Showing papers by "Rutgers University published in 2011"
Book•
23 May 2011TL;DR: It is argued that the alternating direction method of multipliers is well suited to distributed convex optimization, and in particular to large-scale problems arising in statistics, machine learning, and related areas.
Abstract: Many problems of recent interest in statistics and machine learning can be posed in the framework of convex optimization. Due to the explosion in size and complexity of modern datasets, it is increasingly important to be able to solve problems with a very large number of features or training examples. As a result, both the decentralized collection or storage of these datasets as well as accompanying distributed solution methods are either necessary or at least highly desirable. In this review, we argue that the alternating direction method of multipliers is well suited to distributed convex optimization, and in particular to large-scale problems arising in statistics, machine learning, and related areas. The method was developed in the 1970s, with roots in the 1950s, and is equivalent or closely related to many other algorithms, such as dual decomposition, the method of multipliers, Douglas–Rachford splitting, Spingarn's method of partial inverses, Dykstra's alternating projections, Bregman iterative algorithms for l1 problems, proximal methods, and others. After briefly surveying the theory and history of the algorithm, we discuss applications to a wide variety of statistical and machine learning problems of recent interest, including the lasso, sparse logistic regression, basis pursuit, covariance selection, support vector machines, and many others. We also discuss general distributed optimization, extensions to the nonconvex setting, and efficient implementation, including some details on distributed MPI and Hadoop MapReduce implementations.
17,433 citations
Journal Article•
TL;DR: A unified neural network architecture and learning algorithm that can be applied to various natural language processing tasks including part-of-speech tagging, chunking, named entity recognition, and semantic role labeling is proposed.
Abstract: We propose a unified neural network architecture and learning algorithm that can be applied to various natural language processing tasks including part-of-speech tagging, chunking, named entity recognition, and semantic role labeling. This versatility is achieved by trying to avoid task-specific engineering and therefore disregarding a lot of prior knowledge. Instead of exploiting man-made input features carefully optimized for each task, our system learns internal representations on the basis of vast amounts of mostly unlabeled training data. This work is then used as a basis for building a freely available tagging system with good performance and minimal computational requirements.
6,734 citations
TL;DR: Above an annealing temperature of 300 °C, chemically exfoliated MoS2 exhibit prominent band gap photoluminescence, similar to mechanically exfoliate monolayers, indicating that their semiconducting properties are largely restored.
Abstract: A two-dimensional crystal of molybdenum disulfide (MoS2) monolayer is a photoluminescent direct gap semiconductor in striking contrast to its bulk counterpart. Exfoliation of bulk MoS2 via Li intercalation is an attractive route to large-scale synthesis of monolayer crystals. However, this method results in loss of pristine semiconducting properties of MoS2 due to structural changes that occur during Li intercalation. Here, we report structural and electronic properties of chemically exfoliated MoS2. The metastable metallic phase that emerges from Li intercalation was found to dominate the properties of as-exfoliated material, but mild annealing leads to gradual restoration of the semiconducting phase. Above an annealing temperature of 300 °C, chemically exfoliated MoS2 exhibit prominent band gap photoluminescence, similar to mechanically exfoliated monolayers, indicating that their semiconducting properties are largely restored.
3,403 citations
Pennsylvania State University1, Harvard University2, Stony Brook University3, Winthrop-University Hospital4, Cornell University5, Ohio State University6, Loyola University Chicago7, Creighton University8, University of California, San Diego9, Queen's University10, Memorial University of Newfoundland11, Yale University12, Maine Medical Center13, Rutgers University14
TL;DR: The Committee concluded that the prevalence of vitamin D inadequacy in North America has been overestimated and urgent research and clinical priorities were identified, including reassessment of laboratory ranges for 25-hydroxyvitamin D, to avoid problems of both undertreatment and overtreatment.
Abstract: This article summarizes the new 2011 report on dietary requirements for calcium and vitamin D from the Institute of Medicine (IOM). An IOM Committee charged with determining the population needs for these nutrients in North America conducted a comprehensive review of the evidence for both skeletal and extraskeletal outcomes. The Committee concluded that available scientific evidence supports a key role of calcium and vitamin D in skeletal health, consistent with a cause-and-effect relationship and providing a sound basis for determination of intake requirements. For extraskeletal outcomes, including cancer, cardiovascular disease, diabetes, and autoimmune disorders, the evidence was inconsistent, inconclusive as to causality, and insufficient to inform nutritional requirements. Randomized clinical trial evidence for extraskeletal outcomes was limited and generally uninformative. Based on bone health, Recommended Dietary Allowances (RDAs; covering requirements of ≥97.5% of the population) for calcium range...
3,328 citations
Space Telescope Science Institute1, University of California, Santa Cruz2, Johns Hopkins University3, Rutgers University4, Durham University5, University of Nottingham6, Harvard University7, University of Innsbruck8, University of Michigan9, DSM10, University of Edinburgh11, University of Massachusetts Amherst12, California Institute of Technology13, UK Astronomy Technology Centre14, University of California, Irvine15, Swinburne University of Technology16, University of Arizona17, Goddard Space Flight Center18, The Catholic University of America19, Hebrew University of Jerusalem20, University of Victoria21, University of California, Berkeley22, Texas A&M University23, University of Notre Dame24, Carnegie Institution for Science25, Smithsonian Institution26, Yale University27, University of Missouri–Kansas City28, University of California, Riverside29, Max Planck Society30, University of Pittsburgh31, Inter-University Centre for Astronomy and Astrophysics32, University of Barcelona33, European Southern Observatory34, University of Minnesota35, National Research Council36, Western Kentucky University37, Stanford University38, Atacama Large Millimeter Submillimeter Array39, University of Missouri40
TL;DR: The Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey (CANDELS) as discussed by the authors was designed to document the first third of galactic evolution, from z approx. 8 - 1.5 to test their accuracy as standard candles for cosmology.
Abstract: The Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey (CANDELS) is designed to document the first third of galactic evolution, from z approx. 8 - 1.5. It will image > 250,000 distant galaxies using three separate cameras on the Hubble Space Tele8cope, from the mid-UV to near-IR, and will find and measure Type Ia supernovae beyond z > 1.5 to test their accuracy as standard candles for cosmology. Five premier multi-wavelength sky regions are selected, each with extensive ancillary data. The use of five widely separated fields mitigates cosmic variance and yields statistically robust and complete samples of galaxies down to a stellar mass of 10(exp 9) solar mass to z approx. 2, reaching the knee of the UV luminosity function of galaxies to z approx. 8. The survey covers approximately 800 square arc minutes and is divided into two parts. The CANDELS/Deep survey (5(sigma) point-source limit H =27.7mag) covers approx. 125 square arcminutes within GOODS-N and GOODS-S. The CANDELS/Wide survey includes GOODS and three additional fields (EGS, COSMOS, and UDS) and covers the full area to a 50(sigma) point-source limit of H ? or approx. = 27.0 mag. Together with the Hubble Ultradeep Fields, the strategy creates a three-tiered "wedding cake" approach that has proven efficient for extragalactic surveys. Data from the survey are non-proprietary and are useful for a wide variety of science investigations. In this paper, we describe the basic motivations for the survey, the CANDELS team science goals and the resulting observational requirements, the field selection and geometry, and the observing design.
2,088 citations
Harvard University1, Cincinnati Children's Hospital Medical Center2, Duke University3, University of Arkansas for Medical Sciences4, Icahn School of Medicine at Mount Sinai5, Johns Hopkins University School of Medicine6, National Institutes of Health7, University of Southampton8, St Mary's Hospital9, LSU Health Sciences Center Shreveport10, University of Rochester Medical Center11, Rutgers University12, University of California, San Diego13, Boston Children's Hospital14, University of Colorado Denver15, Oregon Health & Science University16, University of Tennessee Health Science Center17, Food and Drug Administration18, University of California, Irvine19, Scripps Health20, University of Manitoba21, Children's National Medical Center22, University of Rochester23, University of Minnesota24
TL;DR: The National Institute of Allergy and Infectious Diseases, working with 34 professional organizations, federal agencies, and patient advocacy groups, led the development of clinical guidelines for the diagnosis and management of food allergy, which include a consensus definition for food allergy.
Abstract: Food allergy is an important public health problem that affects children and adults and may be increasing in prevalence. Despite the risk of severe allergic reactions and even death, there is no current treatment for food allergy: the disease can only be managed by allergen avoidance or treatment of symptoms. The diagnosis and management of food allergy also may vary from one clinical practice setting to another. Finally, because patients frequently confuse nonallergic food reactions, such as food intolerance, with food allergies, there is an unfounded belief among the public that food allergy prevalence is higher than it truly is. In response to these concerns, the National Institute of Allergy and Infectious Diseases, working with 34 professional organizations, federal agencies, and patient advocacy groups, led the development of clinical guidelines for the diagnosis and management of food allergy. These Guidelines are intended for use by a wide variety of health care professionals, including family practice physicians, clinical specialists, and nurse practitioners. The Guidelines include a consensus definition for food allergy, discuss comorbid conditions often associated with food allergy, and focus on both IgE-mediated and non-IgE-mediated reactions to food. Topics addressed include the epidemiology, natural history, diagnosis, and management of food allergy, as well as the management of severe symptoms and anaphylaxis. These Guidelines provide 43 concise clinical recommendations and additional guidance on points of current controversy in patient management. They also identify gaps in the current scientific knowledge to be addressed through future research.
2,014 citations
Space Telescope Science Institute1, University of California, Santa Cruz2, Johns Hopkins University3, Western Kentucky University4, University of Massachusetts Amherst5, Carnegie Institution for Science6, European Southern Observatory7, Ohio State University8, Rutgers University9, Durham University10, University of Nottingham11, Max Planck Society12, University of Innsbruck13, University of Michigan14, French Alternative Energies and Atomic Energy Commission15, University of Edinburgh16, Harvard University17, California Institute of Technology18, University of California, Irvine19, Swinburne University of Technology20, University of Arizona21, Goddard Space Flight Center22, Hebrew University of Jerusalem23, Victoria University, Australia24, DSM25, University of California, Berkeley26, Texas A&M University27, University of Notre Dame28, Smithsonian Institution29, Yale University30, University of Missouri–Kansas City31, University of California, Riverside32, Imperial College London33, University of Pittsburgh34, Inter-University Centre for Astronomy and Astrophysics35, National Research Council36, Stanford University37
TL;DR: In this paper, the authors describe the Hubble Space Telescope imaging data products and data reduction procedures for the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS).
Abstract: This paper describes the Hubble Space Telescope imaging data products and data reduction procedures for the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS). This survey is designed to document the evolution of galaxies and black holes at z 1.5-8, and to study Type Ia supernovae at z > 1.5. Five premier multi-wavelength sky regions are selected, each with extensive multi-wavelength observations. The primary CANDELS data consist of imaging obtained in the Wide Field Camera 3 infrared channel (WFC3/IR) and the WFC3 ultraviolet/optical channel, along with the Advanced Camera for Surveys (ACS). The CANDELS/Deep survey covers ~125 arcmin2 within GOODS-N and GOODS-S, while the remainder consists of the CANDELS/Wide survey, achieving a total of ~800 arcmin2 across GOODS and three additional fields (Extended Groth Strip, COSMOS, and Ultra-Deep Survey). We summarize the observational aspects of the survey as motivated by the scientific goals and present a detailed description of the data reduction procedures and products from the survey. Our data reduction methods utilize the most up-to-date calibration files and image combination procedures. We have paid special attention to correcting a range of instrumental effects, including charge transfer efficiency degradation for ACS, removal of electronic bias-striping present in ACS data after Servicing Mission 4, and persistence effects and other artifacts in WFC3/IR. For each field, we release mosaics for individual epochs and eventual mosaics containing data from all epochs combined, to facilitate photometric variability studies and the deepest possible photometry. A more detailed overview of the science goals and observational design of the survey are presented in a companion paper.
2,011 citations
TL;DR: In this paper, the authors used the Wide Field Camera 3 (WFC3) on the Hubble Space Telescope (HST) to determine the Hubble constant from optical and infrared observations of over 600 Cepheid variables in the host galaxies of eight recent Type Ia supernovae (SNe Ia), providing the calibration for a magnitude-redshift relation based on 253 SNeIa.
Abstract: We use the Wide Field Camera 3 (WFC3) on the Hubble Space Telescope (HST) to determine the Hubble constant from optical and infrared observations of over 600 Cepheid variables in the host galaxies of eight recent Type Ia supernovae (SNe Ia), providing the calibration for a magnitude-redshift relation based on 253 SNe Ia. Increased precision over past measurements of the Hubble constant comes from five improvements: (1) more than doubling the number of infrared observations of Cepheids in the nearby SN hosts; (2) increasing the sample size of ideal SN Ia calibrators from six to eight; (3) increasing by 20% the number of Cepheids with infrared observations in the megamaser host NGC 4258; (4) reducing the difference in the mean metallicity of the Cepheid comparison samples between NGC 4258 and the SN hosts from Δlog [O/H] = 0.08 to 0.05; and (5) calibrating all optical Cepheid colors with a single camera, WFC3, to remove cross-instrument zero-point errors. The result is a reduction in the uncertainty in H 0 due to steps beyond the first rung of the distance ladder from 3.5% to 2.3%. The measurement of H 0 via the geometric distance to NGC 4258 is 74.8 ± 3.1 km s–1 Mpc–1, a 4.1% measurement including systematic uncertainties. Better precision independent of the distance to NGC 4258 comes from the use of two alternative Cepheid absolute calibrations: (1) 13 Milky Way Cepheids with trigonometric parallaxes measured with HST/fine guidance sensor and Hipparcos and (2) 92 Cepheids in the Large Magellanic Cloud for which multiple accurate and precise eclipsing binary distances are available, yielding 74.4 ± 2.5 km s–1 Mpc–1, a 3.4% uncertainty including systematics. Our best estimate uses all three calibrations but a larger uncertainty afforded from any two: H 0 = 73.8 ± 2.4 km s–1 Mpc–1 including systematic errors, corresponding to a 3.3% uncertainty. The improved measurement of H 0, when combined with the Wilkinson Microwave Anisotropy Probe (WMAP) 7 year data, results in a tighter constraint on the equation-of-state parameter of dark energy of w = –1.08 ± 0.10. It also rules out the best-fitting gigaparsec-scale void models, posited as an alternative to dark energy. The combined H 0 + WMAP results yield N eff = 4.2 ± 0.7 for the number of relativistic particle species in the early universe, a low-significance excess for the value expected from the three known neutrino flavors.
1,680 citations
TL;DR: In this paper, the authors provide a detailed and up-to-date description of the literature on the subject as well as highlighting challenges that must be overcome for the utilization of graphene deposited on copper substrates by chemical vapour deposition.
Abstract: The discovery of uniform deposition of high-quality single layered graphene on copper has generated significant interest. That interest has been translated into rapid progress in terms of large area deposition of thin films via transfer onto plastic and glass substrates. The opto-electronic properties of the graphene thin films reveal that they are of very high quality with transmittance and conductance values of >90% and 30Ω/sq, both are comparable to the current state-of-the-art indium tin oxide transparent conductor. In this Feature Article, we provide a detailed and up to date description of the literature on the subject as well as highlighting challenges that must be overcome for the utilization of graphene deposited on copper substrates by chemical vapour deposition.
1,405 citations
TL;DR: It is concluded that, unlike many other mutualisms, the symbiont cannot be “enslaved,” and the mutualism is evolutionarily stable because control is bidirectional, and partners offering the best rate of exchange are rewarded.
Abstract: Plants and their arbuscular mycorrhizal fungal symbionts interact in complex underground networks involving multiple partners. This increases the potential for exploitation and defection by individuals, raising the question of how partners maintain a fair, two-way transfer of resources. We manipulated cooperation in plants and fungal partners to show that plants can detect, discriminate, and reward the best fungal partners with more carbohydrates. In turn, their fungal partners enforce cooperation by increasing nutrient transfer only to those roots providing more carbohydrates. On the basis of these observations we conclude that, unlike many other mutualisms, the symbiont cannot be "enslaved." Rather, the mutualism is evolutionarily stable because control is bidirectional, and partners offering the best rate of exchange are rewarded.
1,346 citations
Broad Institute1, Mayo Clinic2, Harvard University3, Multiple Myeloma Research Foundation4, Translational Genomics Research Institute5, Howard Hughes Medical Institute6, Weizmann Institute of Science7, Ohio State University8, Catholic Medical Center9, University of Michigan10, City of Hope National Medical Center11, Emory University12, Rutgers University13, Washington University in St. Louis14, University of Chicago15, Massachusetts Institute of Technology16
TL;DR: The massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs indicates that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge.
Abstract: Multiple myeloma is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood. Here we report the massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs. Several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set. These include the mutation of genes involved in protein translation (seen in nearly half of the patients), genes involved in histone methylation, and genes involved in blood coagulation. In addition, a broader than anticipated role of NF-κB signalling was indicated by mutations in 11 members of the NF-κB pathway. Of potential immediate clinical relevance, activating mutations of the kinase BRAF were observed in 4% of patients, suggesting the evaluation of BRAF inhibitors in multiple myeloma clinical trials. These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge.
TL;DR: A novel region-based method for image segmentation, which is able to simultaneously segment the image and estimate the bias field, and the estimated bias field can be used for intensity inhomogeneity correction (or bias correction).
Abstract: Intensity inhomogeneity often occurs in real-world images, which presents a considerable challenge in image segmentation. The most widely used image segmentation algorithms are region-based and typically rely on the homogeneity of the image intensities in the regions of interest, which often fail to provide accurate segmentation results due to the intensity inhomogeneity. This paper proposes a novel region-based method for image segmentation, which is able to deal with intensity inhomogeneities in the segmentation. First, based on the model of images with intensity inhomogeneities, we derive a local intensity clustering property of the image intensities, and define a local clustering criterion function for the image intensities in a neighborhood of each point. This local clustering criterion function is then integrated with respect to the neighborhood center to give a global criterion of image segmentation. In a level set formulation, this criterion defines an energy in terms of the level set functions that represent a partition of the image domain and a bias field that accounts for the intensity inhomogeneity of the image. Therefore, by minimizing this energy, our method is able to simultaneously segment the image and estimate the bias field, and the estimated bias field can be used for intensity inhomogeneity correction (or bias correction). Our method has been validated on synthetic images and real images of various modalities, with desirable performance in the presence of intensity inhomogeneities. Experiments show that our method is more robust to initialization, faster and more accurate than the well-known piecewise smooth model. As an application, our method has been used for segmentation and bias correction of magnetic resonance (MR) images with promising results.
Yale University1, University of Michigan2, University of California, Los Angeles3, Emory University4, Carnegie Mellon University5, Rutgers University6, Vanderbilt University7, Cornell University8, Baylor College of Medicine9, University of Illinois at Chicago10, Stanford University11, University of Pittsburgh12, University of Washington13, Princeton University14, Boston Children's Hospital15, Columbia University16, Howard Hughes Medical Institute17, Brown University18, Geisinger Health System19, Montreal Children's Hospital20
TL;DR: A genome-wide analysis of rare copy-number variation in 1124 autism spectrum disorder families, each comprised of a single proband, unaffected parents, and, in most kindreds, an unaffected sibling, finds significant association of ASD with de novo duplications of 7q11.23, where the reciprocal deletion causes Williams-Beuren syndrome.
TL;DR: It is found that neomycin-sensitive bacteria are associated with the induction of productive immune responses in the lung and local or distal injection of Toll-like receptor (TLR) ligands could rescue the immune impairment in the antibiotic-treated mice.
Abstract: Although commensal bacteria are crucial in maintaining immune homeostasis of the intestine, the role of commensal bacteria in immune responses at other mucosal surfaces remains less clear. Here, we show that commensal microbiota composition critically regulates the generation of virus-specific CD4 and CD8 T cells and antibody responses following respiratory influenza virus infection. By using various antibiotic treatments, we found that neomycin-sensitive bacteria are associated with the induction of productive immune responses in the lung. Local or distal injection of Toll-like receptor (TLR) ligands could rescue the immune impairment in the antibiotic-treated mice. Intact microbiota provided signals leading to the expression of mRNA for pro–IL-1β and pro–IL-18 at steady state. Following influenza virus infection, inflammasome activation led to migration of dendritic cells (DCs) from the lung to the draining lymph node and T-cell priming. Our results reveal the importance of commensal microbiota in regulating immunity in the respiratory mucosa through the proper activation of inflammasomes.
TL;DR: The Society for Vascular Surgery and the American Venous Forum have developed clinical practice guidelines for the care of patients with varicose veins of the lower limbs and pelvis, including recommendations on the management of superficial and perforating vein incompetence in patients with associated, more advanced chronic venous diseases.
TL;DR: This "autophagy addiction" suggests that targeting autophagy and mitochondrial metabolism are valuable new approaches to treat these aggressive cancers.
Abstract: Autophagy is a catabolic pathway used by cells to support metabolism in response to starvation and to clear damaged proteins and organelles in response to stress. We report here that expression of a H-rasV12 or K-rasV12 oncogene up-regulates basal autophagy, which is required for tumor cell survival in starvation and in tumorigenesis. In Ras-expressing cells, defective autophagosome formation or cargo delivery causes accumulation of abnormal mitochondria and reduced oxygen consumption. Autophagy defects also lead to tricarboxylic acid (TCA) cycle metabolite and energy depletion in starvation. As mitochondria sustain viability of Ras-expressing cells in starvation, autophagy is required to maintain the pool of functional mitochondria necessary to support growth of Ras-driven tumors. Human cancer cell lines bearing activating mutations in Ras commonly have high levels of basal autophagy, and, in a subset of these, down-regulating the expression of essential autophagy proteins impaired cell growth. As cancers with Ras mutations have a poor prognosis, this “autophagy addiction” suggests that targeting autophagy and mitochondrial metabolism are valuable new approaches to treat these aggressive cancers.
Broad Institute1, Mayo Clinic2, Harvard University3, Multiple Myeloma Research Foundation4, Translational Genomics Research Institute5, Howard Hughes Medical Institute6, Weizmann Institute of Science7, Ohio State University8, Catholic Medical Center9, University of Michigan10, City of Hope National Medical Center11, Emory University12, Rutgers University13, Washington University in St. Louis14, University of Chicago15, Massachusetts Institute of Technology16
TL;DR: In this paper, a massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs was reported, and several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set.
Abstract: Multiple myeloma is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood. Here we report the massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs. Several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set. These include the mutation of genes involved in protein translation (seen in nearly half of the patients), genes involved in histone methylation, and genes involved in blood coagulation. In addition, a broader than anticipated role of NF-κB signalling was indicated by mutations in 11 members of the NF-κB pathway. Of potential immediate clinical relevance, activating mutations of the kinase BRAF were observed in 4% of patients, suggesting the evaluation of BRAF inhibitors in multiple myeloma clinical trials. These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge.
University of North Texas1, East Malling Research Station2, Plant & Food Research3, Oregon State University4, University of Maryland, College Park5, Indiana University6, Virginia Tech7, Georgia Institute of Technology8, University of New Hampshire9, United States Department of Agriculture10, Hoffmann-La Roche11, University of Auckland12, Rutgers University13, University of the Western Cape14, University of Florida15, University of Chile16, Andrés Bello National University17, Weizmann Institute of Science18, University of Pittsburgh19, University of Georgia20, Technische Universität München21, University of Illinois at Urbana–Champaign22, Institut national de la recherche agronomique23
TL;DR: New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted, and macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes.
Abstract: The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria × ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.
TL;DR: A highly luminescent three-dimensional microporous metal-organic framework, [Zn(2)(oba)(2)(bpy)]·DMA, demonstrates unique selectivity for the detection of high explosives and other aromatics via a fluorescence quenching and enhancement mechanism.
Abstract: A highly luminescent three-dimensional microporous metal−organic framework, [Zn2(oba)2(bpy)]·DMA, demonstrates unique selectivity for the detection of high explosives and other aromatics via a fluorescence quenching and enhancement mechanism.
TL;DR: In this paper, a review summarizes the current knowledge on aqueous phase organic reactions and combines evidence that points to a significant role of aqSOA formation in the atmosphere.
Abstract: . Progress has been made over the past decade in predicting secondary organic aerosol (SOA) mass in the atmosphere using vapor pressure-driven partitioning, which implies that SOA compounds are formed in the gas phase and then partition to an organic phase (gasSOA). However, discrepancies in predicting organic aerosol oxidation state, size and product (molecular mass) distribution, relative humidity (RH) dependence, color, and vertical profile suggest that additional SOA sources and aging processes may be important. The formation of SOA in cloud and aerosol water (aqSOA) is not considered in these models even though water is an abundant medium for atmospheric chemistry and such chemistry can form dicarboxylic acids and "humic-like substances" (oligomers, high-molecular-weight compounds), i.e. compounds that do not have any gas phase sources but comprise a significant fraction of the total SOA mass. There is direct evidence from field observations and laboratory studies that organic aerosol is formed in cloud and aerosol water, contributing substantial mass to the droplet mode. This review summarizes the current knowledge on aqueous phase organic reactions and combines evidence that points to a significant role of aqSOA formation in the atmosphere. Model studies are discussed that explore the importance of aqSOA formation and suggestions for model improvements are made based on the comprehensive set of laboratory data presented here. A first comparison is made between aqSOA and gasSOA yields and mass predictions for selected conditions. These simulations suggest that aqSOA might contribute almost as much mass as gasSOA to the SOA budget, with highest contributions from biogenic emissions of volatile organic compounds (VOC) in the presence of anthropogenic pollutants (i.e. NOx) at high relative humidity and cloudiness. Gaps in the current understanding of aqSOA processes are discussed and further studies (laboratory, field, model) are outlined to complement current data sets.
Pennsylvania State University1, Harvard University2, Stony Brook University3, Winthrop-University Hospital4, Cornell University5, Ohio State University6, Loyola University Chicago7, Creighton University8, University of California, San Diego9, Queen's University10, Memorial University of Newfoundland11, Yale University12, Maine Medical Center13, Rutgers University14
TL;DR: Prevalence of vitamin D deficiency in North America has been overestimated; the data show that almost all individuals in this population meet their RDA for vitamin D.
Abstract: This report summarizes the findings of the 2011 Institute of Medicine Committee on dietary intake requirements for calcium and vitamin D in North America, and provides updated data from the previous Institute of Medicine report of 1997. The Committee extensively reviewed existing published evidence on dietary and supplemental intake requirements for calcium and vitamin D with respect to both skeletal health and extraskeletal chronic disease outcomes. Calcium and vitamin D intake requirements were examined for several risk indictors of bone and skeletal health as well as extraskeletal outcomes (including cancer, cardiovascular disease, diabetes, and autoimmune disorders, infectious diseases, neuropsychological function, and disorders of pregnancy). Recommended Dietary Allowance (RDA) was defined as the level of intake of calcium or serum 25-hydroxyvitamin D that would meet the requirements of at least 97.5% of the population. The available scientific data supported an important role for calcium and vitamin D in bone and skeletal health outcomes that was consistent with a cause-and-effect relationship. However, data from randomized clinical trials for extraskeletal health outcomes were limited and inconclusive regarding a possible relationship with calcium and vitamin D intake requirements, and no evidence was found for dose-response or other established criteria for cause-and-effect. For bone health outcome, RDAs of calcium ranged from 700 to 1300 mg/d for life-stage groups at ≥1 year of age, and RDAs of vitamin D were 600 IU/d for ages 1 to 70 years and 800 IU/d for ages ≥71 (corresponding to a serum 25-hydroxyvitamin D level of at least 20 ng/mL [50 nmol/L]). There was an assumption of minimal or no sun exposure for estimation of RDA levels because of the wide variation in vitamin D synthesis from ultraviolet light and concern over risk of skin cancer. No consistent evidence was found that dietary or supplemental intake of vitamin D levels above the RDA provides additional benefit for bone health or extraskeletal outcomes; several investigators have found an U-shaped curve for several outcomes related to vitamin D intake, with increased risks at both low and high levels. The findings of this report suggest that prevalence of vitamin D deficiency in North America has been overestimated. The data show that almost all individuals in this population meet their RDA for vitamin D.
TL;DR: In this paper, the authors provide an overview of machining induced surface integrity in titanium and nickel alloys and conclude that further modeling studies are needed to create predictive physics-based models that is in good agreement with reliable experiments.
Abstract: Titanium and nickel alloys represent a significant metal portion of the aircraft structural and engine components. When these critical structural components in aerospace industry are manufactured with the objective to reach high reliability levels, surface integrity is one of the most relevant parameters used for evaluating the quality of finish machined surfaces. The residual stresses and surface alteration (white etch layer and depth of work hardening) induced by machining of titanium alloys and nickel-based alloys are very critical due to safety and sustainability concerns. This review paper provides an overview of machining induced surface integrity in titanium and nickel alloys. There are many different types of surface integrity problems reported in literature, and among these, residual stresses, white layer and work hardening layers, as well as microstructural alterations can be studied in order to improve surface qualities of end products. Many parameters affect the surface quality of workpieces, and cutting speed, feed rate, depth of cut, tool geometry and preparation, tool wear, and workpiece properties are among the most important ones worth to investigate. Experimental and empirical studies as well as analytical and Finite Element modeling based approaches are offered in order to better understand machining induced surface integrity. In the current state-of-the-art however, a comprehensive and systematic modeling approach based on the process physics and applicable to the industrial processes is still missing. It is concluded that further modeling studies are needed to create predictive physics-based models that is in good agreement with reliable experiments, while explaining the effects of many parameters, for machining of titanium alloys and nickel-based alloys.
Stanford University1, Harvard University2, University of Washington3, University of Florida4, Boston University5, University of Colorado Denver6, University of Texas Southwestern Medical Center7, University of Rochester8, University of Pittsburgh9, University of Toronto10, University of California, San Francisco11, Washington University in St. Louis12, University of Texas Medical Branch13, Loyola University Chicago14, Rutgers University15, Princeton University16
TL;DR: It is shown that critical injury in humans induces a genomic storm with simultaneous changes in expression of innate and adaptive immunity genes that alter the status of these genes in the immune system.
Abstract: Human survival from injury requires an appropriate inflammatory and immune response. We describe the circulating leukocyte transcriptome after severe trauma and burn injury, as well as in healthy subjects receiving low-dose bacterial endotoxin, and show that these severe stresses produce a global reprioritization affecting >80% of the cellular functions and pathways, a truly unexpected “genomic storm.” In severe blunt trauma, the early leukocyte genomic response is consistent with simultaneously increased expression of genes involved in the systemic inflammatory, innate immune, and compensatory antiinflammatory responses, as well as in the suppression of genes involved in adaptive immunity. Furthermore, complications like nosocomial infections and organ failure are not associated with any genomic evidence of a second hit and differ only in the magnitude and duration of this genomic reprioritization. The similarities in gene expression patterns between different injuries reveal an apparently fundamental human response to severe inflammatory stress, with genomic signatures that are surprisingly far more common than different. Based on these transcriptional data, we propose a new paradigm for the human immunological response to severe injury.
TL;DR: In this article, the authors discuss aspects of global and gauged symmetries in quantum field theory and quantum gravity, focusing on discrete gauge symmetsries, and show that all continuous and continuous gauge symmetry are compact and all charges allowed by Dirac quantization are present in the spectrum.
Abstract: We discuss aspects of global and gauged symmetries in quantum field theory and quantum gravity, focusing on discrete gauge symmetries. An effective Lagrangian description of Zp gauge theories shows that they are associated with an emergent Zp one-form (KalbRamond) gauge symmetry. This understanding leads us to uncover new observables and new phenomena in nonlinear σ-models. It also allows us to expand on Polchinski’s classification of cosmic strings. We argue that in models of quantum gravity, there are no global symmetries, all continuous gauge symmetries are compact, and all charges allowed by Dirac quantization are present in the spectrum. These conjectures are not new, but we present them from a streamlined and unified perspective. Finally, our discussion about string charges and symmetries leads to a more physical and more complete understanding of recently found consistency conditions of supergravity.
TL;DR: The International Soil Moisture Network (ISMN) as discussed by the authors is a centralized data hosting facility where globally available in situ soil moisture measurements from operational networks and validation campaigns are collected, harmonized, and made available to users.
Abstract: . In situ measurements of soil moisture are invaluable for calibrating and validating land surface models and satellite-based soil moisture retrievals. In addition, long-term time series of in situ soil moisture measurements themselves can reveal trends in the water cycle related to climate or land cover change. Nevertheless, on a worldwide basis the number of meteorological networks and stations measuring soil moisture, in particular on a continuous basis, is still limited and the data they provide lack standardization of technique and protocol. To overcome many of these limitations, the International Soil Moisture Network (ISMN; http://www.ipf.tuwien.ac.at/insitu ) was initiated to serve as a centralized data hosting facility where globally available in situ soil moisture measurements from operational networks and validation campaigns are collected, harmonized, and made available to users. Data collecting networks share their soil moisture datasets with the ISMN on a voluntary and no-cost basis. Incoming soil moisture data are automatically transformed into common volumetric soil moisture units and checked for outliers and implausible values. Apart from soil water measurements from different depths, important metadata and meteorological variables (e.g., precipitation and soil temperature) are stored in the database. These will assist the user in correctly interpreting the soil moisture data. The database is queried through a graphical user interface while output of data selected for download is provided according to common standards for data and metadata. Currently (status May 2011), the ISMN contains data of 19 networks and more than 500 stations located in North America, Europe, Asia, and Australia. The time period spanned by the entire database runs from 1952 until the present, although most datasets have originated during the last decade. The database is rapidly expanding, which means that both the number of stations and the time period covered by the existing stations are still growing. Hence, it will become an increasingly important resource for validating and improving satellite-derived soil moisture products and studying climate related trends. As the ISMN is animated by the scientific community itself, we invite potential networks to enrich the collection by sharing their in situ soil moisture data.
Posted Content•
TL;DR: The authors proposed a unified neural network architecture and learning algorithm that can be applied to various natural language processing tasks including: part-of-speech tagging, chunking, named entity recognition, and semantic role labeling.
Abstract: We propose a unified neural network architecture and learning algorithm that can be applied to various natural language processing tasks including: part-of-speech tagging, chunking, named entity recognition, and semantic role labeling. This versatility is achieved by trying to avoid task-specific engineering and therefore disregarding a lot of prior knowledge. Instead of exploiting man-made input features carefully optimized for each task, our system learns internal representations on the basis of vast amounts of mostly unlabeled training data. This work is then used as a basis for building a freely available tagging system with good performance and minimal computational requirements.
TL;DR: It is shown that at least 20% of CAFs originate from bone marrow (BM) and derive from mesenchymal stem cells (MSCs), and αSMA+ myofibroblasts (MFs) are niche cells normally present in BM and increase markedly during cancer progression.
TL;DR: McDonald et al. as mentioned in this paper proposed a method to solve the problem of protein synthesis in the context of the 239th American Chemical Society (ACS) National Meeting of Organometallics 2010.
Abstract: s of Papers, 221st ACS National Meeting, San Diego, CA, April 1-5, 2001; American Chemical Society:Washington, DC, 2001; INOR287. (b) Dijkstra, H. P.; Slagt, M. Q.; McDonald, A.; Kruithof, C. A.; Kreiter, R.; Mills, A. M.; Lutz, M.; Spek, A. L.; Klopper, W.; van Klink, G. P. M.; van Koten, G. Eur. J. Inorg. Chem. 2003, 830. (c) Mehendale, N. C.; Bezemer, C.; van Walree, C. A.; Klein Gebbink, R. J. M.; van Koten, G. J. Mol. Catal. A 2006, 257, 167. (d)Mehendale, N. C.; Sietsma, J. R. A.; de Jong, K. P.; vanWalree, C. A.; Gebbink, R. J. M. K.; van Koten, G. Adv. Synth. Catal. 2007, 349, 2619. (e) Mehendale, N. C.; Lutz, M.; Spek, A. L.; Klein Gebbink, R. J. M.; van Koten, G. J. Organomet. Chem. 2008, 693, 2971. (f)McDonald, A. R.; Dijkstra, H. P.; Suijkerbuijk, B.M. J. M.; van Klink, G. P. M.; van Koten, G.Organometallics 2009, 28, 4689. (g) McDonald, A. R.; Franssen, N.; van Klink, G. P. M.; van Koten, G. J. Organomet. Chem. 2009, 694, 2153. (h) O’Leary, P.; vanWalree, C. A.; Mehendale, N. C.; Sumerel, J.; Morse, D. E.; Kaska, W. C.; van Koten, G.; Klein Gebbink, R. J. M. Dalton Trans. 2009, 4289. (164) Gimenez, R.; Swager, T. M. J. Mol. Catal. A 2001, 166, 265. (165) Poyatos, M.; Marquez, F.; Peris, E.; Claver, C.; Fernandez, E. New J. Chem. 2003, 27, 425. (166) Yu, K.; Sommer, W.; Weck, M.; Jones, C. W. J. Catal. 2004, 226, 101. (167) Sommer,W. J.; Yu, K.; Sears, J. S.; Ji, Y.; Zheng, X.; Davis, R. J.; Sherrill, C. D.; Jones, C. W.; Weck, M. Organometallics 2005, 24, 4351. (168) Brookhart, M.; Huang, Z.; MacArthur, A. H.; Carson, E. C.; Goldman, A.; Scott, S. L.; Vicente, B. C. Abstracts of Papers, 239th ACS National Meeting, San Francisco, CA, March 21-25, 2010; American Chemical Society: Washington, DC, 2010; CATL-79. (169) del Pozo, C.; Corma, A.; Iglesias, M.; Sanchez, F. Organometallics 2010, 29, 4491.
Macalester College1, Arizona State University2, University of Western Australia3, United States Forest Service4, University of Florida5, University of California, Davis6, University of New Mexico7, University of Arizona8, Charles Darwin Foundation9, University of Sheffield10, Institute of Ecosystem Studies11, University of California, Berkeley12, Rutgers University13, Stanford University14, University of South Florida15
TL;DR: Conservationists should assess organisms on environmental impact rather than on whether they are natives, argue Mark Davis and 18 other ecologists.
Abstract: Conservationists should assess organisms on environmental impact rather than on whether they are natives, argue Mark Davis and 18 other ecologists.
TL;DR: The current understanding of the core components of the autophagy machinery and the functional relevance of autophile within the tumor microenvironment is described and how this knowledge has informed preclinical investigations combining the autophile inhibitor hydroxychloroquine (HCQ) with chemotherapy, targeted therapy, and immunotherapy is outlined.
Abstract: Autophagy is an evolutionarily conserved, intracellular self-defense mechanism in which organelles and proteins are sequestered into autophagic vesicles that are subsequently degraded through fusion with lysosomes. Cells, thereby, prevent the toxic accumulation of damaged or unnecessary components, but also recycle these components to sustain metabolic homoeostasis. Heightened autophagy is a mechanism of resistance for cancer cells faced with metabolic and therapeutic stress, revealing opportunities for exploitation as a therapeutic target in cancer. We summarize recent developments in the field of autophagy and cancer and build upon the results presented at the Cancer Therapy Evaluation Program (CTEP) Early Drug Development meeting in March 2010. Herein, we describe our current understanding of the core components of the autophagy machinery and the functional relevance of autophagy within the tumor microenvironment, and we outline how this knowledge has informed preclinical investigations combining the autophagy inhibitor hydroxychloroquine (HCQ) with chemotherapy, targeted therapy, and immunotherapy. Finally, we describe ongoing clinical trials involving HCQ as a first generation autophagy inhibitor, as well as strategies for the development of novel, more potent, and specific inhibitors of autophagy.