medical education (CME) activities, studies have shown a sizable difference between real and ideal performance, suggesting a lack of effect of formal CME.ObjectiveTo review, collate, and interpret the effect of formal CME interventions on physician performance and health care outcomes.Data SourcesSources included searches of the complete Research and Development Resource Base in Continuing Medical Education and the Specialised Register of the Cochrane Effective Practice and Organisation of Care Group, supplemented by searches of MEDLINE from 1993 to January 1999.Study SelectionStudies were included in the analyses if they were randomized controlled trials of formal didactic and/or interactive CME interventions (conferences, courses, rounds, meetings, symposia, lectures, and other formats) in which at least 50% of the participants were practicing physicians. Fourteen of 64 studies identified met these criteria and were included in the analyses. Articles were reviewed independently by 3 of the authors.Data ExtractionDeterminations were made about the nature of the CME intervention (didactic, interactive, or mixed), its occurrence as a 1-time or sequenced event, and other information about its educational content and format. Two of 3 reviewers independently applied all inclusion/exclusion criteria. Data were then subjected to meta-analytic techniques.Data SynthesisThe 14 studies generated 17 interventions fitting our criteria. Nine generated positive changes in professional practice, and 3 of 4 interventions altered health care outcomes in 1 or more measures. In 7 studies, sufficient data were available for effect sizes to be calculated; overall, no significant effect of these educational methods was detected (standardized effect size, 0.34; 95% confidence interval [CI], −0.22 to 0.97). However, interactive and mixed educational sessions were associated with a significant effect on practice (standardized effect size, 0.67; 95% CI, 0.01-1.45).ConclusionsOur data show some evidence that interactive CME sessions that enhance participant activity and provide the opportunity to practice skills can effect change in professional practice and, on occasion, health care outcomes. Based on a small number of well-conducted trials, didactic sessions do not appear to be effective in changing physician performance.

Effects of Risedronate Treatment on Vertebral and Nonvertebral Fractures in Women With Postmenopausal Osteoporosis: A Randomized Controlled Trial

Abstract: Context Risedronate, a potent bisphosphonate, has been shown to be effective in the treatment of Paget disease of bone and other metabolic bone diseases but, to our knowledge, it has not been evaluated in the treatment of established postmenopausal osteoporosis.

Does Stakeholder Orientation Matter? The Relationship Between Stakeholder Management Models and Firm Financial Performance

Abstract: Little empirical work has been done on the effect of stakeholder management on corporate performance. In this study, we contributed to stakeholder theory development by (1) deriving two distinct stakeholder management models from extant research, (2) testing the descriptive accuracy of these models, and (3) including important variables from the strategy literature in the tested models. The results provide support for a strategic stakeholder management model but no support for an intrinsic stakeholder commitment model. Implications of these findings for management practice and future research are discussed.

Direct analysis of protein complexes using mass spectrometry

Abstract: We describe a rapid, sensitive process for comprehensively identifying proteins in macromolecular complexes that uses multidimensional liquid chromatography (LC) and tandem mass spectrometry (MS/MS) to separate and fragment peptides. The SEQUEST algorithm, relying upon translated genomic sequences, infers amino acid sequences from the fragment ions. The method was applied to the Saccharomyces cerevisiae ribosome leading to the identification of a novel protein component of the yeast and human 40S subunit. By offering the ability to identify >100 proteins in a single run, this process enables components in even the largest macromolecular complexes to be analyzed comprehensively.

Latent infection of CD4 + T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy

Abstract: Combination therapy for HIV-1 infection can reduce plasma virus to undetectable levels, indicating that prolonged treatment might eradicate the infection. However, HIV-1 can persist in a latent form in resting CD4+ T cells. We measured the decay rate of this latent reservoir in 34 treated adults whose plasma virus levels were undetectable. The mean half-life of the latent reservoir was very long (43.9 months). If the latent reservoir consists of only 1 x 10(5) cells, eradication could take as long as 60 years. Thus, latent infection of resting CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective anti-retroviral therapy.

Impact: Toward a Framework for Understanding the Ecological Effects of Invaders

Abstract: Although ecologists commonly talk about the impacts of nonindigenous species, little formal attention has been given to defining what we mean by impact, or connecting ecological theory with particular measures of impact. The resulting lack of generalizations regarding invasion impacts is more than an academic problem; we need to be able to distinguish invaders with minor effects from those with large effects in order to prioritize management efforts. This paper focuses on defining, evaluating, and comparing a variety of measures of impact drawn from empirical examples and theoretical reasoning. We begin by arguing that the total impact of an invader includes three fundamental dimensions: range, abundance, and the per-capita or per-biomass effect of the invader. Then we summarize previous approaches to measuring impact at different organizational levels, and suggest some new approaches. Reviewing mathematical models of impact, we argue that theoretical studies using community assembly models could act as a basis for better empirical studies and monitoring programs, as well as provide a clearer understanding of the relationship among different types of impact. We then discuss some of the particular challenges that come from the need to prioritize invasive species in a management or policy context. We end with recommendations about how the field of invasion biology might proceed in order to build a general framework for understanding and predicting impacts. In particular, we advocate studies designed to explore the correlations among different measures: Are the results of complex multivariate methods adequately captured by simple composite metrics such as species richness? How well are impacts on native populations correlated with impacts on ecosystem functions? Are there useful bioindicators for invasion impacts? To what extent does the impact of an invasive species depend on the system in which it is measured? Three approaches would provide new insights in this line of inquiry: (1) studies that measure impacts at multiple scales and multiple levels of organization, (2) studies that synthesize currently available data on different response variables, and (3) models designed to guide empirical work and explore generalities.

BIRDSONG AND HUMAN SPEECH: Common Themes and Mechanisms

Abstract: Human speech and birdsong have numerous parallels. Both humans and songbirds learn their complex vocalizations early in life, exhibiting a strong dependence on hearing the adults they will imitate, as well as themselves as they practice, and a waning of this dependence as they mature. Innate predispositions for perceiving and learning the correct sounds exist in both groups, although more evidence of innate descriptions of species-specific signals exists in songbirds, where numerous species of vocal learners have been compared. Humans also share with songbirds an early phase of learning that is primarily perceptual, which then serves to guide later vocal production. Both humans and songbirds have evolved a complex hierarchy of specialized forebrain areas in which motor and auditory centers interact closely, and which control the lower vocal motor areas also found in nonlearners. In both these vocal learners, however, how auditory feedback of self is processed in these brain areas is surprisingly unclear. Finally, humans and songbirds have similar critical periods for vocal learning, with a much greater ability to learn early in life. In both groups, the capacity for late vocal learning may be decreased by the act of learning itself, as well as by biological factors such as the hormones of puberty. Although some features of birdsong and speech are clearly not analogous, such as the capacity of language for meaning, abstraction, and flexible associations, there are striking similarities in how sensory experience is internalized and used to shape vocal outputs, and how learning is enhanced during a critical period of development. Similar neural mechanisms may therefore be involved.

Unconventional Methods for Fabricating and Patterning Nanostructures.

Abstract: 4.1. Nanomachining with Scanning Probes 1831 4.2. Soft Lithography 1832 4.3. Embossing with Rigid Masters 1835 4.4. Near-Field Phase-Shifting Photolithography 1835 4.5. Topographically Directed Photolithography 1837 4.6. Topographically Directed Etching 1837 4.7. Lithography with Neutral Metastable Atoms 1838 4.8. Approaches to Size Reduction 1839 5. Techniques for Making Regular or Simple Patterns 1839

Convergent Stakeholder Theory

Abstract: We describe two divergent approaches to stakeholder theory—a social science approach and a normative ethics approach—and examine their differences and similarities. Since neither approach is complete without the other, we propose a new way of theorizing about organizations: the development of normatively and instrumentally sound convergent stakeholder theory. This form of theory is explicitly and unabashedly normative, demonstrating how managers can create morally sound approaches to business and make them work.

Environmental Significance of Anthocyanins in Plant Stress Responses

Abstract: — Anthocyanins are water-soluble pigments found in all plant tissues throughout the plant kingdom. Our understanding of anthocyanin biosynthesis and its molecular control has greatly improved in the last decade. The adaptive advantages of anthocyanins, especially in non-reproductive tissues, is much less clear. Anthocyanins often appear transiently at specific developmental stages and may be induced by a number of environmental factors including visible and UVB radiation, cold temperatures and water stress. The subsequent production and localization of anthocyanins in root, stem and especially leaf tissues may allow the plant to develop resistance to a number of environmental stresses. This article reviews the environmental induction of anthocyanins and their proposed importance in ameliorating environmental stresses induced by visible and UVB radiation, drought and cold temperatures.

The Toll-like receptor 2 is recruited to macrophage phagosomes and discriminates between pathogens

Abstract: Macrophages orchestrate innate immunity by phagocytosing pathogens and coordinating inflammatory responses. Effective defence requires the host to discriminate between different pathogens. The specificity of innate immune recognition in Drosophila is mediated by the Toll family of receptors; Toll mediates anti-fungal responses, whereas 18-wheeler mediates anti-bacterial defence. A large number of Toll homologues have been identified in mammals, and Toll-like receptor 4 is critical in responses to Gram-negative bacteria. Here we show that Toll-like receptor 2 is recruited specifically to macrophage phagosomes containing yeast, and that a point mutation in the receptor abrogates inflammatory responses to yeast and Gram-positive bacteria, but not to Gram-negative bacteria. Thus, during the phagocytosis of pathogens, two classes of innate immune receptors cooperate to mediate host defence: phagocytic receptors, such as the mannose receptor, signal particle internalization, and the Toll-like receptors sample the contents of the vacuole and trigger an inflammatory response appropriate to defence against the specific organism.

Effective field theory, black holes, and the cosmological constant

Abstract: Bekenstein has proposed the bound S{le}{pi}M{sup 2}{sub P}L{sup 2} on the total entropy S in a volume L{sup 3} . This nonextensive scaling suggests that quantum field theory breaks down in large volume. To reconcile this breakdown with the success of local quantum field theory in describing observed particle phenomenology, we propose a relationship between UV and IR cutoffs such that an effective field theory should be a good description of nature. We discuss implications for the cosmological constant problem. We find a limitation on the accuracy which can be achieved by conventional effective field theory. {copyright} {ital 1999} {ital The American Physical Society}

Bronchiolitis-associated hospitalizations among US children, 1980-1996.

Abstract: ContextRespiratory syncytial virus (RSV) causes more lower respiratory tract infections, often manifested as bronchiolitis, among young children than any other pathogen. Few national estimates exist of the hospitalizations attributable to RSV, and recent advances in prophylaxis warrant an update of these estimates.ObjectivesTo describe rates of bronchiolitis-associated hospitalizations and to estimate current hospitalizations associated with RSV infection.Design and SettingDescriptive analysis of US National Hospital Discharge Survey data from 1980 through 1996.ParticipantsChildren younger than 5 years who were hospitalized in short-stay, nonfederal hospitals for bronchiolitis.Main Outcome MeasureBronchiolitis-associated hospitalization rates by age and year.ResultsDuring the 17-year study period, an estimated 1.65 million hospitalizations for bronchiolitis occurred among children younger than 5 years, accounting for 7.0 million inpatient days. Fifty-seven percent of these hospitalizations occurred among children younger than 6 months and 81% among those younger than 1 year. Among children younger than 1 year, annual bronchiolitis hospitalization rates increased 2.4-fold, from 12.9 per 1000 in 1980 to 31.2 per 1000 in 1996. During 1988-1996, infant hospitalization rates for bronchiolitis increased significantly (P for trend <.001), while hospitalization rates for lower respiratory tract diseases excluding bronchiolitis did not vary significantly (P for trend = .20). The proportion of hospitalizations for lower respiratory tract illnesses among children younger than 1 year associated with bronchiolitis increased from 22.2% in 1980 to 47.4% in 1996; among total hospitalizations, this proportion increased from 5.4% to 16.4%. Averaging bronchiolitis hospitalizations during 1994-1996 and assuming that RSV was the etiologic agent in 50% to 80% of November through April hospitalizations, an estimated 51,240 to 81,985 annual bronchiolitis hospitalizations among children younger than 1 year were related to RSV infection.ConclusionsDuring 1980-1996, rates of hospitalization of infants with bronchiolitis increased substantially, as did the proportion of total and lower respiratory tract hospitalizations associated with bronchiolitis. Annual bronchiolitis hospitalizations associated with RSV infection among infants may be greater than previous estimates for RSV bronchiolitis and pneumonia hospitalizations combined.

Twice-daily compared with once-daily thoracic radiotherapy in limited small-cell lung cancer treated concurrently with cisplatin and etoposide

Abstract: Background For small-cell lung cancer confined to one hemithorax (limited small-cell lung cancer), thoracic radiotherapy improves survival, but the best ways of integrating chemotherapy and thoracic radiotherapy remain unsettled. Twice-daily accelerated thoracic radiotherapy has potential advantages over once-daily radiotherapy. Methods We studied 417 patients with limited small-cell lung cancer. All the patients received four 21-day cycles of cisplatin plus etoposide. We randomly assigned these patients to receive a total of 45 Gy of concurrent thoracic radiotherapy, given either twice daily over a three-week period or once daily over a period of five weeks. Results Twice-daily treatment beginning with the first cycle of chemotherapy significantly improved survival as compared with concurrent once-daily radiotherapy (P=0.04 by the log-rank test). After a median follow-up of almost 8 years, the median survival was 19 months for the once-daily group and 23 months for the twice-daily group. The survival rat...

The Effective Number of Spatial Degrees of Freedom of a Time-Varying Field

Abstract: The authors systematically investigate two easily computed measures of the effective number of spatial degrees of freedom (ESDOF), or number of independently varying spatial patterns, of a time-varying field of data. The first measure is based on matching the mean and variance of the time series of the spatially integrated squared anomaly of the field to a chi-squared distribution. The second measure, which is equivalent to the first for a long time sample of normally distributed field values, is based on the partitioning of variance between the EOFs. Although these measures were proposed almost 30 years ago, this paper aims to provide a comprehensive discussion of them that may help promote their more widespread use. The authors summarize the theoretical basis of the two measures and considerations when estimating them with a limited time sample or from nonnormally distributed data. It is shown that standard statistical significance tests for the difference or correlation between two realizations of a field (e.g., a forecast and an observation) are approximately valid if the number of degrees of freedom is chosen using an appropriate combination of the two ESDOF measures. Also described is a method involving ESDOF for deciding whether two time-varying fields are significantly correlated to each other. A discussion of the parallels between ESDOF and the effective sample size of an autocorrelated time series is given, and the authors review how an appropriate measure of effective sample size can be computed for assessing the significance of correlations between two time series.

Intermittent Administration of Inhaled Tobramycin in Patients with Cystic Fibrosis

Abstract: Background and Methods We conducted two multicenter, double-blind, placebo-controlled trials of intermittent administration of inhaled tobramycin in patients with cystic fibrosis and Pseudomonas aeruginosa infection. A total of 520 patients (mean age, 21 years) were randomly assigned to receive either 300 mg of inhaled tobramycin or placebo twice daily for four weeks, followed by four weeks with no study drug. Patients received treatment or placebo in three on–off cycles for a total of 24 weeks. The end points included pulmonary function, the density of P. aeruginosa in sputum, and hospitalization. Results The patients treated with inhaled tobramycin had an average increase in forced expiratory volume in one second (FEV1) of 10 percent at week 20 as compared with week 0, whereas the patients receiving placebo had a 2 percent decline in FEV1 (P<0.001). In the tobramycin group, the density of P. aeruginosa decreased by an average of 0.8 log10 colony-forming units (CFU) per gram of expectorated sputum from w...