Showing papers by "Cornell University published in 2009"
Queen's University Belfast1, Collège de France2, English Heritage3, University of Arizona4, University of Sheffield5, University of Oxford6, University of Minnesota7, University of Hohenheim8, University of Kiel9, Lawrence Livermore National Laboratory10, University of Bergen11, ETH Zurich12, University of Waikato13, Woods Hole Oceanographic Institution14, Swiss Federal Institute for Forest, Snow and Landscape Research15, Cornell University16, University of Bristol17, University of Glasgow18, University of California, Irvine19, University of New South Wales20
TL;DR: In this paper, Heaton, AG Hogg, KA Hughen, KF Kaiser, B Kromer, SW Manning, RW Reimer, DA Richards, JR Southon, S Talamo, CSM Turney, J van der Plicht, CE Weyhenmeyer
Abstract: Additional co-authors: TJ Heaton, AG Hogg, KA Hughen, KF Kaiser, B Kromer, SW Manning, RW Reimer, DA Richards, JR Southon, S Talamo, CSM Turney, J van der Plicht, CE Weyhenmeyer
13,605 citations
National Institutes of Health1, University of Chicago2, Duke University3, Harvard University4, University of Oxford5, GlaxoSmithKline6, Johns Hopkins University7, Yale University8, deCODE genetics9, Howard Hughes Medical Institute10, Princeton University11, Washington University in St. Louis12, University of California, Berkeley13, Stanford University14, University of Michigan15, Cornell University16, University of Washington17, University of Queensland18, Vanderbilt University19, North Carolina State University20, QIMR Berghofer Medical Research Institute21
TL;DR: This paper examined potential sources of missing heritability and proposed research strategies, including and extending beyond current genome-wide association approaches, to illuminate the genetics of complex diseases and enhance its potential to enable effective disease prevention or treatment.
Abstract: Genome-wide association studies have identified hundreds of genetic variants associated with complex human diseases and traits, and have provided valuable insights into their genetic architecture. Most variants identified so far confer relatively small increments in risk, and explain only a small proportion of familial clustering, leading many to question how the remaining, 'missing' heritability can be explained. Here we examine potential sources of missing heritability and propose research strategies, including and extending beyond current genome-wide association approaches, to illuminate the genetics of complex diseases and enhance its potential to enable effective disease prevention or treatment.
7,797 citations
TL;DR: The sequence of the maize genome reveals it to be the most complex genome known to date and the correlation of methylation-poor regions with Mu transposon insertions and recombination and how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state is reported.
Abstract: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.
3,761 citations
20 Jun 2009
TL;DR: This paper introduces a method for salient region detection that outputs full resolution saliency maps with well-defined boundaries of salient objects that outperforms the five algorithms both on the ground-truth evaluation and on the segmentation task by achieving both higher precision and better recall.
Abstract: Detection of visually salient image regions is useful for applications like object segmentation, adaptive compression, and object recognition. In this paper, we introduce a method for salient region detection that outputs full resolution saliency maps with well-defined boundaries of salient objects. These boundaries are preserved by retaining substantially more frequency content from the original image than other existing techniques. Our method exploits features of color and luminance, is simple to implement, and is computationally efficient. We compare our algorithm to five state-of-the-art salient region detection methods with a frequency domain analysis, ground truth, and a salient object segmentation application. Our method outperforms the five algorithms both on the ground-truth evaluation and on the segmentation task by achieving both higher precision and better recall.
3,723 citations
TL;DR: The results lend empirical support for the validity and reliability of this set of facial expressions as determined by accurate identification of expressions and high intra-participant agreement across two testing sessions, respectively.
Abstract: A set of face stimuli called the NimStim Set of Facial Expressions is described. The goal in creating this set was to provide facial expressions that untrained individuals, characteristic of research participants, would recognize. This set is large in number, multiracial, and available to the scientific community online. The results of psychometric evaluations of these stimuli are presented. The results lend empirical support for the validity and reliability of this set of facial expressions as determined by accurate identification of expressions and high intra-participant agreement across two testing sessions, respectively.
3,040 citations
University of Georgia1, Rutgers University2, United States Department of Energy3, Stanford University4, University of California, Berkeley5, North China University of Science and Technology6, University of Zurich7, Clemson University8, University of Düsseldorf9, Cold Spring Harbor Laboratory10, Purdue University11, International Crops Research Institute for the Semi-Arid Tropics12, Texas A&M University13, Cornell University14, University of Illinois at Urbana–Champaign15, Mississippi State University16, National Institute for Biotechnology and Genetic Engineering17, United States Department of Agriculture18
TL;DR: An initial analysis of the ∼730-megabase Sorghum bicolor (L.) Moench genome is presented, placing ∼98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information.
Abstract: Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.
2,809 citations
TL;DR: Improvements in the water quality of many freshwater and most coastal marine ecosystems requires reductions in both nitrogen and phosphorus inputs.
Abstract: Improvements in the water quality of many freshwater and most coastal marine ecosystems requires reductions in both nitrogen and phosphorus inputs.
2,773 citations
TL;DR: In this article, a field is emerging that leverages the capacity to collect and analyze data at a scale that may reveal patterns of individual and group behaviors at a large scale, such as behavior patterns.
Abstract: A field is emerging that leverages the capacity to collect and analyze data at a scale that may reveal patterns of individual and group behaviors.
2,619 citations
University of Washington1, University of Paris2, Queen Mary University of London3, McMaster University4, Cornell University5, University of Pennsylvania6, University of New South Wales7, Medical University of Vienna8, Sapienza University of Rome9, Scripps Research Institute10, Boston Children's Hospital11, University of Toronto12, University of Oklahoma Health Sciences Center13
TL;DR: An International Working Group of recognized expert clinicians convened a 2-day structured meeting to define standard terminology and definitions for primary ITP and its different phases and criteria for the grading of severity, and clinically meaningful outcomes and response.
2,127 citations
TL;DR: It is shown that 44-nm-diameter nanoparticles with a gold core and dye-doped silica shell allow us to completely overcome the loss of localized surface plasmons by gain and realize a spaser, and that outcoupling of surface plasmon oscillations to photonic modes at a wavelength of 531 nm makes this system the smallest nanolaser reported to date—and to the authors' knowledge the first operating at visible wavelengths.
Abstract: Nanoplasmonics — the nanoscale manipulation of surface plasmons (fluctuations in the electron density at a metallic surface) — could revolutionize applications ranging from sensing and biomedicine to imaging and information technology. But first, we need a simple and efficient method for actively generating coherent plasmonic fields. This is in theory possible with the spaser, first proposed in 2003 as a device that generates and amplifies surface plasmons in the same way that a laser generates and amplifies photons. Now Noginov et al. present the first unambiguous experimental demonstration of spasing, using 44-nm diameter nanoparticles with a gold core and dye-doped silica shell. The system generates stimulated emission of surface plasmons in the same way as a laser generates stimulated emission of coherent photons, and has been used to implement the smallest nanolaser reported to date, and the first operating at visible wavelengths. Nanoplasmonics promises to revolutionize applications ranging from sensing and biomedicine to imaging and information technology, but its full development is hindered by the lack of devices that can generate coherent plasmonic fields. In theory, this is possible with a so-called 'spaser' — analogous to a laser — which would generate stimulated emission of surface plasmons. This is now realized experimentally, and should enable many new technological developments. One of the most rapidly growing areas of physics and nanotechnology focuses on plasmonic effects on the nanometre scale, with possible applications ranging from sensing and biomedicine to imaging and information technology1,2. However, the full development of nanoplasmonics is hindered by the lack of devices that can generate coherent plasmonic fields. It has been proposed3 that in the same way as a laser generates stimulated emission of coherent photons, a ‘spaser’ could generate stimulated emission of surface plasmons (oscillations of free electrons in metallic nanostructures) in resonating metallic nanostructures adjacent to a gain medium. But attempts to realize a spaser face the challenge of absorption loss in metal, which is particularly strong at optical frequencies. The suggestion4,5,6 to compensate loss by optical gain in localized and propagating surface plasmons has been implemented recently7,8,9,10 and even allowed the amplification of propagating surface plasmons in open paths11. Still, these experiments and the reported enhancement of the stimulated emission of dye molecules in the presence of metallic nanoparticles12,13,14 lack the feedback mechanism present in a spaser. Here we show that 44-nm-diameter nanoparticles with a gold core and dye-doped silica shell allow us to completely overcome the loss of localized surface plasmons by gain and realize a spaser. And in accord with the notion that only surface plasmon resonances are capable of squeezing optical frequency oscillations into a nanoscopic cavity to enable a true nanolaser15,16,17,18, we show that outcoupling of surface plasmon oscillations to photonic modes at a wavelength of 531 nm makes our system the smallest nanolaser reported to date—and to our knowledge the first operating at visible wavelengths. We anticipate that now it has been realized experimentally, the spaser will advance our fundamental understanding of nanoplasmonics and the development of practical applications.
1,998 citations
01 Jan 2009
TL;DR: In this article, Flannery presented a Biochar Classification and Test Methods for determining the quantity of Biochar within Soils and its effect on Nutrient Transformations and Nutrient Leaching.
Abstract: Preface Foreword by Tim Flannery 1. Biochar for Environmental Management: An Introduction 2. Physical Properties of Biochar 3. Characteristics of Biochar: Microchemical Properties 4. Characteristics of Biochar: Organo-chemical Properties 5. Biochar: Nutrient Properties and Their Enhancement 6. Characteristics of Biochar: Biological Properties 7. Developing a Biochar Classification and Test Methods 8. Biochar Production Technology 9. Biochar Systems 10. Changes of Biochar in Soil 11. Stability of Biochar in Soil 12. Biochar Application to Soil 13. Biochar and Emissions of Non-CO2 Greenhouse Gases from Soil 14. Biochar Effects on Soil Nutrient Transformations 15. Biochar Effects on Nutrient Leaching 16. Biochar and Sorption of Organic Compounds 17. Test Procedures for Determining the Quantity of Biochar within Soils 18. Biochar, Greenhouse Gas Accounting and Emissions Trading 19. Economics of Biochar Production, Utilization and Greenhouse Gas Offsets 20. Socio-economic Assessment and Implementation of Small-scale Biochar Projects 21. Taking Biochar to Market: Some Essential Concepts for Commercial Success 22. Policy to Address the Threat of Dangerous Climate Change: A Leading Role for Biochar Index
TL;DR: In this article, the authors proposed a method for automatically searching motion-tracking data captured from various physical systems, ranging from simple harmonic oscillators to chaotic double-pendula, without any prior knowledge about physics, kinematics, or geometry, the algorithm discovered Hamiltonians, Lagrangians, and other laws of geometric and momentum conservation.
Abstract: For centuries, scientists have attempted to identify and document analytical laws that underlie physical phenomena in nature. Despite the prevalence of computing power, the process of finding natural laws and their corresponding equations has resisted automation. A key challenge to finding analytic relations automatically is defining algorithmically what makes a correlation in observed data important and insightful. We propose a principle for the identification of nontriviality. We demonstrated this approach by automatically searching motion-tracking data captured from various physical systems, ranging from simple harmonic oscillators to chaotic double-pendula. Without any prior knowledge about physics, kinematics, or geometry, the algorithm discovered Hamiltonians, Lagrangians, and other laws of geometric and momentum conservation. The discovery rate accelerated as laws found for simpler systems were used to bootstrap explanations for more complex systems, gradually uncovering the "alphabet" used to describe those systems.
TL;DR: Combining the demographic model with a previously estimated distribution of selective effects among newly arising amino acid mutations accurately predicts the frequency spectrum of nonsynonymous variants across three continental populations (YRI, CHB, CEU).
Abstract: Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic variants within and between populations. For candidate models we numerically compute the expected spectrum using a diffusion approximation to the one-locus, two-allele Wright-Fisher process, involving up to three simultaneous populations. Our approach is a composite likelihood scheme, since linkage between neutral loci alters the variance but not the expectation of the frequency spectrum. We thus use bootstraps incorporating linkage to estimate uncertainties for parameters and significance values for hypothesis tests. Our method can also incorporate selection on single sites, predicting the joint distribution of selected alleles among populations experiencing a bevy of evolutionary forces, including expansions, contractions, migrations, and admixture. We model human expansion out of Africa and the settlement of the New World, using 5 Mb of noncoding DNA resequenced in 68 individuals from 4 populations (YRI, CHB, CEU, and MXL) by the Environmental Genome Project. We infer divergence between West African and Eurasian populations 140 thousand years ago (95% confidence interval: 40–270 kya). This is earlier than other genetic studies, in part because we incorporate migration. We estimate the European (CEU) and East Asian (CHB) divergence time to be 23 kya (95% c.i.: 17–43 kya), long after archeological evidence places modern humans in Europe. Finally, we estimate divergence between East Asians (CHB) and Mexican-Americans (MXL) of 22 kya (95% c.i.: 16.3–26.9 kya), and our analysis yields no evidence for subsequent migration. Furthermore, combining our demographic model with a previously estimated distribution of selective effects among newly arising amino acid mutations accurately predicts the frequency spectrum of nonsynonymous variants across three continental populations (YRI, CHB, CEU).
28 Jun 2009
TL;DR: This work develops a framework for tracking short, distinctive phrases that travel relatively intact through on-line text; developing scalable algorithms for clustering textual variants of such phrases, and identifies a broad class of memes that exhibit wide spread and rich variation on a daily basis.
Abstract: Tracking new topics, ideas, and "memes" across the Web has been an issue of considerable interest. Recent work has developed methods for tracking topic shifts over long time scales, as well as abrupt spikes in the appearance of particular named entities. However, these approaches are less well suited to the identification of content that spreads widely and then fades over time scales on the order of days - the time scale at which we perceive news and events.We develop a framework for tracking short, distinctive phrases that travel relatively intact through on-line text; developing scalable algorithms for clustering textual variants of such phrases, we identify a broad class of memes that exhibit wide spread and rich variation on a daily basis. As our principal domain of study, we show how such a meme-tracking approach can provide a coherent representation of the news cycle - the daily rhythms in the news media that have long been the subject of qualitative interpretation but have never been captured accurately enough to permit actual quantitative analysis. We tracked 1.6 million mainstream media sites and blogs over a period of three months with the total of 90 million articles and we find a set of novel and persistent temporal patterns in the news cycle. In particular, we observe a typical lag of 2.5 hours between the peaks of attention to a phrase in the news media and in blogs respectively, with divergent behavior around the overall peak and a "heartbeat"-like pattern in the handoff between news and blogs. We also develop and analyze a mathematical model for the kinds of temporal variation that the system exhibits.
TL;DR: The extent to which social disconnectedness and perceived isolation have distinct associations with physical and mental health among older adults is examined and it is concluded that health researchers need to consider social disconnectednesses and perceived isolatedness simultaneously.
Abstract: Previous research has identified a wide range of indicators of social isolation that pose health risks, including living alone, having a small social network, infrequent participation in social activities, and feelings of loneliness. However multiple forms of isolation are rarely studied together making it difficult to determine which aspects of isolation are most deleterious for health. Using population-based data from the National Social Life, Health, and Aging Project, we combine multiple indicators of social isolation into scales assessing social disconnectedness (e.g., small social network, infrequent participation in social activities) and perceived isolation (e.g., loneliness, perceived lack of social support). We examine the extent to which social disconnectedness and perceived isolation have distinct associations with physical and mental health among older adults. Results indicate that social disconnectedness and perceived isolation are independently associated with lower levels of self-rated physical health. However, the association between disconnectedness and mental health may operate through the strong relationship between perceived isolation and mental health. We conclude that health researchers need to consider social disconnectedness and perceived isolation simultaneously.
TL;DR: The authors survey 1,050 CFOs in the US, Europe, and Asia to assess whether their firms are credit constrained during the global financial crisis of 2008 and find that constrained firms planned deeper cuts in tech spending, employment, and capital spending.
Abstract: We survey 1,050 CFOs in the US, Europe, and Asia to directly assess whether their firms are credit constrained during the global financial crisis of 2008 We study whether corporate spending plans differ conditional on this survey-based measure of financial constraint Our evidence indicates that constrained firms planned deeper cuts in tech spending, employment, and capital spending Constrained firms also burned through more cash, drew more heavily on lines of credit for fear banks would restrict access in the future, and sold more assets to fund their operations We also find that the inability to borrow externally caused many firms to bypass attractive investment opportunities, with 86% of constrained US CFOs saying their investment in attractive projects was restricted during the credit crisis of 2008 More than half of the respondents said they canceled or postponed their planned investments Our results also hold in Europe and Asia, and in many cases are stronger in those economies Our analysis adds to the portfolio of approaches and knowledge about the impact of credit constraints on real firm behavior
01 Sep 2009
TL;DR: A system that can match and reconstruct 3D scenes from extremely large collections of photographs such as those found by searching for a given city on Internet photo sharing sites and is designed to scale gracefully with both the size of the problem and the amount of available computation.
Abstract: We present a system that can match and reconstruct 3D scenes from extremely large collections of photographs such as those found by searching for a given city (e.g., Rome) on Internet photo sharing sites. Our system uses a collection of novel parallel distributed matching and reconstruction algorithms, designed to maximize parallelism at each stage in the pipeline and minimize serialization bottlenecks. It is designed to scale gracefully with both the size of the problem and the amount of available computation. We have experimented with a variety of alternative algorithms at each stage of the pipeline and report on which ones work best in a parallel computing environment. Our experimental results demonstrate that it is now possible to reconstruct cities consisting of 150K images in less than a day on a cluster with 500 compute cores.
TL;DR: This paper presents an innovative use of the Internet and information technologies that better enhances the opportunity for citizens to contribute their observations to science and the conservation of bird populations.
United States Department of Agriculture1, Cornell University2, North Carolina State University3, University of Missouri4, University of Wisconsin-Madison5, Monsanto6, Beijing Normal University7, University of Illinois at Urbana–Champaign8, Purdue University9, Spanish National Research Council10, International Maize and Wheat Improvement Center11, Cold Spring Harbor Laboratory12, Kansas State University13
TL;DR: A simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis.
Abstract: Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis.
Broad Institute1, Sainsbury Laboratory2, Ohio Agricultural Research and Development Center3, Uppsala University4, Wageningen University and Research Centre5, Virginia Bioinformatics Institute6, University of California, Riverside7, University of Aberdeen8, Scottish Crop Research Institute9, University of Warwick10, Agricultural Research Service11, Royal Institute of Technology12, Cornell University13, Oregon State University14, Lafayette College15, University of Glasgow16, Harvard University17, Delaware Biotechnology Institute18, North Carolina State University19, University of Delaware20, University of Tennessee21, University of Maryland, Baltimore22, Vanderbilt University23, College of Wooster24, Bowling Green State University25, Edinburgh Cancer Research Centre26, J. Craig Venter Institute27, Tel Aviv University28, University of Wisconsin-Madison29, University of Hohenheim30, University of Dundee31
TL;DR: The sequence of the P. infestans genome is reported, which at ∼240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates and probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
Abstract: Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement(1). To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world's population(1). Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion(2). Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars(3,4). Here we report the sequence of the P. infestans genome, which at similar to 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for similar to 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.
TL;DR: The overall risk of death and other adverse outcomes after bariatric surgery was low and varied considerably according to patient characteristics, andExtreme values of body-mass index were significantly associated with an increased risk of the composite end point, whereas age, sex, race, ethnic group, and other coexisting conditions were not.
Abstract: BACKGROUND To improve decision making in the treatment of extreme obesity, the risks of bariatric surgical procedures require further characterization. METHODS We performed a prospective, multicenter, observational study of 30-day outcomes in consecutive patients undergoing bariatric surgical procedures at 10 clinical sites in the United States from 2005 through 2007. A composite end point of 30-day major adverse outcomes (including death; venous thromboembolism; percutaneous, endoscopic, or operative reintervention; and failure to be discharged from the hospital) was evaluated among patients undergoing first-time bariatric surgery. RESULTS There were 4776 patients who had a first-time bariatric procedure (mean age, 44.5 years; 21.1% men; 10.9% nonwhite; median body-mass index [the weight in kilograms divided by the square of the height in meters], 46.5). More than half had at least two coexisting conditions. A Roux-en-Y gastric bypass was performed in 3412 patients (with 87.2% of the procedures performed laparoscopically), and laparoscopic adjustable gastric banding was performed in 1198 patients; 166 patients underwent other procedures and were not included in the analysis. The 30-day rate of death among patients who underwent a Roux-en-Y gastric bypass or laparoscopic adjustable gastric banding was 0.3%; a total of 4.3% of patients had at least one major adverse outcome. A history of deep-vein thrombosis or pulmonary embolus, a diagnosis of obstructive sleep apnea, and impaired functional status were each independently associated with an increased risk of the composite end point. Extreme values of body-mass index were significantly associated with an increased risk of the composite end point, whereas age, sex, race, ethnic group, and other coexisting conditions were not. CONCLUSIONS The overall risk of death and other adverse outcomes after bariatric surgery was low and varied considerably according to patient characteristics. In helping patients make appropriate choices, short-term safety should be considered in conjunction with both the long-term effects of bariatric surgery and the risks associated with being extremely obese. (ClinicalTrials.gov number, NCT00433810.)
TL;DR: Genomic selection would substantially accelerate the breeding cycle, enhancing gains per unit time and dramatically change the role of phenotyping, which would then serve to update prediction models and no longer to select lines.
Abstract: Despite important strides in marker technologies, the use of marker-assisted selection has stagnated for the improvement of quantitative traits. Biparental mating designs for the detection of loci affecting these traits (quantitative trait loci [QTL]) impede their application, and the statistical methods used are ill-suited to the traits' polygenic nature. Genomic selection (GS) has been proposed to address these deficiencies. Genomic selection predicts the breeding values of lines in a population by analyzing their phenotypes and high-density marker scores. A key to the success of GS is that it incorporates all marker information in the prediction model, thereby avoiding biased marker effect estimates and capturing more of the variation due to small-effect QTL. In simulations, the correlation between true breeding value and the genomic estimated breeding value has reached levels of 0.85 even for polygenic low heritability traits. This level of accuracy is sufficient to consider selecting for agronomic performance using marker information alone. Such selection would substantially accelerate the breeding cycle, enhancing gains per unit time. It would dramatically change the role of phenotyping, which would then serve to update prediction models and no longer to select lines. While research to date shows the exceptional promise of GS, work remains to be done to validate it empirically and to incorporate it into breeding schemes.
TL;DR: The biology of latent tuberculosis is discussed as part of a broad range of responses that occur following infection with Mycobacterium tuberculosis, which result in the formation of physiologically distinct granulomatous lesions that provide microenvironments with differential ability to support or suppress the persistence of viable bacteria.
Abstract: Immunological tests provide evidence of latent tuberculosis in one third of the global population, which corresponds to more than two billion individuals. Latent tuberculosis is defined by the absence of clinical symptoms but carries a risk of subsequent progression to clinical disease, particularly in the context of co-infection with HIV. In this Review we discuss the biology of latent tuberculosis as part of a broad range of responses that occur following infection with Mycobacterium tuberculosis, which result in the formation of physiologically distinct granulomatous lesions that provide microenvironments with differential ability to support or suppress the persistence of viable bacteria. We then show how this model can be used to develop a rational programme to discover effective drugs for the eradication of M. tuberculosis infection.
TL;DR: Three post hoc strategies and the strategy of doing nothing within three sets of assumptions about CMV are evaluated, finding potential benefits and likely risks of using the different techniques.
Abstract: Many researchers who use same-source data face concerns about common method variance (CMV). Although post hoc statistical detection and correction techniques for CMV have been proposed, there is a lack of empirical evidence regarding their efficacy. Because of disagreement among scholars regarding the likelihood and nature of CMV in self-report data, the current study evaluates three post hoc strategies and the strategy of doing nothing within three sets of assumptions about CMV: that CMV does not exist, that CMV exists and has equal effects across constructs, and that CMV exists and has unequal effects across constructs. The implications of using each strategy within each of the three assumptions are examined empirically using 691,200 simulated data sets varying factors such as the amount of true variance and the amount and nature of CMV modeled. Based on analyses of these data, potential benefits and likely risks of using the different techniques are detailed.
TL;DR: This first comprehensive examination of built-environment measures demonstrates considerable progress over the past decade, showing diverse environmental variables available that use multiple modes of assessment.
TL;DR: Change in resilience mediated the relation between positive emotions and increased life satisfaction, suggesting that happy people become more satisfied not simply because they feel better but because they develop resources for living well.
Abstract: Happiness—a composite of life satisfaction, coping resources, and positive emotions—predicts desirable life outcomes in many domains. The broaden-and-build theory suggests that this is because positive emotions help people build lasting resources. To test this hypothesis, the authors measured emotions daily for 1 month in a sample of students (N 86) and assessed life satisfaction and trait resilience at the beginning and end of the month. Positive emotions predicted increases in both resilience and life satisfaction. Negative emotions had weak or null effects and did not interfere with the benefits of positive emotions. Positive emotions also mediated the relation between baseline and final resilience, but life satisfaction did not. This suggests that it is in-the-moment positive emotions, and not more general positive evaluations of one’s life, that form the link between happiness and desirable life outcomes. Change in resilience mediated the relation between positive emotions and increased life satisfaction, suggesting that happy people become more satisfied not simply because they feel better but because they develop resources for living well.
TL;DR: It is shown that the hypercitrullination of histones by PAD4 mediates chromatin decondensation in granulocytes/neutrophils, and citrullinations of biochemically defined avian nucleosome arrays inhibits their compaction by the linker histone H5 to form higher order chromatin structures.
Abstract: Peripheral blood neutrophils form highly decondensed chromatin structures, termed neutrophil extracellular traps (NETs), that have been implicated in innate immune response to bacterial infection. Neutrophils express high levels of peptidylarginine deiminase 4 (PAD4), which catalyzes histone citrullination. However, whether PAD4 or histone citrullination plays a role in chromatin structure in neutrophils is unclear. In this study, we show that the hypercitrullination of histones by PAD4 mediates chromatin decondensation. Histone hypercitrullination is detected on highly decondensed chromatin in HL-60 granulocytes and blood neutrophils. The inhibition of PAD4 decreases histone hypercitrullination and the formation of NET-like structures, whereas PAD4 treatment of HL-60 cells facilitates these processes. The loss of heterochromatin and multilobular nuclear structures is detected in HL-60 granulocytes after PAD4 activation. Importantly, citrullination of biochemically defined avian nucleosome arrays inhibits their compaction by the linker histone H5 to form higher order chromatin structures. Together, these results suggest that histone hypercitrullination has important functions in chromatin decondensation in granulocytes/neutrophils.
Stanford University1, Prescott College2, University of Illinois at Urbana–Champaign3, Cornell University4, National Center for Atmospheric Research5, University of Bristol6, University of São Paulo7, Columbia University8, Michigan State University9, University of Colorado Boulder10, China Agricultural University11
TL;DR: Solutions to the nutrient challenges that face global agriculture can be informed by analyses of trajectories of change within, as well as across, agricultural systems.
Abstract: Nutrient cycles link agricultural systems to their societies and surroundings; inputs of nitrogen and phosphorus in particular are essential for high crop yields, but downstream and downwind losses of these same nutrients diminish environmental quality and human well-being. Agricultural nutrient balances differ substantially with economic development, from inputs that are inadequate to maintain soil fertility in parts of many developing countries, particularly those of sub-Saharan Africa, to excessive and environmentally damaging surpluses in many developed and rapidly growing economies. National and/or regional policies contribute to patterns of nutrient use and their environmental consequences in all of these situations ( 1 ). Solutions to the nutrient challenges that face global agriculture can be informed by analyses of trajectories of change within, as well as across, agricultural systems.
TL;DR: Emerging data that support the 'seed and soil' hypothesis for metastasis are presented and the potential mechanism and temporal sequence by which changes occur in tissues distant from the primary tumour are outlined.
Abstract: The 'seed and soil' hypothesis for metastasis sets forth the concept that a conducive microenvironment, or niche, is required for disseminating tumour cells to engraft distant sites. This Opinion presents emerging data that support this concept and outlines the potential mechanism and temporal sequence by which changes occur in tissues distant from the primary tumour. To enable improvements in the prognosis of advanced malignancy, early interventions that target both the disseminating seed and the metastatic soil are likely to be required.
TL;DR: This paper explores how cutting-plane methods can provide fast training not only for classification SVMs, but also for structural SVMs and presents an extensive empirical evaluation of the method applied to binary classification, multi-class classification, HMM sequence tagging, and CFG parsing.
Abstract: Discriminative training approaches like structural SVMs have shown much promise for building highly complex and accurate models in areas like natural language processing, protein structure prediction, and information retrieval. However, current training algorithms are computationally expensive or intractable on large datasets. To overcome this bottleneck, this paper explores how cutting-plane methods can provide fast training not only for classification SVMs, but also for structural SVMs. We show that for an equivalent "1-slack" reformulation of the linear SVM training problem, our cutting-plane method has time complexity linear in the number of training examples. In particular, the number of iterations does not depend on the number of training examples, and it is linear in the desired precision and the regularization parameter. Furthermore, we present an extensive empirical evaluation of the method applied to binary classification, multi-class classification, HMM sequence tagging, and CFG parsing. The experiments show that the cutting-plane algorithm is broadly applicable and fast in practice. On large datasets, it is typically several orders of magnitude faster than conventional training methods derived from decomposition methods like SVM-light, or conventional cutting-plane methods. Implementations of our methods are available at www.joachims.org .