Showing papers by "University of Washington published in 2008"
31 Mar 2008
TL;DR: This whitepaper proposes OpenFlow: a way for researchers to run experimental protocols in the networks they use every day, based on an Ethernet switch, with an internal flow-table, and a standardized interface to add and remove flow entries.
Abstract: This whitepaper proposes OpenFlow: a way for researchers to run experimental protocols in the networks they use every day. OpenFlow is based on an Ethernet switch, with an internal flow-table, and a standardized interface to add and remove flow entries. Our goal is to encourage networking vendors to add OpenFlow to their switch products for deployment in college campus backbones and wiring closets. We believe that OpenFlow is a pragmatic compromise: on one hand, it allows researchers to run experiments on heterogeneous switches in a uniform way at line-rate and with high port-density; while on the other hand, vendors do not need to expose the internal workings of their switches. In addition to allowing researchers to evaluate their ideas in real-world traffic settings, OpenFlow could serve as a useful campus component in proposed large-scale testbeds like GENI. Two buildings at Stanford University will soon run OpenFlow networks, using commercial Ethernet switches and routers. We will work to encourage deployment at other schools; and We encourage you to consider deploying OpenFlow in your university network too
9,138 citations
TL;DR: It is shown here that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity and established the measurement of tumor-derived mi RNAs in serum or plasma as an important approach for the blood-based detection of human cancer.
Abstract: Improved approaches for the detection of common epithelial malignancies are urgently needed to reduce the worldwide morbidity and mortality caused by cancer. MicroRNAs (miRNAs) are small (≈22 nt) regulatory RNAs that are frequently dysregulated in cancer and have shown promise as tissue-based markers for cancer classification and prognostication. We show here that miRNAs are present in human plasma in a remarkably stable form that is protected from endogenous RNase activity. miRNAs originating from human prostate cancer xenografts enter the circulation, are readily measured in plasma, and can robustly distinguish xenografted mice from controls. This concept extends to cancer in humans, where serum levels of miR-141 (a miRNA expressed in prostate cancer) can distinguish patients with prostate cancer from healthy controls. Our results establish the measurement of tumor-derived miRNAs in serum or plasma as an important approach for the blood-based detection of human cancer.
7,296 citations
TL;DR: In this paper, the authors investigated whether intensive therapy to target normal glycated hemoglobin levels would reduce cardiovascular events in patients with type 2 diabetes who had either established cardiovascular disease or additional cardiovascular risk factors.
Abstract: BACKGROUND Epidemiologic studies have shown a relationship between glycated hemoglobin levels and cardiovascular events in patients with type 2 diabetes. We investigated whether intensive therapy to target normal glycated hemoglobin levels would reduce cardiovascular events in patients with type 2 diabetes who had either established cardiovascular disease or additional cardiovascular risk factors. METHODS In this randomized study, 10,251 patients (mean age, 62.2 years) with a median glycated hemoglobin level of 8.1% were assigned to receive intensive therapy (targeting a glycated hemoglobin level below 6.0%) or standard therapy (targeting a level from 7.0 to 7.9%). Of these patients, 38% were women, and 35% had had a previous cardiovascular event. The primary outcome was a composite of nonfatal myocardial infarction, nonfatal stroke, or death from cardiovascular causes. The finding of higher mortality in the intensive-therapy group led to a discontinuation of intensive therapy after a mean of 3.5 years of follow-up. RESULTS At 1 year, stable median glycated hemoglobin levels of 6.4% and 7.5% were achieved in the intensive-therapy group and the standard-therapy group, respectively. During follow-up, the primary outcome occurred in 352 patients in the intensive-therapy group, as compared with 371 in the standard-therapy group (hazard ratio, 0.90; 95% confidence interval [CI], 0.78 to 1.04; P=0.16). At the same time, 257 patients in the intensive-therapy group died, as compared with 203 patients in the standard-therapy group (hazard ratio, 1.22; 95% CI, 1.01 to 1.46; P=0.04). Hypoglycemia requiring assistance and weight gain of more than 10 kg were more frequent in the intensive-therapy group (P<0.001). CONCLUSIONS As compared with standard therapy, the use of intensive therapy to target normal glycated hemoglobin levels for 3.5 years increased mortality and did not significantly reduce major cardiovascular events. These findings identify a previously unrecognized harm of intensive glucose lowering in high-risk patients with type 2 diabetes. (ClinicalTrials.gov number, NCT00000620.)
6,621 citations
TL;DR: Next-generation DNA sequencing has the potential to dramatically accelerate biological and biomedical research, by enabling the comprehensive analysis of genomes, transcriptomes and interactomes to become inexpensive, routine and widespread, rather than requiring significant production-scale efforts.
Abstract: DNA sequence represents a single format onto which a broad range of biological phenomena can be projected for high-throughput data collection. Over the past three years, massively parallel DNA sequencing platforms have become widely available, reducing the cost of DNA sequencing by over two orders of magnitude, and democratizing the field by putting the sequencing capacity of a major genome center in the hands of individual investigators. These new technologies are rapidly evolving, and near-term challenges include the development of robust protocols for generating sequencing libraries, building effective new approaches to data-analysis, and often a rethinking of experimental design. Next-generation DNA sequencing has the potential to dramatically accelerate biological and biomedical research, by enabling the comprehensive analysis of genomes, transcriptomes and interactomes to become inexpensive, routine and widespread, rather than requiring significant production-scale efforts.
4,458 citations
TL;DR: An information theoretic approach is introduced that reveals community structure in weighted and directed networks of large-scale biological and social systems and reveals a directional pattern of citation from the applied fields to the basic sciences.
Abstract: To comprehend the multipartite organization of large-scale biological and social systems, we introduce an information theoretic approach that reveals community structure in weighted and directed networks. We use the probability flow of random walks on a network as a proxy for information flows in the real system and decompose the network into modules by compressing a description of the probability flow. The result is a map that both simplifies and highlights the regularities in the structure and their relationships. We illustrate the method by making a map of scientific communication as captured in the citation patterns of >6,000 journals. We discover a multicentric organization with fields that vary dramatically in size and degree of integration into the network of science. Along the backbone of the network—including physics, chemistry, molecular biology, and medicine—information flows bidirectionally, but the map reveals a directional pattern of citation from the applied fields to the basic sciences.
4,051 citations
Federal University of Bahia1, McMaster University2, University of Amsterdam3, National Institutes of Health4, Charité5, Catholic University of Cordoba6, University of Genoa7, Radboud University Nijmegen8, Transilvania University of Brașov9, Ghent University10, University of Tennessee Health Science Center11, University of Naples Federico II12, Laval University13, Universidade Federal de Minas Gerais14, University of Oslo15, University of Manchester16, Aarhus University17, Imperial College London18, Erasmus University Rotterdam19, George Washington University20, Seoul National University21, Medical University of Łódź22, Hai phong University Of Medicine and Pharmacy23, Université de Montréal24, Guangzhou Medical University25, University of South Florida26, University of California, San Diego27, University of California28, University of Chicago29, Monash University30, Teikyo University31, National and Kapodistrian University of Athens32, Nippon Medical School33, Sofia Medical University34, Leiden University35, Leiden University Medical Center36, University College London37, University of Manitoba38, University of Helsinki39, Finnish Institute of Occupational Health40, National University of Singapore41, Karolinska Institutet42, University of Minnesota43, Celal Bayar University44, University of Cape Town45, Pierre-and-Marie-Curie University46, Tunis University47, University of Ghana48, University of Wisconsin-Madison49, University of British Columbia50, Georgia Regents University51, Vilnius University52, University of Washington53, University of Dundee54, University of Poitiers55, University of Mississippi56, Federal University of São Paulo57, German Red Cross58, Jagiellonian University Medical College59, Chiba University60, American Pharmacists Association61, University of Aberdeen62, University of Nevada, Reno63, University of North Carolina at Chapel Hill64
TL;DR: The ARIA guidelines for the management of allergic rhinitis and asthma are similar in both the 1999 ARIA workshop report and the 2008 Update as discussed by the authors, but the GRADE approach is not yet available.
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.
3,769 citations
TL;DR: Climate change undermines a basic assumption that historically has facilitated management of water supplies, demands, and risks and threatens to derail efforts to conserve and manage water resources.
Abstract: Climate change undermines a basic assumption that historically has facilitated management of water supplies, demands, and risks.
3,438 citations
TL;DR: The results show that warming in the tropics, although relatively small in magnitude, is likely to have the most deleterious consequences because tropical insects are relatively sensitive to temperature change and are currently living very close to their optimal temperature, so that warming may even enhance their fitness.
Abstract: The impact of anthropogenic climate change on terrestrial organisms is often predicted to increase with latitude, in parallel with the rate of warming. Yet the biological impact of rising temperatures also depends on the physiological sensitivity of organisms to temperature change. We integrate empirical fitness curves describing the thermal tolerance of terrestrial insects from around the world with the projected geographic distribution of climate change for the next century to estimate the direct impact of warming on insect fitness across latitude. The results show that warming in the tropics, although relatively small in magnitude, is likely to have the most deleterious consequences because tropical insects are relatively sensitive to temperature change and are currently living very close to their optimal temperature. In contrast, species at higher latitudes have broader thermal tolerance and are living in climates that are currently cooler than their physiological optima, so that warming may even enhance their fitness. Available thermal tolerance data for several vertebrate taxa exhibit similar patterns, suggesting that these results are general for terrestrial ectotherms. Our analyses imply that, in the absence of ameliorating factors such as migration and adaptation, the greatest extinction risks from global warming may be in the tropics, where biological diversity is also greatest.
2,996 citations
University of Rochester1, University of Washington2, Saint Louis University3, University of Toronto4, University of Texas MD Anderson Cancer Center5, University of Pennsylvania6, Johns Hopkins University7, Yale University8, National Institutes of Health9, Pfizer10, Food and Drug Administration11, NorthShore University HealthSystem12, Merck & Co.13, Allergan14, University of Copenhagen15, Purdue Pharma16, Celgene17, University of Oxford18, Élan19, GlaxoSmithKline20, Johnson & Johnson21, Duke University22, Oregon Health & Science University23, Endo International plc24, AstraZeneca25
TL;DR: A consensus meeting was convened by the Initiative on Methods, Measurement, and Pain Assessment in Clinical Trials (IMMPACT) to provide recommendations for interpreting clinical importance of treatment outcomes in clinical trials of the efficacy and effectiveness of chronic pain treatments as discussed by the authors.
2,581 citations
Book•
01 Dec 2008
TL;DR: Markov Chains and Mixing Times as mentioned in this paper is an introduction to the modern approach to the theory of Markov chains and its application in the field of probability theory and linear algebra, where the main goal is to determine the rate of convergence of a Markov chain to the stationary distribution.
Abstract: This book is an introduction to the modern approach to the theory of Markov chains. The main goal of this approach is to determine the rate of convergence of a Markov chain to the stationary distribution as a function of the size and geometry of the state space. The authors develop the key tools for estimating convergence times, including coupling, strong stationary times, and spectral methods. Whenever possible, probabilistic methods are emphasized. The book includes many examples and provides brief introductions to some central models of statistical mechanics. Also provided are accounts of random walks on networks, including hitting and cover times, and analyses of several methods of shuffling cards. As a prerequisite, the authors assume a modest understanding of probability theory and linear algebra at an undergraduate level. ""Markov Chains and Mixing Times"" is meant to bring the excitement of this active area of research to a wide audience.
2,573 citations
University of California, Irvine1, Saint Francis University2, Wake Forest University3, National Institutes of Health4, University of Minnesota5, Northwestern University6, Columbia University7, Johns Hopkins University8, Carney Hospital9, University of Vermont10, University of California, Los Angeles11, University of Washington12
TL;DR: The coronary calcium score is a strong predictor of incident coronary heart disease and provides predictive information beyond that provided by standard risk factors in four major racial and ethnic groups in the United States.
Abstract: BACKGROUND In white populations, computed tomographic measurements of coronary-artery calcium predict coronary heart disease independently of traditional coronary risk factors. However, it is not known whether coronary-artery calcium predicts coronary heart disease in other racial or ethnic groups. METHODS We collected data on risk factors and performed scanning for coronary calcium in a population-based sample of 6722 men and women, of whom 38.6% were white, 27.6% were black, 21.9% were Hispanic, and 11.9% were Chinese. The study subjects had no clinical cardiovascular disease at entry and were followed for a median of 3.8 years. RESULTS There were 162 coronary events, of which 89 were major events (myocardial infarction or death from coronary heart disease). In comparison with participants with no coronary calcium, the adjusted risk of a coronary event was increased by a factor of 7.73 among participants with coronary calcium scores between 101 and 300 and by a factor of 9.67 among participants with scores above 300 (P<0.001 for both comparisons). Among the four racial and ethnic groups, a doubling of the calcium score increased the risk of a major coronary event by 15 to 35% and the risk of any coronary event by 18 to 39%. The areas under the receiver-operating-characteristic curves for the prediction of both major coronary events and any coronary event were higher when the calcium score was added to the standard risk factors. CONCLUSIONS The coronary calcium score is a strong predictor of incident coronary heart disease and provides predictive information beyond that provided by standard risk factors in four major racial and ethnic groups in the United States. No major differences among racial and ethnic groups in the predictive value of calcium scores were detected.
Harvard University1, University of California, Santa Cruz2, University of British Columbia3, University of Oxford4, University of Washington5, University of California, San Diego6, Oak Ridge National Laboratory7, Arizona State University8, Brown University9, Case Western Reserve University10, Boston University11, University of North Carolina at Chapel Hill12, North Carolina State University13, National Institutes of Health14
TL;DR: A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility.
Abstract: A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore. The nanopore provides a highly confined space within which single nucleic acid polymers can be analyzed at high throughput by one of a variety of means, and the perfect processivity that can be enforced in a narrow pore ensures that the native order of the nucleobases in a polynucleotide is reflected in the sequence of signals that is detected. Kilobase length polymers (single-stranded genomic DNA or RNA) or small molecules (e.g., nucleosides) can be identified and characterized without amplification or labeling, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Further research and development to overcome current challenges to nanopore identification of each successive nucleotide in a DNA strand offers the prospect of 'third generation' instruments that will sequence a diploid mammalian genome for ∼$1,000 in ∼24 h.
TL;DR: A background on applications of MNPs as MR imaging contrast agents and as carriers for drug delivery and an overview of the recent developments in this area of research are provided.
TL;DR: This paper presents structure-from-motion and image-based rendering algorithms that operate on hundreds of images downloaded as a result of keyword-based image search queries like “Notre Dame” or “Trevi Fountain,” and presents these algorithms and results as a first step towards 3D modeled sites, cities, and landscapes from Internet imagery.
Abstract: There are billions of photographs on the Internet, comprising the largest and most diverse photo collection ever assembled. How can computer vision researchers exploit this imagery? This paper explores this question from the standpoint of 3D scene modeling and visualization. We present structure-from-motion and image-based rendering algorithms that operate on hundreds of images downloaded as a result of keyword-based image search queries like "Notre Dame" or "Trevi Fountain." This approach, which we call Photo Tourism, has enabled reconstructions of numerous well-known world sites. This paper presents these algorithms and results as a first step towards 3D modeling of the world's well-photographed sites, cities, and landscapes from Internet imagery, and discusses key open problems and challenges for the research community.
TL;DR: The results show that using COPE at the forwarding layer, without modifying routing and higher layers, increases network throughput, and the gains vary from a few percent to several folds depending on the traffic pattern, congestion level, and transport protocol.
Abstract: This paper proposes COPE, a new architecture for wireless mesh networks. In addition to forwarding packets, routers mix (i.e., code) packets from different sources to increase the information content of each transmission. We show that intelligently mixing packets increases network throughput. Our design is rooted in the theory of network coding. Prior work on network coding is mainly theoretical and focuses on multicast traffic. This paper aims to bridge theory with practice; it addresses the common case of unicast traffic, dynamic and potentially bursty flows, and practical issues facing the integration of network coding in the current network stack. We evaluate our design on a 20-node wireless network, and discuss the results of the first testbed deployment of wireless network coding. The results show that using COPE at the forwarding layer, without modifying routing and higher layers, increases network throughput. The gains vary from a few percent to several folds depending on the traffic pattern, congestion level, and transport protocol.
TL;DR: NanoString nCounter as mentioned in this paper is a system for gene expression measurement with high multiplex capability and digital readout, which can detect individual mRNA transcripts without enzymatic reactions or bias.
Abstract: We describe a technology, the NanoString nCounter gene expression system, which captures and counts individual mRNA transcripts. Advantages over existing platforms include direct measurement of mRNA expression levels without enzymatic reactions or bias, sensitivity coupled with high multiplex capability, and digital readout. Experiments performed on 509 human genes yielded a replicate correlation coefficient of 0.999, a detection limit between 0.1 fM and 0.5 fM, and a linear dynamic range of over 500-fold. Comparison of the NanoString nCounter gene expression system with microarrays and TaqMan PCR demonstrated that the nCounter system is more sensitive than microarrays and similar in sensitivity to real-time PCR. Finally, a comparison of transcript levels for 21 genes across seven samples measured by the nCounter system and SYBR Green real-time PCR demonstrated similar patterns of gene expression at all transcript levels.
TL;DR: CTC are the most accurate and independent predictor of OS in CRPC, and this data led to Food and Drug Administration clearance of this assay for the evaluation of CRPC.
Abstract: Purpose: A method for enumerating circulating tumor cells (CTC) has received regulatory clearance. The primary objective of this prospective study was to establish the relationship between posttreatment CTC count and overall survival (OS) in castration-resistant prostate cancer (CRPC). Secondary objectives included determining the prognostic utility of CTC measurement before initiating therapy, and the relationship of CTC to prostate-specific antigen (PSA) changes and OS at these and other time points. Experimental Design: Blood was drawn from CRPC patients with progressive disease starting a new line of chemotherapy before treatment and monthly thereafter. Patients were stratified into predetermined Favorable or Unfavorable groups ( Results: Two hundred thirty-one of 276 enrolled patients (84%) were evaluable. Patients with Unfavorable pretreatment CTC (57%) had shorter OS (median OS, 11.5 versus 21.7 months; Cox hazard ratio, 3.3; P P P = 0.0218). Prognosis for patients with ( a ) Unfavorable baseline CTC who converted to Favorable CTC improved (6.8 to 21.3 months); ( b ) Favorable baseline CTC who converted to Unfavorable worsened (>26 to 9.3 months). Conclusions: CTC are the most accurate and independent predictor of OS in CRPC. These data led to Food and Drug Administration clearance of this assay for the evaluation of CRPC.
TL;DR: If higher SES is a causal determinant of diet quality, then the reported associations between diet quality and better health may have been confounded by unobserved indexes of social class, and some current strategies for health promotion, based on recommending high-cost foods to low-income people, may prove to be wholly ineffective.
TL;DR: In this study involving 10 geographic regions in North America, there were significant and important regional differences in out-of-hospital cardiac arrest incidence and outcome.
Abstract: Context The health and policy implications of regional variation in incidence and outcome of out-of-hospital cardiac arrest remain to be determined. Objective To evaluate whether cardiac arrest incidence and outcome differ across geographic regions. Design, Setting, and Patients Prospective observational study (the Resuscitation Outcomes Consortium) of all out-of-hospital cardiac arrests in 10 North American sites (8 US and 2 Canadian) from May 1, 2006, to April 30, 2007, followed up to hospital discharge, and including data available as of June 28, 2008. Cases (aged 0-108 years) were assessed by organized emergency medical services (EMS) personnel, did not have traumatic injury, and received attempts at external defibrillation or chest compressions or resuscitation was not attempted. Census data were used to determine rates adjusted for age and sex. Main Outcome Measures Incidence rate, mortality rate, case-fatality rate, and survival to discharge for patients assessed or treated by EMS personnel or with an initial rhythm of ventricular fibrillation. Results Among the 10 sites, the total catchment population was 21.4 million, and there were 20 520 cardiac arrests. A total of 11 898 (58.0%) had resuscitation attempted; 2729 (22.9% of treated) had initial rhythm of ventricular fibrillation or ventricular tachycardia or rhythms that were shockable by an automated external defibrillator; and 954(4.6% of total) were discharged alive. The median incidence of EMS-treated cardiac arrest across sites was 52.1 (interquartile range [IQR], 48.0-70.1) per 100 000 population; survival ranged from 3.0% to 16.3%, with a median of 8.4% (IQR, 5.4%-10.4%). Median ventricular fibrillation incidence was 12.6 (IQR, 10.6-5.2) per 100 000 population; survival ranged from 7.7% to 39.9%, with a median of 22.0% (IQR, 15.0%-24.4%), with significant differences across sites for incidence and survival (P Conclusion In this study involving 10 geographic regions in North America, there were significant and important regional differences in out-of-hospital cardiac arrest incidence and outcome.
TL;DR: The results suggest that multiple, individually rare mutations altering genes in neurodevelopmental pathways contribute to schizophrenia, and disrupted genes disproportionately from signaling networks controlling neurodevelopment, including neuregulin and glutamate pathways.
Abstract: Schizophrenia is a devastating neurodevelopmental disorder whose genetic influences remain elusive. We hypothesize that individually rare structural variants contribute to the illness. Microdeletions and microduplications >100 kilobases were identified by microarray comparative genomic hybridization of genomic DNA from 150 individuals with schizophrenia and 268 ancestry-matched controls. All variants were validated by high-resolution platforms. Novel deletions and duplications of genes were present in 5% of controls versus 15% of cases and 20% of young-onset cases, both highly significant differences. The association was independently replicated in patients with childhood-onset schizophrenia as compared with their parents. Mutations in cases disrupted genes disproportionately from signaling networks controlling neurodevelopment, including neuregulin and glutamate pathways. These results suggest that multiple, individually rare mutations altering genes in neurodevelopmental pathways contribute to schizophrenia.
University of Freiburg1, United States Department of Energy2, Lawrence Berkeley National Laboratory3, Kanazawa University4, University of Washington5, University of Leeds6, Graduate University for Advanced Studies7, National Institute for Basic Biology, Japan8, Monash University, Clayton campus9, Hokkaido University10, National Institute of Genetics11, University of Tokyo12, National Institute of Informatics13, Southern Illinois University Carbondale14, Nagoya University15, University of Regina16, Donald Danforth Plant Science Center17, University of Georgia18, Indiana University19, Ghent University20, Michigan State University21, Kenyon College22, Max Planck Society23, University of Giessen24, University of Mainz25, Arizona State University26, University of Tennessee Health Science Center27, San Diego State University28, University of Virginia29, University of Minnesota30, Rothamsted Research31, University of California, Berkeley32
TL;DR: This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments; acquisition of genes for tolerating terrestrial stresses; and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response.
Abstract: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.
TL;DR: Evidence on correlates appears sufficient to support policy changes and more recent evidence supports the conclusions of prior reviews, and new studies address some of the limitations of earlier studies.
Abstract: Introduction:The past decade has seen a dramatic increase in empirical investigation into the relations between built environment and physical activity. To create places that facilitate and encourage walking, practitioners need an understanding of the specific characteristics of the built en
TL;DR: In this paper, the authors present a single complete and straightforward method that reflects currently accepted practices and is consistent with existing production rate calibration measurements, which is intended to enable geoscientists, who wish to use cosmogenic-nuclide exposure age or erosion rate measurements in their work, to calculate exposure ages and erosion rates; compare previously published exposure ages on a common basis; and evaluate the sensitivity of their results to differences between published production rate scaling schemes.
TL;DR: In this article, the authors demonstrate that, together with pro-inflammatory cytokines, TGF-beta orchestrates T helper cells that produce IL-17 (T(H)17 cells) in a concentration-dependent manner.
Abstract: T helper cells that produce IL-17 (T(H)17 cells) promote autoimmunity in mice and have been implicated in the pathogenesis of human inflammatory diseases. At mucosal surfaces, T(H)17 cells are thought to protect the host from infection, whereas regulatory T (T(reg)) cells control immune responses and inflammation triggered by the resident microflora. Differentiation of both cell types requires transforming growth factor-beta (TGF-beta), but depends on distinct transcription factors: RORgammat (encoded by Rorc(gammat)) for T(H)17 cells and Foxp3 for T(reg) cells. How TGF-beta regulates the differentiation of T cells with opposing activities has been perplexing. Here we demonstrate that, together with pro-inflammatory cytokines, TGF-beta orchestrates T(H)17 cell differentiation in a concentration-dependent manner. At low concentrations, TGF-beta synergizes with interleukin (IL)-6 and IL-21 (refs 9-11) to promote IL-23 receptor (Il23r) expression, favouring T(H)17 cell differentiation. High concentrations of TGF-beta repress IL23r expression and favour Foxp3+ T(reg) cells. RORgammat and Foxp3 are co-expressed in naive CD4+ T cells exposed to TGF-beta and in a subset of T cells in the small intestinal lamina propria of the mouse. In vitro, TGF-beta-induced Foxp3 inhibits RORgammat function, at least in part through their interaction. Accordingly, lamina propria T cells that co-express both transcription factors produce less IL-17 (also known as IL-17a) than those that express RORgammat alone. IL-6, IL-21 and IL-23 relieve Foxp3-mediated inhibition of RORgammat, thereby promoting T(H)17 cell differentiation. Therefore, the decision of antigen-stimulated cells to differentiate into either T(H)17 or T(reg) cells depends on the cytokine-regulated balance of RORgammat and Foxp3.
TL;DR: The potential to generate virtually any differentiated cell type from embryonic stem cells (ESCs) offers the possibility to establish new models of mammalian development and to create new sources of cells for regenerative medicine, but it is essential to be able to control ESC differentiation and to direct the development of these cells along specific pathways.
TL;DR: The number of CTCs before and during treatment is an independent predictor of PFS and OS in patients with metastatic colorectal cancer and Baseline and follow-up CTC levels remained strong predictors of P FS and OS after adjustment for clinically significant factors.
Abstract: Purpose As treatment options expand for metastatic colorectal cancer (mCRC), a blood marker with a prognostic and predictive role could guide treatment. We tested the hypothesis that circulating tumor cells (CTCs) could predict clinical outcome in patients with mCRC. Patients and Methods In a prospective multicenter study, CTCs were enumerated in the peripheral blood of 430 patients with mCRC at baseline and after starting first-, second-, or third-line therapy. CTCs were measured using an immunomagnetic separation technique. Results Patients were stratified into unfavorable and favorable prognostic groups based on CTC levels of three or more or less than three CTCs/7.5 mL, respectively. Patients with unfavorable compared with favorable baseline CTCs had shorter median progression-free survival (PFS; 4.5 v 7.9 months; P = .0002) and overall survival (OS; 9.4 v 18.5 months; P < .0001). Differences persisted at 1 to 2, 3 to 5, 6 to 12, and 13 to 20 weeks after therapy. Conversion of baseline unfavorable CTC...
TL;DR: Proposed MIC values are not the final answer but offer a common starting point for future research and facilitate the use of these measures in clinical practice and the comparability of future studies.
Abstract: Study Design. Literature review, expert panel, and a workshop during the "VIII International Forum on Primary Care Research on Low Back Pain" (Amsterdam, June 2006). Objective. To develop practical guidance regarding the minimal important change (MIC) on frequently used measures of pain and functional status for low back pain. of Background Data. Empirical studies have tried to determine meaningful changes for back pain, using different methodologies. This has led to confusion about what change is clinically important for commonly used back pain outcome measures. Methods. This study covered the Visual Analogue Scale (0-100) and the Numerical Rating Scale (0-10) for pain and for function, the Roland Disability Questionnaire (0-24), the Oswestry Disability Index (0-100), and the Quebec Back Pain Disability Questionnaire (0-100). The literature was reviewed for empirical evidence. Additionally, experts and participants of the VIII International Forum on Primary Care Research on Low Back Pain were consulted to develop international consensus on clinical interpretation. Results. There was wide variation in study design and the methods used to estimate MICs, and in values found for MIC, where MIC is the improvement in clinical status of an individual patient. However, after discussion among experts and workshop participants a reasonable consensus was achieved. Proposed MIC values are: 15 for the Visual Analogue Scale, 2 for the Numerical Rating Scale, 5 for the Roland Disability Questionnaire, 10 for the Oswestry Disability Index, and 20 for the QBDQ. When the baseline score is taken into account, a 30% improvement was considered a useful threshold for identifying clinically meaningful improvement on each of these measures. Conclusion. For a range of commonly used back pain outcome measures, a 30% change from baseline may be considered clinically meaningful improvement when comparing before and after measures for individual patients. It is hoped that these proposals facilitate the use of these measures in clinical practice and the comparability of future studies. The proposed MIC values are not the final answer but offer a common starting point for future research.
TL;DR: The Sixth Data Release of the Sloan Digital Sky Survey (SDS) as discussed by the authors contains images and parameters of roughly 287 million objects over 9583 deg(2), including scans over a large range of Galactic latitudes and longitudes.
Abstract: This paper describes the Sixth Data Release of the Sloan Digital Sky Survey. With this data release, the imaging of the northern Galactic cap is now complete. The survey contains images and parameters of roughly 287 million objects over 9583 deg(2), including scans over a large range of Galactic latitudes and longitudes. The survey also includes 1.27 million spectra of stars, galaxies, quasars, and blank sky ( for sky subtraction) selected over 7425 deg2. This release includes much more stellar spectroscopy than was available in previous data releases and also includes detailed estimates of stellar temperatures, gravities, and metallicities. The results of improved photometric calibration are now available, with uncertainties of roughly 1% in g, r, i, and z, and 2% in u, substantially better than the uncertainties in previous data releases. The spectra in this data release have improved wavelength and flux calibration, especially in the extreme blue and extreme red, leading to the qualitatively better determination of stellar types and radial velocities. The spectrophotometric fluxes are now tied to point-spread function magnitudes of stars rather than fiber magnitudes. This gives more robust results in the presence of seeing variations, but also implies a change in the spectrophotometric scale, which is now brighter by roughly 0.35 mag. Systematic errors in the velocity dispersions of galaxies have been fixed, and the results of two independent codes for determining spectral classifications and red-shifts are made available. Additional spectral outputs are made available, including calibrated spectra from individual 15 minute exposures and the sky spectrum subtracted from each exposure. We also quantify a recently recognized underestimation of the brightnesses of galaxies of large angular extent due to poor sky subtraction; the bias can exceed 0.2 mag for galaxies brighter than r = 14 mag.
TL;DR: In this article, a method to constrain parton distribution function (PDF) uncertainties in LHC observables, by effectively exploiting PDF-induced correlations with benchmark standard model cross sections, is presented.
Abstract: The latest CTEQ6.6 parton distributions, obtained by global analysis of hard-scattering data in the framework of general-mass perturbative QCD, are employed to study theoretical predictions and their uncertainties for significant processes at the Fermilab Tevatron and CERN Large Hadron Collider. The previously observed increase in predicted cross sections for the standard-candle W and Z boson production processes in the general-mass scheme (compared to those in the zero-mass scheme) is further investigated and quantified. A novel method to constrain parton distribution function (PDF) uncertainties in LHC observables, by effectively exploiting PDF-induced correlations with benchmark standard model cross sections, is presented. Using this method, we show that the tt cross section can potentially serve as a standard-candle observable for the LHC processes dominated by initial-state gluon scattering. Among other benefits, precise measurements of tt cross sections would reduce PDF uncertainties in predictions for single top-quark and Higgs boson production in the standard model and minimal supersymmetric standard model.
École Normale Supérieure1, J. Craig Venter Institute2, Joint Genome Institute3, Alfred Wegener Institute for Polar and Marine Research4, University of Konstanz5, University of Wisconsin–Milwaukee6, University of Melbourne7, University of Washington8, University of Nantes9, University of Wisconsin-Madison10, Ghent University11, University of Rhode Island12, Sewanee: The University of the South13, University of Arizona14, Hebrew University of Jerusalem15, Georgia Institute of Technology16, Leibniz Institute for Neurobiology17, Stazione Zoologica Anton Dohrn18, University of British Columbia19, Stanford University20, Scottish Association for Marine Science21, University of North Carolina at Wilmington22
TL;DR: Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms, and documents the presence of hundreds of genes from bacteria, likely to provide novel possibilities for metabolite management and for perception of environmental signals.
Abstract: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one- fifth of the primary productivity on Earth(1,2). The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology(3-5). Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (similar to 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.