Showing papers by "National Autonomous University of Mexico published in 2016"
TL;DR: In this paper, the authors present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macro-autophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes.
For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy.
Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.
5,187 citations
University of California, San Diego1, University of Montana2, Stanford University3, Scripps Institution of Oceanography4, National Autonomous University of Mexico5, Salk Institute for Biological Studies6, San Diego State University7, Strathclyde Institute of Pharmacy and Biomedical Sciences8, Lawrence Berkeley National Laboratory9, Harvard University10, University of Rennes11, University of Minnesota12, University of Lorraine13, Technical University of Denmark14, J. Craig Venter Institute15, University of California, Los Angeles16, University of Washington17, ETH Zurich18, University of Illinois at Chicago19, National Sun Yat-sen University20, Academia Sinica21, University of Münster22, Victoria University of Wellington23, University of North Carolina at Chapel Hill24, Indiana University25, Smithsonian Tropical Research Institute26, Federal University of Mato Grosso do Sul27, University of São Paulo28, University of Notre Dame29, University of California, Santa Cruz30, Oregon State University31, University of California, Berkeley32, Florida International University33, University of Hawaii at Manoa34, University of Geneva35, Institut de Chimie des Substances Naturelles36, Pacific Northwest National Laboratory37, National Institutes of Health38, Chinese Academy of Sciences39
TL;DR: In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations and data-driven social-networking should facilitate identification of spectra and foster collaborations.
Abstract: The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
2,365 citations
University of British Columbia1, National Autonomous University of Mexico2, Arizona State University3, National University of Cordoba4, University of Oxford5, University of Vermont6, Helmholtz Centre for Environmental Research - UFZ7, Charles Sturt University8, Lüneburg University9, Oregon State University10, Georgia Institute of Technology11, University of Kiel12, Ikerbasque13, University of Victoria14
TL;DR: It is proposed that focusing only on instrumental or intrinsic values may fail to resonate with views on personal and collective well-being, or “what is right,” with regard to nature and the environment, and it is time to engage seriously with a third class of values, one with diverse roots and current expressions: relational values.
Abstract: A cornerstone of environmental policy is the debate over protecting nature for humans’ sake (instrumental values) or for nature’s (intrinsic values) (1). We propose that focusing only on instrumental or intrinsic values may fail to resonate with views on personal and collective well-being, or “what is right,” with regard to nature and the environment. Without complementary attention to other ways that value is expressed and realized by people, such a focus may inadvertently promote worldviews at odds with fair and desirable futures. It is time to engage seriously with a third class of values, one with diverse roots and current expressions: relational values. By doing so, we reframe the discussion about environmental protection, and open the door to new, potentially more productive policy approaches.
977 citations
Wageningen University and Research Centre1, University of Puerto Rico2, University of Alabama3, National Autonomous University of Mexico4, Brown University5, University of Connecticut6, University of São Paulo7, Leipzig University8, Smithsonian Tropical Research Institute9, Federal University of Pernambuco10, Tulane University11, University of Stirling12, Clemson University13, University of Alberta14, National Institute of Amazonian Research15, Colorado Mesa University16, State University of New York at Purchase17, World Agroforestry Centre18, University of Wisconsin-Madison19, Columbia University20, Aarhus University21, University of Minnesota22, Pedagogical and Technological University of Colombia23, University of California, Santa Barbara24, University of Maryland, College Park25, Yale-NUS College26, National University of Singapore27, Puerto Rico Department of Agriculture28, University of Amsterdam29, Museu Paraense Emílio Goeldi30, Louisiana State University31, University of Regina32
TL;DR: A biomass recovery map of Latin America is presented, which illustrates geographical and climatic variation in carbon sequestration potential during forest regrowth and will support policies to minimize forest loss in areas where biomass resilience is naturally low and promote forest regeneration and restoration in humid tropical lowland areas with high biomass resilience.
Abstract: Land-use change occurs nowhere more rapidly than in the tropics, where the imbalance between deforestation and forest regrowth has large consequences for the global carbon cycle. However, considerable uncertainty remains about the rate of biomass recovery in secondary forests, and how these rates are influenced by climate, landscape, and prior land use. Here we analyse aboveground biomass recovery during secondary succession in 45 forest sites and about 1,500 forest plots covering the major environmental gradients in the Neotropics. The studied secondary forests are highly productive and resilient. Aboveground biomass recovery after 20 years was on average 122 megagrams per hectare (Mg ha(-1)), corresponding to a net carbon uptake of 3.05 Mg C ha(-1) yr(-1), 11 times the uptake rate of old-growth forests. Aboveground biomass stocks took a median time of 66 years to recover to 90% of old-growth values. Aboveground biomass recovery after 20 years varied 11.3-fold (from 20 to 225 Mg ha(-1)) across sites, and this recovery increased with water availability (higher local rainfall and lower climatic water deficit). We present a biomass recovery map of Latin America, which illustrates geographical and climatic variation in carbon sequestration potential during forest regrowth. The map will support policies to minimize forest loss in areas where biomass resilience is naturally low (such as seasonally dry forest regions) and promote forest regeneration and restoration in humid tropical lowland areas with high biomass resilience.
724 citations
TL;DR: This review gives an overview about the membrane lipid structures known in bacteria, the different metabolic pathways involved in their formation, and the distribution of membrane lipids and metabolic pathways across taxonomical groups.
Abstract: For many decades, Escherichia coli was the main model organism for the study of bacterial membrane lipids. The results obtained served as a blueprint for membrane lipid biochemistry, but it is clear now that there is no such thing as a typical bacterial membrane lipid composition. Different bacterial species display different membrane compositions and even the membrane composition of cells belonging to a single species is not constant, but depends on the environmental conditions to which the cells are exposed. Bacterial membranes present a large diversity of amphiphilic lipids, including the common phospholipids phosphatidylglycerol, phosphatidylethanolamine and cardiolipin, the less frequent phospholipids phosphatidylcholine, and phosphatidylinositol and a variety of other membrane lipids, such as for example ornithine lipids, glycolipids, sphingolipids or hopanoids among others. In this review, we give an overview about the membrane lipid structures known in bacteria, the different metabolic pathways involved in their formation, and the distribution of membrane lipids and metabolic pathways across taxonomical groups.
703 citations
TL;DR: Kirschvink et al. as discussed by the authors used magnetic analyses and electron microscopy to identify the abundant presence in the brain of magnetite nanoparticles that are consistent with high-temperature formation, suggesting, therefore, an external, not internal, source.
Abstract: Biologically formed nanoparticles of the strongly magnetic mineral, magnetite, were first detected in the human brain over 20 y ago [Kirschvink JL, Kobayashi-Kirschvink A, Woodford BJ (1992) Proc Natl Acad Sci USA 89(16):7683-7687]. Magnetite can have potentially large impacts on the brain due to its unique combination of redox activity, surface charge, and strongly magnetic behavior. We used magnetic analyses and electron microscopy to identify the abundant presence in the brain of magnetite nanoparticles that are consistent with high-temperature formation, suggesting, therefore, an external, not internal, source. Comprising a separate nanoparticle population from the euhedral particles ascribed to endogenous sources, these brain magnetites are often found with other transition metal nanoparticles, and they display rounded crystal morphologies and fused surface textures, reflecting crystallization upon cooling from an initially heated, iron-bearing source material. Such high-temperature magnetite nanospheres are ubiquitous and abundant in airborne particulate matter pollution. They arise as combustion-derived, iron-rich particles, often associated with other transition metal particles, which condense and/or oxidize upon airborne release. Those magnetite pollutant particles which are <∼200 nm in diameter can enter the brain directly via the olfactory bulb. Their presence proves that externally sourced iron-bearing nanoparticles, rather than their soluble compounds, can be transported directly into the brain, where they may pose hazard to human health.
697 citations
TL;DR: The Extended Baryon Oscillation Spectroscopic Survey (eBOSS) as mentioned in this paper uses four different tracers of the underlying matter density field to expand the volume covered by BOSS and map the large-scale structures over the relatively unconstrained redshift range 0.6 0.87.
Abstract: In a six-year program started in 2014 July, the Extended Baryon Oscillation Spectroscopic Survey (eBOSS) will conduct novel cosmological observations using the BOSS spectrograph at Apache Point Observatory. These observations will be conducted simultaneously with the Time Domain Spectroscopic Survey (TDSS) designed for variability studies and the Spectroscopic Identification of eROSITA Sources (SPIDERS) program designed for studies of X-ray sources. In particular, eBOSS will measure with percent-level precision the distance-redshift relation with baryon acoustic oscillations (BAO) in the clustering of matter. eBOSS will use four different tracers of the underlying matter density field to vastly expand the volume covered by BOSS and map the large-scale-structures over the relatively unconstrained redshift range 0.6 0.6 sample of BOSS galaxies. With ~195,000 new emission line galaxy redshifts, we expect BAO measurements of d_A(z) to an accuracy of 3.1% and H(z) to 4.7% at an effective redshift of z = 0.87. A sample of more than 500,000 spectroscopically confirmed quasars will provide the first BAO distance measurements over the redshift range 0.9 2.1; these new data will enhance the precision of dA(z) and H(z) at z > 2.1 by a factor of 1.44 relative to BOSS. Furthermore, eBOSS will provide improved tests of General Relativity on cosmological scales through redshift-space distortion measurements, improved tests for non-Gaussianity in the primordial density field, and new constraints on the summed mass of all neutrino species. Here, we provide an overview of the cosmological goals, spectroscopic target sample, demonstration of spectral quality from early data, and projected cosmological constraints from eBOSS.
648 citations
Royal Botanic Garden Edinburgh1, National Autonomous University of Mexico2, University of Edinburgh3, Smithsonian Conservation Biology Institute4, National Agrarian University5, Universidade Federal de Minas Gerais6, National University of Rosario7, Pontificia Universidad Católica del Ecuador8, Spanish National Research Council9, National Museum of Natural History10, University of Los Andes11, South Colombian University12, University of Atlántico13, Venezuelan Institute for Scientific Research14, Arizona State University15, Alexander von Humboldt Biological Resources Research Institute16, Del Rosario University17, International Institute of Minnesota18, University of Antioquia19, District University of Bogotá20, National University of Salta21, Bangor University22, University of the West Indies23, Universidad del Tolima24, National University of Colombia25, Royal Botanic Gardens26, University of Pamplona27
TL;DR: Using 835 inventories covering 4660 species of woody plants, marked floristic turnover among inventories and regions indicates that numerous conservation areas across many countries will be needed to protect the full diversity of tropical dry forests.
Abstract: Seasonally dry tropical forests are distributed across Latin America and the Caribbean and are highly threatened, with less than 10% of their original extent remaining in many countries. Using 835 inventories covering 4660 species of woody plants, we show marked floristic turnover among inventories and regions, which may be higher than in other neotropical biomes, such as savanna. Such high floristic turnover indicates that numerous conservation areas across many countries will be needed to protect the full diversity of tropical dry forests. Our results provide a scientific framework within which national decision-makers can contextualize the floristic significance of their dry forest at a regional and continental scale.
473 citations
TL;DR: The semiautomatic strategy to accelerate curation, including datasets from high-throughput experiments, a novel coexpression distance to search for ‘neighborhood’ genes to known operons and regulons, and computational developments are described.
Abstract: RegulonDB (http://regulondb.ccg.unam.mx) is one of the most useful and important resources on bacterial gene regulation, as it integrates the scattered scientific knowledge of the best-characterized organism, Escherichia coli K-12, in a database that organizes large amounts of data. Its electronic format enables researchers to compare their results with the legacy of previous knowledge and supports bioinformatics tools and model building. Here, we summarize our progress with RegulonDB since our last Nucleic Acids Research publication describing RegulonDB, in 2013. In addition to maintaining curation up-to-date, we report a collection of 232 interactions with small RNAs affecting 192 genes, and the complete repertoire of 189 Elementary Genetic Sensory-Response units (GENSOR units), integrating the signal, regulatory interactions, and metabolic pathways they govern. These additions represent major progress to a higher level of understanding of regulated processes. We have updated the computationally predicted transcription factors, which total 304 (184 with experimental evidence and 120 from computational predictions); we updated our position-weight matrices and have included tools for clustering them in evolutionary families. We describe our semiautomatic strategy to accelerate curation, including datasets from high-throughput experiments, a novel coexpression distance to search for `neighborhood' genes to known operons and regulons, and computational developments.
466 citations
TL;DR: In the absolute rigidity range ∼60 to ∼500 GV, the antiproton p[over ¯], proton p, and positron e^{+} fluxes are found to have nearly identical rigidity dependence and the electron e^{-} flux exhibits a different rigidity dependent.
Abstract: A precision measurement by AMS of the antiproton flux and the antiproton-to-proton flux ratio in
primary cosmic rays in the absolute rigidity range from 1 to 450 GV is presented based on 3.49 × 105
antiproton events and 2.42 × 109 proton events. The fluxes and flux ratios of charged elementary particles
in cosmic rays are also presented. In the absolute rigidity range ∼60 to ∼500 GV, the antiproton ¯p, proton
p, and positron eþ fluxes are found to have nearly identical rigidity dependence and the electron e− flux
exhibits a different rigidity dependence. Below 60 GV, the ( ¯ p=p), ( ¯ p=eþ), and (p=eþ) flux ratios each
reaches a maximum. From ∼60 to ∼500 GV, the ( ¯ p=p), ( ¯ p=eþ), and (p=eþ) flux ratios show no rigidity
dependence. These are new observations of the properties of elementary particles in the cosmos.
464 citations
National Autonomous University of Mexico1, National Institutes of Health2, University of California, Davis3, Laura and John Arnold Foundation4, BioMed Central5, University of Texas at Austin6, Center for Open Science7, University of California, Berkeley8, University of Virginia9, Mozilla Foundation10
TL;DR: There is evidence that open research practices bring significant benefits to researchers relative to more traditional closed practices, including increases in citations, media attention, potential collaborators, job opportunities and funding opportunities.
Abstract: Open access, open data, open source and other open scholarship practices are growing in popularity and necessity. However, widespread adoption of these practices has not yet been achieved. One reason is that researchers are uncertain about how sharing their work will affect their careers. We review literature demonstrating that open research is associated with increases in citations, media attention, potential collaborators, job opportunities and funding opportunities. These findings are evidence that open research practices bring significant benefits to researchers relative to more traditional closed practices.
TL;DR: A new dimensionality reduction technique, demixed principal component analysis (dPCA), that decomposes population activity into a few components and exposes the dependence of the neural representation on task parameters such as stimuli, decisions, or rewards is demonstrated.
Abstract: Neurons in higher cortical areas, such as the prefrontal cortex, are often tuned to a variety of sensory and motor variables, and are therefore said to display mixed selectivity. This complexity of single neuron responses can obscure what information these areas represent and how it is represented. Here we demonstrate the advantages of a new dimensionality reduction technique, demixed principal component analysis (dPCA), that decomposes population activity into a few components. In addition to systematically capturing the majority of the variance of the data, dPCA also exposes the dependence of the neural representation on task parameters such as stimuli, decisions, or rewards. To illustrate our method we reanalyze population data from four datasets comprising different species, different cortical areas and different experimental tasks. In each case, dPCA provides a concise way of visualizing the data that summarizes the task-dependent features of the population response in a single figure.
TL;DR: The number of species places Mexico as the country with the fourth largest floristic richness in the world, although among the non-insular countries, by its number of endemic species (about 50%) is second only surpassed by South Africa.
Abstract: An updated inventory of the native vascular plants of Mexico records 23,314 species, distributed in 2,854 genera, 297 families, and 73 orders. The flora includes 1,039 species of ferns and lycophytes, 149 gymnosperms, and 22,126 angiosperms. On average, the number of synonyms per species is 1.3 (mode = 1). The number of species places Mexico as the country with the fourth largest floristic richness in the world, although among the non-insular countries, by its number of endemic species (about 50%) is second only surpassed by South Africa. The species distribution among higher taxonomic categories, and the richness and endemism values in the 32 states of Mexico are discussed. This compilation allows us to assess the flora's contribution to the overall Mexican biodiversity.
Queen's University1, Polytechnic University of Valencia2, Pacific Northwest National Laboratory3, Northwestern University4, Indiana University5, Saha Institute of Nuclear Physics6, Fermilab7, University of Toronto8, University of Chicago9, Université de Montréal10, Laurentian University11, Czech Technical University in Prague12, University of Alberta13, Virginia Tech14, Drexel University15, National Autonomous University of Mexico16
TL;DR: These data provide the most sensitive direct detection constraints on WIMP-proton spin-dependent scattering to date, with significant sensitivity at low W IMP masses for spin-independent WIMp-nucleon scattering.
Abstract: New results are reported from the operation of the PICO-60 dark matter detector, a bubble chamber filled with 52 kg of C_{3}F_{8} located in the SNOLAB underground laboratory. As in previous PICO bubble chambers, PICO-60 C_{3}F_{8} exhibits excellent electron recoil and alpha decay rejection, and the observed multiple-scattering neutron rate indicates a single-scatter neutron background of less than one event per month. A blind analysis of an efficiency-corrected 1167-kg day exposure at a 3.3-keV thermodynamic threshold reveals no single-scattering nuclear recoil candidates, consistent with the predicted background. These results set the most stringent direct-detection constraint to date on the weakly interacting massive particle (WIMP)-proton spin-dependent cross section at 3.4×10^{-41} cm^{2} for a 30-GeV c^{-2} WIMP, more than 1 order of magnitude improvement from previous PICO results.
Harvard University1, Yale University2, University of Bologna3, INAF4, Instituto Politécnico Nacional5, University of Hawaii6, Durham University7, University of Helsinki8, Max Planck Society9, California Institute of Technology10, University of Hawaii at Hilo11, Rochester Institute of Technology12, University of Bonn13, University of California, San Diego14, National Autonomous University of Mexico15, University of Sussex16, ETH Zurich17, National Radio Astronomy Observatory18, Institute for the Physics and Mathematics of the Universe19, University of Zagreb20, University of Copenhagen21, University of Concepción22
TL;DR: The COSMOS-Legacy survey as discussed by the authors is a 4.6Ms Chandra program that has imaged 2.2 deg2 of the COS-MOS field with an effective exposure of ≃ 160 ks over the central 1.5 deg^2 and ≃ 80 ks in the remaining area.
Abstract: The COSMOS-Legacy survey is a 4.6 Ms Chandra program that has imaged 2.2 deg2 of the COSMOS field with an effective exposure of ≃ 160 ks over the central 1.5 deg^2 and of ≃ 80 ks in the remaining area. The survey is the combination of 56 new observations obtained as an X-ray Visionary Project with the previous C-COSMOS survey. We describe the reduction and analysis of the new observations and the properties of 2273 point sources detected above a spurious probability of 2 × 10^(−5). We also present the updated properties of the C-COSMOS sources detected in the new data. The whole survey includes 4016 point sources (3814, 2920 and 2440 in the full, soft, and hard band). The limiting depths are 2.2 × 10^(−16), 1.5 × 10^(−15), and 8.9 × 10^(−16) erg cm^(-2)s^(-1) in the 0.5–2, 2–10, and 0.5–10 keV bands, respectively. The observed fraction of obscured active galactic nuclei with a column density >10^(22) cm^(−2) from the hardness ratio (HR) is 50_(-16)^(+17)%. Given the large sample we compute source number counts in the hard and soft bands, significantly reducing the uncertainties of 5%–10%. For the first time we compute number counts for obscured (HR > −0.2) and unobscured (HR < −0.2) sources and find significant differences between the two populations in the soft band. Due to the unprecedent large exposure, COSMOS-Legacy area is three times larger than surveys at similar depths and its depth is three times fainter than surveys covering similar areas. The area-flux region occupied by COSMOS-Legacy is likely to remain unsurpassed for years to come.
International Institute of Minnesota1, University of Connecticut2, University of Alabama3, University of Regina4, Wageningen University and Research Centre5, University of Puerto Rico6, National Autonomous University of Mexico7, Brown University8, University of São Paulo9, Leipzig University10, Smithsonian Tropical Research Institute11, Federal University of Pernambuco12, Tulane University13, University of Stirling14, Clemson University15, University of Alberta16, National Institute of Amazonian Research17, Colorado Mesa University18, State University of New York at Purchase19, World Agroforestry Centre20, Aarhus University21, Columbia University22, University of Minnesota23, University of California, Santa Barbara24, Pedagogical and Technological University of Colombia25, University of Maryland, College Park26, National University of Singapore27, Yale-NUS College28, University of Amsterdam29, Puerto Rico Department of Agriculture30, Museu Paraense Emílio Goeldi31, Louisiana State University32
TL;DR: This study estimates the age and spatial extent of lowland second-growth forests in the Latin American tropics and model their potential aboveground carbon accumulation over four decades to guide national-level forest-based carbon mitigation plans.
Abstract: Regrowth of tropical secondary forests following complete or nearly complete removal of forest vegetation actively stores carbon in aboveground biomass, partially counterbalancing carbon emissions from deforestation, forest degradation, burning of fossil fuels, and other anthropogenic sources. We estimate the age and spatial extent of lowland second-growth forests in the Latin American tropics and model their potential aboveground carbon accumulation over four decades. Our model shows that, in 2008, second-growth forests (1 to 60 years old) covered 2.4 million km2 of land (28.1% of the total study area). Over 40 years, these lands can potentially accumulate a total aboveground carbon stock of 8.48 Pg C (petagrams of carbon) in aboveground biomass via low-cost natural regeneration or assisted regeneration, corresponding to a total CO2 sequestration of 31.09 Pg CO2. This total is equivalent to carbon emissions from fossil fuel use and industrial processes in all of Latin America and the Caribbean from 1993 to 2014. Ten countries account for 95% of this carbon storage potential, led by Brazil, Colombia, Mexico, and Venezuela. We model future land-use scenarios to guide national carbon mitigation policies. Permitting natural regeneration on 40% of lowland pastures potentially stores an additional 2.0 Pg C over 40 years. Our study provides information and maps to guide national-level forest-based carbon mitigation plans on the basis of estimated rates of natural regeneration and pasture abandonment. Coupled with avoided deforestation and sustainable forest management, natural regeneration of second-growth forests provides a low-cost mechanism that yields a high carbon sequestration potential with multiple benefits for biodiversity and ecosystem services.
TL;DR: Use of opioid analgesics has increased, but remains low in Africa, Asia, Central America, the Caribbean, South America, and eastern and southeastern Europe.
TL;DR: Modelling with Stakeholders is updated and builds on Voinov and Bousquet, 2010, and structured mechanisms to examine and account for human biases and beliefs in participatory modelling are suggested.
Abstract: This paper updates and builds on 'Modelling with Stakeholders' Voinov and Bousquet, 2010 which demonstrated the importance of, and demand for, stakeholder participation in resource and environmental modelling. This position paper returns to the concepts of that publication and reviews the progress made since 2010. A new development is the wide introduction and acceptance of social media and web applications, which dramatically changes the context and scale of stakeholder interactions and participation. Technology advances make it easier to incorporate information in interactive formats via visualization and games to augment participatory experiences. Citizens as stakeholders are increasingly demanding to be engaged in planning decisions that affect them and their communities, at scales from local to global. How people interact with and access models and data is rapidly evolving. In turn, this requires changes in how models are built, packaged, and disseminated: citizens are less in awe of experts and external authorities, and they are increasingly aware of their own capabilities to provide inputs to planning processes, including models. The continued acceleration of environmental degradation and natural resource depletion accompanies these societal changes, even as there is a growing acceptance of the need to transition to alternative, possibly very different, life styles. Substantive transitions cannot occur without significant changes in human behaviour and perceptions. The important and diverse roles that models can play in guiding human behaviour, and in disseminating and increasing societal knowledge, are a feature of stakeholder processes today. Display Omitted Participatory modelling has become mainstream in resource and environmental management.We review recent contributions to participatory environmental modelling to identify the tools, methods and processes applied.Global internet connectivity, social media and crowdsourcing create opportunities for participatory modelling.We suggest structured mechanisms to examine and account for human biases and beliefs in participatory modelling.Advanced visualization tools, gaming, and virtual environments improve communication with stakeholders.
University of California, Berkeley1, Lawrence Berkeley National Laboratory2, Carnegie Mellon University3, Yale University4, University of Portsmouth5, New York University6, University of St Andrews7, Harvard University8, Ohio State University9, Max Planck Society10, Brookhaven National Laboratory11, Princeton University12, Open University13, University of Wisconsin-Madison14, Moscow State University15, New Mexico State University16, University of Utah17, Autonomous University of Madrid18, Case Western Reserve University19, Leibniz Institute for Astrophysics Potsdam20, University of Tokyo21, King's College22, Centre national de la recherche scientifique23, Spanish National Research Council24, Ludwig Maximilian University of Munich25, Abastumani Astrophysical Observatory26, Kansas State University27, Pennsylvania State University28, National University of La Plata29, National Scientific and Technical Research Council30, National Autonomous University of Mexico31
TL;DR: The Baryon Oscillation Spectroscopic Survey (BOSS) as discussed by the authors provides the largest survey of galaxy redshifts available to date, in terms of both the number of galaxies measured by a single survey, and the effective cosmological volume covered.
Abstract: The Baryon Oscillation Spectroscopic Survey (BOSS), part of the Sloan Digital Sky Survey (SDSS) III project, has provided the largest survey of galaxy redshifts available to date, in terms of both the number of galaxy redshifts measured by a single survey, and the effective cosmological volume covered. Key to analysing the clustering of these data to provide cosmological measurements is understanding the detailed properties of this sample. Potential issues include variations in the target catalogue caused by changes either in the targeting algorithm or properties of the data used, the pattern of spectroscopic observations, the spatial distribution of targets for which redshifts were not obtained, and variations in the target sky density due to observational systematics. We document here the target selection algorithms used to create the galaxy samples that comprise BOSS. We also present the algorithms used to create large-scale structure catalogues for the final Data Release (DR12) samples and the associated random catalogues that quantify the survey mask. The algorithms are an evolution of those used by the BOSS team to construct catalogues from earlier data, and have been designed to accurately quantify the galaxy sample. The code used, designated MKSAMPLE, is released with this paper.
University of Alberta1, Leiden University Medical Center2, University of Southern Denmark3, Charité4, Ruhr University Bochum5, National Autonomous University of Mexico6, Paris Descartes University7, University of Copenhagen8, Aarhus University Hospital9, Leeds Teaching Hospitals NHS Trust10, Ghent University Hospital11, VU University Medical Center12, Academic Medical Center13
TL;DR: The definition of a positive MRI for classification of axial SpA should continue to primarily depend on the imaging features of ‘active sacroiliitis’ until more data are available regarding MRI features of structural damage in the sacrosiliac joint and MRI features in the spine and their utility when used for classification purposes.
Abstract: Objectives To review and update the existing definition of a positive MRI for classification of axial spondyloarthritis (SpA). Methods The Assessment in SpondyloArthritis International Society (ASAS) MRI working group conducted a consensus exercise to review the definition of a positive MRI for inclusion in the ASAS classification criteria of axial SpA. Existing definitions and new data relevant to the MRI diagnosis and classification of sacroiliitis and spondylitis in axial SpA, published since the ASAS definition first appeared in print in 2009, were reviewed and discussed. The precise wording of the existing definition was examined in detail and the data and a draft proposal were presented to and voted on by the ASAS membership. Results The clear presence of bone marrow oedema on MRI in subchondral bone is still considered to be the defining observation that determines the presence of active sacroiliitis. Structural damage lesions seen on MRI may contribute to a decision by the observer that inflammatory lesions are genuinely due to SpA but are not required to meet the definition. The existing definition was clarified adding guidelines and images to assist in the application of the definition. Conclusion The definition of a positive MRI for classification of axial SpA should continue to primarily depend on the imaging features of ‘active sacroiliitis’ until more data are available regarding MRI features of structural damage in the sacroiliac joint and MRI features in the spine and their utility when used for classification purposes.
Space Telescope Science Institute1, Johns Hopkins University2, University of Kentucky3, University of Pittsburgh4, University of Wisconsin-Madison5, New Mexico State University6, Carnegie Institution for Science7, University of Chile8, New York University9, University of Utah10, Institute for the Physics and Mathematics of the Universe11, Nanjing University12, University of Texas at Austin13, Max Planck Society14, University of Iowa15, University of Washington16, National Autonomous University of Mexico17, Lawrence Berkeley National Laboratory18, Open University19, University of St Andrews20
TL;DR: In this paper, the authors describe the MaNGA Data Reduction Pipeline algorithms and centralized metadata framework that produce sky-subtracted spectrophotometrically calibrated spectra and rectified three-dimensional data cubes that combine individual dithered observations.
Abstract: Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) is an optical fiber-bundle integral-field unit (IFU) spectroscopic survey that is one of three core programs in the fourth-generation Sloan Digital Sky Survey (SDSS-IV). With a spectral coverage of 3622–10354 A and an average footprint of ~500 arcsec2 per IFU the scientific data products derived from MaNGA will permit exploration of the internal structure of a statistically large sample of 10,000 low-redshift galaxies in unprecedented detail. Comprising 174 individually pluggable science and calibration IFUs with a near-constant data stream, MaNGA is expected to obtain ~100 million raw-frame spectra and ~10 million reduced galaxy spectra over the six-year lifetime of the survey. In this contribution, we describe the MaNGA Data Reduction Pipeline algorithms and centralized metadata framework that produce sky-subtracted spectrophotometrically calibrated spectra and rectified three-dimensional data cubes that combine individual dithered observations. For the 1390 galaxy data cubes released in Summer 2016 as part of SDSS-IV Data Release 13, we demonstrate that the MaNGA data have nearly Poisson-limited sky subtraction shortward of ~8500 A and reach a typical 10σ limiting continuum surface brightness μ = 23.5 AB arcsec-2 in a five-arcsecond-diameter aperture in the g-band. The wavelength calibration of the MaNGA data is accurate to 5 km s-1 rms, with a median spatial resolution of 2.54 arcsec FWHM (1.8 kpc at the median redshift of 0.037) and a median spectral resolution of σ = 72 km s-1.
TL;DR: In this paper, the rigidity dependence of the boron to carbon flux ratio (B/C) is studied and a detailed variation with rigidity of the B=C spectral index is reported for the first time.
Abstract: Knowledge of the rigidity dependence of the boron to carbon flux ratio (B/C) is important in
understanding the propagation of cosmic rays. The precise measurement of the B=C ratio from 1.9 GV to
2.6 TV, based on 2.3 million boron and 8.3 million carbon nuclei collected by AMS during the first 5 years
of operation, is presented. The detailed variation with rigidity of the B=C spectral index is reported for the
first time. The B=C ratio does not show any significant structures in contrast to many cosmic ray models
that require such structures at high rigidities. Remarkably, above 65 GV, the B=C ratio is well described by
a single power law RΔ with index Δ ¼ −0.333 + 0.014ðfitÞ + 0.005ðsystÞ, in good agreement with the
Kolmogorov theory of turbulence which predicts Δ ¼ −1=3 asymptotically.
TL;DR: In this article, the sky localization of the first observed compact binary merger is presented, where the authors describe the low-latency analysis of the LIGO data and present a sky localization map.
Abstract: A gravitational-wave (GW) transient was identified in data recorded by the Advanced Laser Interferometer Gravitational-wave Observatory (LIGO) detectors on 2015 September 14. The event, initially designated G184098 and later given the name GW150914, is described in detail elsewhere. By prior arrangement, preliminary estimates of the time, significance, and sky location of the event were shared with 63 teams of observers covering radio, optical, near-infrared, X-ray, and gamma-ray wavelengths with ground- and space-based facilities. In this Letter we describe the low-latency analysis of the GW data and present the sky localization of the first observed compact binary merger. We summarize the follow-up observations reported by 25 teams via private Gamma-ray Coordinates Network circulars, giving an overview of the participating facilities, the GW sky localization coverage, the timeline, and depth of the observations. As this event turned out to be a binary black hole merger, there is little expectation of a detectable electromagnetic (EM) signature. Nevertheless, this first broadband campaign to search for a counterpart of an Advanced LIGO source represents a milestone and highlights the broad capabilities of the transient astronomy community and the observing strategies that have been developed to pursue neutron star binary merger events. Detailed investigations of the EM data and results of the EM follow-up campaign are being disseminated in papers by the individual teams.
TL;DR: A supportive versus permissive model is suggested, where patterns of coordinated activity, rather than the relative amount of activity in these pathways, regulate movement initiation and execution.
TL;DR: Comparisons between theoretical and experimental data confirm that modern theoretical tools are not only able to explain controversial experimental facts but also to predict chemical behavior.
Abstract: In this review, we briefly summarize the reliability of the density functional theory (DFT)-based methods to accurately predict the main antioxidant properties and the reaction mechanisms involved in the free radical-scavenging reactions of chemical compounds present in food. The analyzed properties are the bond dissociation energies, in particular those involving OH bonds, electron transfer enthalpies, adiabatic ionization potentials, and proton affinities. The reaction mechanisms are hydrogen-atom transfer, proton-coupled electron transfer, radical adduct formation, single electron transfer, sequential electron proton transfer, proton-loss electron transfer, and proton-loss hydrogen-atom transfer. Furthermore, the chelating ability of these compounds and its role in decreasing or inhibiting the oxidative stress induced by Fe(III) and Cu(II) are considered. Comparisons between theoretical and experimental data confirm that modern theoretical tools are not only able to explain controversial experimental facts but also to predict chemical behavior.
TL;DR: Results show that, forecasts made with the proposed hybrid methodology are more accurate for medium (5–23 h ahead) short term WSF and WPF than those made with persistence and autoregressive models.
TL;DR: Age-accumulation of circ RNAs in brain tissues was found to be largely independent from linear RNA expression of host genes, suggesting that circRNAs might play biological roles relevant to the aging nervous system.
Abstract: Circular RNAs (circRNAs) are a newly appreciated class of RNAs expressed across diverse phyla. These enigmatic transcripts are most commonly generated by back-splicing events from exons of protein-coding genes. This results in highly stable RNAs due to the lack of free 5' and 3' ends. CircRNAs are enriched in neural tissues, suggesting that they might have neural functions. Here, we sought to determine whether circRNA accumulation occurs during aging in mice. Total RNA-seq profiling of young (1 month old) and aged (22 month old) cortex, hippocampus and heart samples was performed. This led to the confident detection of 6,791 distinct circRNAs across these samples, including 675 novel circRNAs. Analysis uncovered a strong bias for circRNA upregulation during aging in neural tissues. These age-accumulation trends were verified for individual circRNAs by RT-qPCR and Northern analysis. In contrast, comparison of aged versus young hearts failed to reveal a global trend for circRNA upregulation. Age-accumulation of circRNAs in brain tissues was found to be largely independent from linear RNA expression of host genes. These findings suggest that circRNAs might play biological roles relevant to the aging nervous system.
TL;DR: In this article, a review of the state of the art in strain and ripple-induced effects on the electronic and optical properties of graphene is presented, with a focus on the Raman spectrum.
Abstract: This review presents the state of the art in strain and ripple-induced effects on the electronic and optical properties of graphene. It starts by providing the crystallographic description of mechanical deformations, as well as the diffraction pattern for different kinds of representative deformation fields. Then, the focus turns to the unique elastic properties of graphene, and to how strain is produced. Thereafter, various theoretical approaches used to study the electronic properties of strained graphene are examined, discussing the advantages of each. These approaches provide a platform to describe exotic properties, such as a fractal spectrum related with quasicrystals, a mixed Dirac-Schrodinger behavior, emergent gravity, topological insulator states, in molecular graphene and other 2D discrete lattices. The physical consequences of strain on the optical properties are reviewed next, with a focus on the Raman spectrum. At the same time, recent advances to tune the optical conductivity of graphene by strain engineering are given, which open new paths in device applications. Finally, a brief review of strain effects in multilayered graphene and other promising 2D materials like silicene and materials based on other group-IV elements, phosphorene, dichalcogenide- and monochalcogenide-monolayers is presented, with a brief discussion of interplays among strain, thermal effects, and illumination in the latter material family.
TL;DR: The present review describes the most recent advances in understanding the ecological functions of Trichodermaspp.