Showing papers by "University of Arizona published in 2014"
01 Jun 2014
TL;DR: The design and use of the Stanford CoreNLP toolkit is described, an extensible pipeline that provides core natural language analysis, and it is suggested that this follows from a simple, approachable design, straightforward interfaces, the inclusion of robust and good quality analysis components, and not requiring use of a large amount of associated baggage.
Abstract: We describe the design and use of the Stanford CoreNLP toolkit, an extensible pipeline that provides core natural language analysis. This toolkit is quite widely used, both in the research NLP community and also among commercial and government users of open source NLP technology. We suggest that this follows from a simple, approachable design, straightforward interfaces, the inclusion of robust and good quality analysis components, and not requiring use of a large amount of associated baggage.
7,070 citations
TL;DR: This review reports on the top 25 most commonly utilized nitrogen heterocycles found in pharmaceuticals, and reports detailed substitution patterns, highlight common architectural cores, and discuss unusual or rare structures.
Abstract: Nitrogen heterocycles are among the most significant structural components of pharmaceuticals. Analysis of our database of U.S. FDA approved drugs reveals that 59% of unique small-molecule drugs contain a nitrogen heterocycle. In this review we report on the top 25 most commonly utilized nitrogen heterocycles found in pharmaceuticals. The main part of our analysis is divided into seven sections: (1) three- and four-membered heterocycles, (2) five-, (3) six-, and (4) seven- and eight-membered heterocycles, as well as (5) fused, (6) bridged bicyclic, and (7) macrocyclic nitrogen heterocycles. Each section reveals the top nitrogen heterocyclic structures and their relative impact for that ring type. For the most commonly used nitrogen heterocycles, we report detailed substitution patterns, highlight common architectural cores, and discuss unusual or rare structures.
3,241 citations
Tufts Medical Center1, University of Oxford2, Pierre-and-Marie-Curie University3, Erasmus University Rotterdam4, Women's College Hospital5, American Physical Therapy Association6, University of Liège7, Royal North Shore Hospital8, University of Tokyo9, University of Arizona10, Lund University11, Paris Descartes University12, University of Southern Denmark13, Coventry Health Care14
TL;DR: These evidence-based consensus recommendations provide guidance to patients and practitioners on treatments applicable to all individuals with knee OA, as well as therapies that can be considered according to individualized patient needs and preferences.
2,467 citations
University of Évry Val d'Essonne1, Crops Research Institute2, Agriculture and Agri-Food Canada3, Fujian Agriculture and Forestry University4, J. Craig Venter Institute5, Plant Genome Mapping Laboratory6, University of Giessen7, French Alternative Energies and Atomic Energy Commission8, Institut national de la recherche agronomique9, National Research Council10, Australian Centre for Plant Functional Genomics11, University of Cologne12, Purdue University13, University of California, Berkeley14, University of British Columbia15, Fondation Jean Dausset Centre d'Etude du Polymorphisme Humain16, Huazhong Agricultural University17, Hunan Agricultural University18, Chungnam National University19, University of Arizona20, University of York21, University of Missouri22, Southern Cross University23, University of Western Australia24, Centre national de la recherche scientifique25
TL;DR: The polyploid genome of Brassica napus, which originated from a recent combination of two distinct genomes approximately 7500 years ago and gave rise to the crops of rape oilseed, is sequenced.
Abstract: Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
1,743 citations
TL;DR: All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset.
Abstract: IntAct (freely available at http://www.ebi.ac.uk/intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions. IntAct has developed a sophisticated web-based curation tool, capable of supporting both IMEx- and MIMIx-level curation. This tool is now utilized by multiple additional curation teams, all of whom annotate data directly into the IntAct database. Members of the IntAct team supply appropriate levels of training, perform quality control on entries and take responsibility for long-term data maintenance. Recently, the MINT and IntAct databases decided to merge their separate efforts to make optimal use of limited developer resources and maximize the curation output. All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset. Both IntAct and MINT are active contributors to the IMEx consortium (http://www.imexconsortium.org).
1,602 citations
Nicholas J Kassebaum1, Amelia Bertozzi-Villa1, Megan Coggeshall1, Katya Anne Shackelford1 +349 more•Institutions (179)
TL;DR: Global rates of change suggest that only 16 countries will achieve the MDG 5 target by 2015, with evidence of continued acceleration in the MMR, and MMR was highest in the oldest age groups in both 1990 and 2013.
1,383 citations
TL;DR: RNA-directed DNA methylation, the major small RNA-mediated epigenetic pathway in plants, is implicated in pathogen defence, stress responses and reproduction, as well as in interallelic and intercellular communication.
Abstract: RNA-directed DNA methylation (RdDM) is the major small RNA-mediated epigenetic pathway in plants. RdDM requires a specialized transcriptional machinery that comprises two plant-specific RNA polymerases - Pol IV and Pol V - and a growing number of accessory proteins, the functions of which in the RdDM mechanism are only partially understood. Recent work has revealed variations in the canonical RdDM pathway and identified factors that recruit Pol IV and Pol V to specific target sequences. RdDM, which transcriptionally represses a subset of transposons and genes, is implicated in pathogen defence, stress responses and reproduction, as well as in interallelic and intercellular communication.
1,171 citations
Broad Institute1, Harvard University2, University of Tübingen3, Max Planck Society4, University of Mainz5, University of Washington6, University of California, Berkeley7, Massachusetts Institute of Technology8, Stockholm University9, University of Adelaide10, The Heritage Foundation11, National Museum of Natural History12, University of Edinburgh13, Sultan Qaboos University14, University of Costa Rica15, University of Antioquia16, Rambam Health Care Campus17, University of Pécs18, Al Akhawayn University19, Catholic University of the Sacred Heart20, University of Oxford21, Belgorod State University22, University of Toronto23, University of Buenos Aires24, University of Bern25, Russian Academy of Sciences26, Paul Sabatier University27, North-Eastern Federal University28, University of Chicago29, University of Arizona30, Stony Brook University31, University of Bergen32, Illumina33, Sofia Medical University34, Bashkir State University35, University of Cambridge36, Vilnius University37, Estonian Biocentre38, University of Strasbourg39, University College London40, Amgen41, Gladstone Institutes42, University of Tartu43, University of Oulu44, Muhimbili University of Health and Allied Sciences45, University of Palermo46, University of Tarapacá47, University of Chile48, Academy of Sciences of Uzbekistan49, Armenian National Academy of Sciences50, University of North Texas51, University of Santiago de Compostela52, University of Kharkiv53, Higher University of San Andrés54, Novosibirsk State University55, Leidos56, Lebanese American University57, University of Split58, University of Pennsylvania59, Banaras Hindu University60, Centre for Cellular and Molecular Biology61, Estonian Academy of Sciences62, Pompeu Fabra University63, Howard Hughes Medical Institute64
TL;DR: It is shown that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians; and early European farmers, who were mainly of Near Eastern origin but also harboured west Europeanhunter-gatherer related ancestry.
Abstract: We sequenced the genomes of a ∼7,000-year-old farmer from Germany and eight ∼8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations' deep relationships and show that early European farmers had ∼44% ancestry from a 'basal Eurasian' population that split before the diversification of other non-African lineages.
1,077 citations
TL;DR: The addition of bevacizumab to combination chemotherapy in patients with recurrent, persistent, or metastatic cervical cancer was associated with an improvement of 3.7 months in median overall survival.
Abstract: Background Vascular endothelial growth factor (VEGF) promotes angiogenesis, a mediator of disease progression in cervical cancer. Bevacizumab, a humanized anti-VEGF monoclonal antibody, has single-agent activity in previously treated, recurrent disease. Most patients in whom recurrent cervical cancer develops have previously received cisplatin with radiation therapy, which reduces the effectiveness of cisplatin at the time of recurrence. We evaluated the effectiveness of bevacizumab and nonplatinum combination chemotherapy in patients with recurrent, persistent, or metastatic cervical cancer. Methods Using a 2-by-2 factorial design, we randomly assigned 452 patients to chemotherapy with or without bevacizumab at a dose of 15 mg per kilogram of body weight. Chemotherapy consisted of cisplatin at a dose of 50 mg per square meter of body-surface area, plus paclitaxel at a dose of 135 or 175 mg per square meter or topote can at a dose of 0.75 mg per square meter on days 1 to 3, plus paclitaxel at a dose of 175 mg per square meter on day 1. Cycles were repeated every 21 days until disease progression, the development of unacceptable toxic effects, or a complete response was documented. The primary end point was overall survival; a reduction of 30% in the hazard ratio for death was considered clinically important. Results Groups were well balanced with respect to age, histologic findings, performance status, previous use or nonuse of a radiosensitizing platinum agent, and disease status. Topotecan–paclitaxel was not superior to cisplatin–paclitaxel (hazard ratio for death, 1.20). With the data for the two chemotherapy regimens combined, the addition of bevaciz umab to chemotherapy was associated with increased overall survival (17.0 months vs. 13.3 months; hazard ratio for death, 0.71; 98% confidence interval, 0.54 to 0.95; P = 0.004 in a one-sided test) and higher response rates (48% vs. 36%, P = 0.008). Bevacizumab, as compared with chemotherapy alone, was associated with an increased incidence of hypertension of grade 2 or higher (25% vs. 2%), thromboembolic events of grade 3 or higher (8% vs. 1%), and gastrointestinal fistulas of grade 3 or higher (3% vs. 0%). Conclusions The addition of bevacizumab to combination chemotherapy in patients with recurrent, persistent, or metastatic cervical cancer was associated with an improvement of 3.7 months in median overall survival. (Funded by the National Cancer Institute; GOG 240 ClinicalTrials.gov number, NCT00803062.)
1,029 citations
Northwestern University1, University of Texas at Austin2, University of Alberta3, University of Arizona4, University of Georgia5, University of Florida6, American Museum of Natural History7, Eastern Kentucky University8, Pennsylvania State University9, Harvard University10, University of Cologne11, Duke University12, University of British Columbia13, Spanish National Research Council14, New York Botanical Garden15, Ludwig Maximilian University of Munich16, Université de Montréal17, Centre national de la recherche scientifique18, Chinese Academy of Sciences19, University of Michigan20, Donald Danforth Plant Science Center21
TL;DR: Strong and robust support is found for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
Abstract: Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
1,026 citations
United States Department of Energy1, North Dakota State University2, United States Department of Agriculture3, University of Georgia4, Institut national de la recherche agronomique5, Tennessee State University6, Colorado State University7, University of California, Davis8, Michigan State University9, University of Arizona10, University of Paris-Sud11, University of Nebraska–Lincoln12
TL;DR: 2 independent domestications from genetic pools that diverged before human colonization are confirmed and a set of genes linked with increased leaf and seed size are identified and combined with quantitative trait locus data from Mesoamerican cultivars.
Abstract: Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.
TL;DR: The implementation of this classification system is intended to permit more meaningful analysis of outcomes for various forms of therapy in this challenging, but heterogeneous population.
Yale University1, Goddard Space Flight Center2, Space Telescope Science Institute3, Leiden University4, Max Planck Society5, University of Arizona6, University of California, Berkeley7, University of Wisconsin-Madison8, University of California, Santa Cruz9, Tufts University10, Yonsei University11, Carnegie Institution for Science12, Open University13
TL;DR: In this paper, a photometric analysis of the CANDELS and 3D-HST HST imaging and the ancillary imaging data at wavelengths 0.3-8 μm is presented, where objects were selected in the WFC3 near-IR bands and their spectral energy distributions were determined by carefully taking the effects of the point-spread function in each observation into account.
Abstract: The 3D-HST and CANDELS programs have provided WFC3 and ACS spectroscopy and photometry over ≈900 arcmin2 in five fields: AEGIS, COSMOS, GOODS-North, GOODS-South, and the UKIDSS UDS field. All these fields have a wealth of publicly available imaging data sets in addition to the Hubble Space Telescope (HST) data, which makes it possible to construct the spectral energy distributions (SEDs) of objects over a wide wavelength range. In this paper we describe a photometric analysis of the CANDELS and 3D-HST HST imaging and the ancillary imaging data at wavelengths 0.3-8 μm. Objects were selected in the WFC3 near-IR bands, and their SEDs were determined by carefully taking the effects of the point-spread function in each observation into account. A total of 147 distinct imaging data sets were used in the analysis. The photometry is made available in the form of six catalogs: one for each field, as well as a master catalog containing all objects in the entire survey. We also provide derived data products: photometric redshifts, determined with the EAZY code, and stellar population parameters determined with the FAST code. We make all the imaging data that were used in the analysis available, including our reductions of the WFC3 imaging in all five fields. 3D-HST is a spectroscopic survey with the WFC3 and ACS grisms, and the photometric catalogs presented here constitute a necessary first step in the analysis of these grism data. All the data presented in this paper are available through the 3D-HST Web site (http://3dhst.research.yale.edu).
Harvard University1, Ben-Gurion University of the Negev2, University of Illinois at Urbana–Champaign3, University of California, Davis4, University of Pennsylvania5, Department of Environment and Primary Industries6, United States Department of Agriculture7, University of Arizona8, The Nature Conservancy9, University of Melbourne10
TL;DR: It is reported that C3 grains and legumes have lower concentrations of zinc and iron when grown under field conditions at the elevated atmospheric CO2 concentration predicted for the middle of this century.
Abstract: experiments contribute more than tenfold more data regarding both the zinc and iron content of the edible portions of crops grown under FACE conditions than is currently available in the literature. Consistent with earlier meta-analyses of other aspects of plant function under FACE conditions 14,15 , we considered the response comparisons observed from different species, cultivars and stress treatments and from different years to be independent. The natural logarithm of the mean response ratio (r5 response in elevated [CO2]/response in ambient [CO2]) was used as the metric for all analyses. Meta-analysis was used to estimate the overall effect of elevated [CO2] on the concentration of each nutrient in a particular crop and to determine the significance of this effect (see Methods). We found that elevated [CO2] was associated with significant decreases in the concentrations of zinc and iron in all C3 grasses and legumes (Fig. 1 and Extended Data Table 1). For example, wheat grains grown at elevated [CO2] had 9.3% lower zinc (95% confidence interval (CI)212.7% to25.9%) and 5.1% lower iron (95% CI26.5% to23.7%) than those grown at ambient [CO2]. We also found that elevated [CO2] was associated with lower protein content in C3 grasses, with a 6.3% decrease (95% CI27.5% to25.2%) in wheat grains and a 7.8% decrease (95% CI 28.9% to26.8%) in rice grains. Elevated [CO2] was associated with a small decrease in protein in field peas, and there was no significant
TL;DR: The evolution and structural diversity of sulfur and the popular integration of fluorine into drugs introduced over the past 50 years are evaluated and promoted to promote innovative insights into drug development.
Abstract: Among carbon, hydrogen, oxygen, and nitrogen, sulfur and fluorine are both leading constituents of the pharmaceuticals that comprise our medicinal history. In efforts to stimulate the minds of both the general public and expert scientist, statistics were collected from the trends associated with therapeutics spanning 12 disease categories (a total of 1969 drugs) from our new graphical montage compilation: disease focused pharmaceuticals posters. Each poster is a vibrant display of a collection of pharmaceuticals (including structural image, Food and Drug Administration (FDA) approval date, international nonproprietary name (INN), initial market name, and a color-coded subclass of function) organized chronologically and classified according to an association with a particular clinical indication. Specifically, the evolution and structural diversity of sulfur and the popular integration of fluorine into drugs introduced over the past 50 years are evaluated. The presented qualitative conclusions in this arti...
Christopher J L Murray1, Katrina F Ortblad1, Caterina Guinovart1, Stephen S Lim1 +367 more•Institutions (179)
TL;DR: The Global Burden of Disease 2013 study provides a consistent and comprehensive approach to disease estimation for between 1990 and 2013, and an opportunity to assess whether accelerated progress has occured since the Millennium Declaration.
Seoul National University1, Soongsil University2, Agricultural Research Organization, Volcani Center3, Chonnam National University4, Korea Research Institute of Bioscience and Biotechnology5, Myongji University6, New Mexico State University7, University of Arizona8, Rural Development Administration9, University of California, Davis10, Yonsei University11, Andong National University12, Cornell University13, United States Department of Agriculture14
TL;DR: The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements.
Abstract: Doil Choi and colleagues report the genome sequence of the hot pepper, Capsicum annuum, as well as the resequencing of two cultivated peppers and a wild species, Capsicum chinense. Comparative genomic analysis across Solanaceae provides insights into genome expansion, pungency, ripening and disease resistance in hot peppers.
Lawrence Livermore National Laboratory1, Stanford University2, University of California, Berkeley3, University of Toronto4, National Research Council5, Space Telescope Science Institute6, University of Arizona7, Princeton University8, University of California, Los Angeles9, Arizona State University10, University of California, Santa Cruz11, Université de Montréal12, Search for extraterrestrial intelligence13, Ames Research Center14, American Museum of Natural History15, Cornell University16, University of Georgia17, California Institute of Technology18, Johns Hopkins University19
TL;DR: Observations ofBeta Pictoris clearly detect the planet, Beta Pictoris b, in a single 60-s exposure with minimal postprocessing, and fitting the Keplerian orbit of Beta Pic b using the new position together with previous astrometry gives a factor of 3 improvement in most parameters over previous solutions.
Abstract: The Gemini Planet Imager is a dedicated facility for directly imaging and spectroscopically characterizing extrasolar planets. It combines a very high-order adaptive optics system, a diffraction-suppressing coronagraph, and an integral field spectrograph with low spectral resolution but high spatial resolution. Every aspect of the Gemini Planet Imager has been tuned for maximum sensitivity to faint planets near bright stars. During first-light observations, we achieved an estimated H band Strehl ratio of 0.89 and a 5-σ contrast of 10(6) at 0.75 arcseconds and 10(5) at 0.35 arcseconds. Observations of Beta Pictoris clearly detect the planet, Beta Pictoris b, in a single 60-s exposure with minimal postprocessing. Beta Pictoris b is observed at a separation of 434 ± 6 milliarcseconds (mas) and position angle 211.8 ± 0.5°. Fitting the Keplerian orbit of Beta Pic b using the new position together with previous astrometry gives a factor of 3 improvement in most parameters over previous solutions. The planet orbits at a semimajor axis of [Formula: see text] near the 3:2 resonance with the previously known 6-AU asteroidal belt and is aligned with the inner warped disk. The observations give a 4% probability of a transit of the planet in late 2017.
TL;DR: Advanced materials and devices are reported that enable high-efficiency mechanical-to-electrical energy conversion from the natural contractile and relaxation motions of the heart, lung, and diaphragm, demonstrated in several different animal models, each of which has organs with sizes that approach human scales.
Abstract: Here, we report advanced materials and devices that enable high-efficiency mechanical-to-electrical energy conversion from the natural contractile and relaxation motions of the heart, lung, and diaphragm, demonstrated in several different animal models, each of which has organs with sizes that approach human scales. A cointegrated collection of such energy-harvesting elements with rectifiers and microbatteries provides an entire flexible system, capable of viable integration with the beating heart via medical sutures and operation with efficiencies of ∼2%. Additional experiments, computational models, and results in multilayer configurations capture the key behaviors, illuminate essential design aspects, and offer sufficient power outputs for operation of pacemakers, with or without battery assist.
Columbia University1, University of California, San Diego2, Michigan State University3, Stanford University4, Georgia Institute of Technology5, Southern Methodist University6, Florida State University7, Nvidia8, University of Colorado Boulder9, University of Edinburgh10, Oak Ridge National Laboratory11, University of California, Santa Cruz12, University of California, Berkeley13, University of Arizona14, Hokkaido University15, ETH Zurich16, American Museum of Natural History17, Princeton University18
TL;DR: Enzo as discussed by the authors uses block-structured adaptive mesh refinement to provide high spatial and temporal resolution for modeling astrophysical fluid flows, which can be run in one, two, and three dimensions, and supports a wide variety of physics, including hydrodynamics, ideal and non-ideal magnetohydrodynamic, N-body dynamics, primordial gas chemistry, optically thin radiative cooling of primordial and metal-enriched plasmas, and models for star formation and feedback in a cosmological context.
Abstract: This paper describes the open-source code Enzo, which uses block-structured adaptive mesh refinement to provide high spatial and temporal resolution for modeling astrophysical fluid flows. The code is Cartesian, can be run in one, two, and three dimensions, and supports a wide variety of physics including hydrodynamics, ideal and non-ideal magnetohydrodynamics, N-body dynamics (and, more broadly, self-gravity of fluids and particles), primordial gas chemistry, optically thin radiative cooling of primordial and metal-enriched plasmas (as well as some optically-thick cooling models), radiation transport, cosmological expansion, and models for star formation and feedback in a cosmological context. In addition to explaining the algorithms implemented, we present solutions for a wide range of test problems, demonstrate the code's parallel performance, and discuss the Enzo collaboration's code development methodology.
TL;DR: The colon mucus in animal models that spontaneously develop colitis and in patients with active UC allows bacteria to penetrate and reach the epithelium, and this suggests a novel model of UC pathophysiology.
Abstract: Objective The inner mucus layer in mouse colon normally separates bacteria from the epithelium. Do humans have a similar inner mucus layer and are defects in this mucus layer a common denominator for spontaneous colitis in mice models and ulcerative colitis (UC)? Methods and results The colon mucus layer from mice deficient in Muc2 mucin, Core 1 O -glycans, Tlr5, interleukin 10 (IL-10) and Slc9a3 (Nhe3) together with that from dextran sodium sulfate-treated mice was immunostained for Muc2, and bacterial localisation in the mucus was analysed. All murine colitis models revealed bacteria in contact with the epithelium. Additional analysis of the less inflamed IL-10 −/− mice revealed a thicker mucus layer than wild-type, but the properties were different, as the inner mucus layer could be penetrated both by bacteria in vivo and by fluorescent beads the size of bacteria ex vivo. Clear separation between bacteria or fluorescent beads and the epithelium mediated by the inner mucus layer was also evident in normal human sigmoid colon biopsy samples. In contrast, mucus on colon biopsy specimens from patients with UC with acute inflammation was highly penetrable. Most patients with UC in remission had an impenetrable mucus layer similar to that of controls. Conclusions Normal human sigmoid colon has an inner mucus layer that is impenetrable to bacteria. The colon mucus in animal models that spontaneously develop colitis and in patients with active UC allows bacteria to penetrate and reach the epithelium. Thus colon mucus properties can be modulated, and this suggests a novel model of UC pathophysiology.
Haidong Wang1, Chelsea A. Liddell1, Matthew M Coates1, Meghan D. Mooney1 +228 more•Institutions (123)
TL;DR: Decreases since 2000 in under-5 mortality rates are accelerating in many developing countries, especially in sub-Saharan Africa, and rising income per person and maternal education and changes in secular trends led to 4·2 million fewer deaths.
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TL;DR: In this paper, the authors propose a test for disparate impact based on analyzing the information leakage of the protected class from the other data attributes, and present empirical evidence supporting the effectiveness of their test and their approach for masking bias and preserving relevant information in the data.
Abstract: What does it mean for an algorithm to be biased? In U.S. law, unintentional bias is encoded via disparate impact, which occurs when a selection process has widely different outcomes for different groups, even as it appears to be neutral. This legal determination hinges on a definition of a protected class (ethnicity, gender, religious practice) and an explicit description of the process.
When the process is implemented using computers, determining disparate impact (and hence bias) is harder. It might not be possible to disclose the process. In addition, even if the process is open, it might be hard to elucidate in a legal setting how the algorithm makes its decisions. Instead of requiring access to the algorithm, we propose making inferences based on the data the algorithm uses.
We make four contributions to this problem. First, we link the legal notion of disparate impact to a measure of classification accuracy that while known, has received relatively little attention. Second, we propose a test for disparate impact based on analyzing the information leakage of the protected class from the other data attributes. Third, we describe methods by which data might be made unbiased. Finally, we present empirical evidence supporting the effectiveness of our test for disparate impact and our approach for both masking bias and preserving relevant information in the data. Interestingly, our approach resembles some actual selection practices that have recently received legal scrutiny.
University of Pretoria1, Universidade Católica de Brasília2, Empresa Brasileira de Pesquisa Agropecuária3, United States Department of Energy4, Oak Ridge National Laboratory5, Joint Genome Institute6, Ghent University7, Institut national de la recherche agronomique8, University of Toulouse9, University of British Columbia10, University of Münster11, University of Düsseldorf12, Oregon State University13, University of São Paulo14, Federal University of Rio de Janeiro15, Australian National University16, Indian Institute of Chemical Technology17, University of Arizona18, Universidade Federal de Viçosa19, Universidade Federal do Rio Grande do Sul20, Department of Environment and Primary Industries21, University of Melbourne22, University of Tasmania23, University of the Sunshine Coast24, University of Brasília25
TL;DR: Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes, which shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils.
Abstract: Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.
University of Oxford1, Australian National University2, Queen's University Belfast3, University of Maryland, College Park4, University of the Basque Country5, Autonomous University of Madrid6, University of Siena7, Centre national de la recherche scientifique8, University of Tübingen9, University of La Laguna10, University of Cantabria11, University of Trento12, Royal Belgian Institute of Natural Sciences13, University of Massachusetts Amherst14, University of Arizona15, National University of Distance Education16, Weizmann Institute of Science17, Trent University18, University of Genoa19, University of Ferrara20, University of Oviedo21, Université de Montréal22, University College Dublin23, Natural History Museum24
TL;DR: Improved accelerator mass spectrometry 14C techniques are applied to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, showing that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.
Abstract: The timing of Neanderthal disappearance and the extent to which they overlapped with the earliest incoming anatomically modern humans (AMHs) in Eurasia are key questions in palaeoanthropology. Determining the spatiotemporal relationship between the two populations is crucial if we are to understand the processes, timing and reasons leading to the disappearance of Neanderthals and the likelihood of cultural and genetic exchange. Serious technical challenges, however, have hindered reliable dating of the period, as the radiocarbon method reaches its limit at ∼50,000 years ago. Here we apply improved accelerator mass spectrometry (14)C techniques to construct robust chronologies from 40 key Mousterian and Neanderthal archaeological sites, ranging from Russia to Spain. Bayesian age modelling was used to generate probability distribution functions to determine the latest appearance date. We show that the Mousterian ended by 41,030-39,260 calibrated years bp (at 95.4% probability) across Europe. We also demonstrate that succeeding 'transitional' archaeological industries, one of which has been linked with Neanderthals (Châtelperronian), end at a similar time. Our data indicate that the disappearance of Neanderthals occurred at different times in different regions. Comparing the data with results obtained from the earliest dated AMH sites in Europe, associated with the Uluzzian technocomplex, allows us to quantify the temporal overlap between the two human groups. The results reveal a significant overlap of 2,600-5,400 years (at 95.4% probability). This has important implications for models seeking to explain the cultural, technological and biological elements involved in the replacement of Neanderthals by AMHs. A mosaic of populations in Europe during the Middle to Upper Palaeolithic transition suggests that there was ample time for the transmission of cultural and symbolic behaviours, as well as possible genetic exchanges, between the two groups.
TL;DR: The authors examined a 3-week census of articles and comments posted to a local newspaper's website and found that incivility occurs frequently and is associated with key contextual factors, such as the topic of the article and the sources quoted within the article.
Abstract: Incivility in public discussions has received increasing attention from academic and popular commentators in recent years. In an effort to better understand the nature and determinants of such incivility, this study examined a 3-week census of articles and comments posted to a local newspaper’s website—totaling more than 300 articles and 6,400 comments. The results of the content analysis show that incivility occurs frequently and is associated with key contextual factors, such as the topic of the article and the sources quoted within the article. We also find that, contrary to popular perceptions, frequent commenters are more civil than are infrequent commenters, and uncivil commenters are no less likely than civil commenters to use evidence in support of their claims.
Book•
30 Jan 2014TL;DR: This book discusses the service-dominant mindset, the nature, scope, and integration of resources, and the nature and scope of resources in service ecosystems.
Abstract: In 2004, Robert F. Lusch and Stephen L. Vargo published their groundbreaking article on the evolution of marketing theory and practice toward 'service-dominant (S-D) logic', describing the shift from a product-centred view of markets to a service-led model. Now, in this keenly anticipated book, the authors present a thorough primer on the principles and applications of S-D logic. They describe a clear alternative to the dominant worldview of the heavily planned, production-oriented, profit-maximizing firm, presenting a coherent, organizing framework based on ten foundational premises. The foundational premises of S-D logic have much wider implications beyond marketing for the future of the firm, transcending different industries and contexts, and will provide readers with a deeper sense of why the exchange of service is the fundamental basis of all social and economic exchange. This accessible book will appeal to students, as well as to researchers and practitioners.
TL;DR: In this paper, the authors analyzed the physical conditions of the cool, photoionized (T ∼ 10 4 K) circumgalactic medium (CGM) using the COS-Halos suite of gas column density measurements for 44 gaseous halos within 160 kpc of L ∼ L ∗ galaxies at z ∼ 0.2.
Abstract: We analyze the physical conditions of the cool, photoionized (T ∼ 10 4 K) circumgalactic medium (CGM) using the COS-Halos suite of gas column density measurements for 44 gaseous halos within 160 kpc of L ∼ L ∗ galaxies at z ∼ 0.2. These data are well described by simple photoionization models, with the gas highly ionized (nHii/nH 99%) by the extragalactic ultraviolet background. Scaling by estimates for the virial radius, Rvir, we show that the ionization state (tracked by the dimensionless ionization parameter, U) increases with distance from the host galaxy. The ionization parameters imply a decreasing volume density profile nH = (10 −4.2±0.25 )(R/Rvir) −0.8±0.3 . Our derived gas volume densities are several orders of magnitude lower than predictions from standard two-phase models with a cool medium in pressure equilibrium with a hot, coronal medium expected in virialized halos at this mass scale. Applying the ionization corrections to the Hi column densities, we estimate a lower limit to the cool gas mass M cool CGM > 6.5 × 10
University of Tokyo1, University of Edinburgh2, Ludwig Maximilian University of Munich3, University of California, Los Angeles4, University of Greifswald5, University of Würzburg6, University of Marburg7, Janelia Farm Research Campus8, Yale University9, University of Arizona10, University of Mainz11, Rockefeller University12
TL;DR: A consortium of neurobiologists studying arthropod brains, the Insect Brain Name Working Group, has established the present hierarchical nomenclature system, using the brain of Drosophila melanogaster as the reference framework, while taking the brains of other taxa into careful consideration for maximum consistency and expandability.
TL;DR: This study shows experimentally that changes in plant diversity and species composition are caused by fungal pathogens and insect herbivores, and provides an overall test of the Janzen–Connell hypothesis.
Abstract: Tropical forests are important reservoirs of biodiversity, but the processes that maintain this diversity remain poorly understood. The Janzen-Connell hypothesis suggests that specialized natural enemies such as insect herbivores and fungal pathogens maintain high diversity by elevating mortality when plant species occur at high density (negative density dependence; NDD). NDD has been detected widely in tropical forests, but the prediction that NDD caused by insects and pathogens has a community-wide role in maintaining tropical plant diversity remains untested. We show experimentally that changes in plant diversity and species composition are caused by fungal pathogens and insect herbivores. Effective plant species richness increased across the seed-to-seedling transition, corresponding to large changes in species composition. Treating seeds and young seedlings with fungicides significantly reduced the diversity of the seedling assemblage, consistent with the Janzen-Connell hypothesis. Although suppressing insect herbivores using insecticides did not alter species diversity, it greatly increased seedling recruitment and caused a marked shift in seedling species composition. Overall, seedling recruitment was significantly reduced at high conspecific seed densities and this NDD was greatest for the species that were most abundant as seeds. Suppressing fungi reduced the negative effects of density on recruitment, confirming that the diversity-enhancing effect of fungi is mediated by NDD. Our study provides an overall test of the Janzen-Connell hypothesis and demonstrates the crucial role that insects and pathogens have both in structuring tropical plant communities and in maintaining their remarkable diversity.