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Showing papers by "Université du Québec à Montréal published in 2016"


Journal ArticleDOI
Daniel J. Klionsky1, Kotb Abdelmohsen2, Akihisa Abe3, Joynal Abedin4  +2519 moreInstitutions (695)
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


Journal ArticleDOI
TL;DR: ROS play a central role in cell signalling as well as in regulation of the main pathways of apoptosis mediated by mitochondria, death receptors and the endoplasmic reticulum, and current understanding of the role of ROS in each of these three main pathways is focused on.

2,101 citations


Journal ArticleDOI
Jingjing Liang1, Thomas W. Crowther2, Nicolas Picard3, Susan K. Wiser4, Mo Zhou1, Giorgio Alberti5, Ernst Detlef Schulze6, A. David McGuire7, Fabio Bozzato, Hans Pretzsch8, Sergio de-Miguel, Alain Paquette9, Bruno Hérault10, Michael Scherer-Lorenzen11, Christopher B. Barrett12, Henry B. Glick2, Geerten M. Hengeveld13, Gert-Jan Nabuurs13, Sebastian Pfautsch14, Helder Viana15, Helder Viana16, Alexander Christian Vibrans, Christian Ammer17, Peter Schall17, David David Verbyla7, N. M. Tchebakova18, Markus Fischer19, James V. Watson1, Han Y. H. Chen20, Xiangdong Lei, Mart-Jan Schelhaas13, Huicui Lu13, Damiano Gianelle, Elena I. Parfenova18, Christian Salas21, Eungul Lee1, Boknam Lee22, Hyun-Seok Kim, Helge Bruelheide23, David A. Coomes24, Daniel Piotto, Terry Sunderland25, Terry Sunderland26, Bernhard Schmid27, Sylvie Gourlet-Fleury, Bonaventure Sonké28, Rebecca Tavani3, Jun Zhu29, Susanne Brandl8, Jordi Vayreda, Fumiaki Kitahara, Eric B. Searle20, Victor J. Neldner30, Michael R. Ngugi30, Christopher Baraloto31, Christopher Baraloto32, Lorenzo Frizzera, Radomir Bałazy33, Jacek Oleksyn34, Jacek Oleksyn35, Tomasz Zawiła-Niedźwiecki36, Olivier Bouriaud37, Filippo Bussotti38, Leena Finér, Bogdan Jaroszewicz39, Tommaso Jucker24, Fernando Valladares40, Fernando Valladares41, Andrzej M. Jagodziński35, Pablo Luis Peri42, Pablo Luis Peri43, Pablo Luis Peri44, Christelle Gonmadje28, William Marthy45, Timothy G. O'Brien45, Emanuel H. Martin46, Andrew R. Marshall47, Francesco Rovero, Robert Bitariho, Pascal A. Niklaus27, Patricia Alvarez-Loayza48, Nurdin Chamuya49, Renato Valencia50, Frédéric Mortier, Verginia Wortel, Nestor L. Engone-Obiang51, Leandro Valle Ferreira52, David E. Odeke, R. Vásquez, Simon L. Lewis53, Simon L. Lewis54, Peter B. Reich14, Peter B. Reich34 
West Virginia University1, Yale University2, Food and Agriculture Organization3, Landcare Research4, University of Udine5, Max Planck Society6, University of Alaska Fairbanks7, Technische Universität München8, Université du Québec à Montréal9, University of the French West Indies and Guiana10, University of Freiburg Faculty of Biology11, Cornell University12, Wageningen University and Research Centre13, University of Sydney14, Polytechnic Institute of Viseu15, University of Trás-os-Montes and Alto Douro16, University of Göttingen17, Russian Academy of Sciences18, Oeschger Centre for Climate Change Research19, Lakehead University20, University of La Frontera21, Seoul National University22, Martin Luther University of Halle-Wittenberg23, University of Cambridge24, James Cook University25, Center for International Forestry Research26, University of Zurich27, University of Yaoundé I28, University of Wisconsin-Madison29, Queensland Government30, Institut national de la recherche agronomique31, Florida International University32, Forest Research Institute33, University of Minnesota34, Polish Academy of Sciences35, Warsaw University of Life Sciences36, Ştefan cel Mare University of Suceava37, University of Florence38, University of Warsaw39, Spanish National Research Council40, King Juan Carlos University41, National Scientific and Technical Research Council42, International Trademark Association43, National University of Austral Patagonia44, Wildlife Conservation Society45, College of African Wildlife Management46, University of York47, Durham University48, Ontario Ministry of Natural Resources49, Pontificia Universidad Católica del Ecuador50, Centre national de la recherche scientifique51, Museu Paraense Emílio Goeldi52, University of Leeds53, University College London54
14 Oct 2016-Science
TL;DR: A consistent positive concave-down effect of biodiversity on forest productivity across the world is revealed, showing that a continued biodiversity loss would result in an accelerating decline in forest productivity worldwide.
Abstract: The biodiversity-productivity relationship (BPR) is foundational to our understanding of the global extinction crisis and its impacts on ecosystem functioning. Understanding BPR is critical for the accurate valuation and effective conservation of biodiversity. Using ground-sourced data from 777,126 permanent plots, spanning 44 countries and most terrestrial biomes, we reveal a globally consistent positive concave-down BPR, showing that continued biodiversity loss would result in an accelerating decline in forest productivity worldwide. The value of biodiversity in maintaining commercial forest productivity alone-US$166 billion to 490 billion per year according to our estimation-is more than twice what it would cost to implement effective global conservation. This highlights the need for a worldwide reassessment of biodiversity values, forest management strategies, and conservation priorities.

889 citations


Journal ArticleDOI
Marielle Saunois1, Philippe Bousquet1, Ben Poulter2, Anna Peregon1, Philippe Ciais1, Josep G. Canadell3, Edward J. Dlugokencky4, Giuseppe Etiope5, David Bastviken6, Sander Houweling7, Greet Janssens-Maenhout, Francesco N. Tubiello8, Simona Castaldi, Robert B. Jackson9, Mihai Alexe, Vivek K. Arora, David J. Beerling10, Peter Bergamaschi, Donald R. Blake11, Gordon Brailsford12, Victor Brovkin13, Lori Bruhwiler4, Cyril Crevoisier14, Patrick M. Crill, Kristofer R. Covey15, Charles L. Curry16, Christian Frankenberg17, Nicola Gedney18, Lena Höglund-Isaksson19, Misa Ishizawa20, Akihiko Ito20, Fortunat Joos21, Heon Sook Kim20, Thomas Kleinen13, Paul B. Krummel3, Jean-Francois Lamarque22, Ray L. Langenfelds3, Robin Locatelli1, Toshinobu Machida20, Shamil Maksyutov20, Kyle C. McDonald23, Julia Marshall13, Joe R. Melton, Isamu Morino18, Vaishali Naik24, Simon O'Doherty25, Frans-Jan W. Parmentier26, Prabir K. Patra27, Changhui Peng28, Shushi Peng1, Glen P. Peters29, Isabelle Pison1, Catherine Prigent30, Ronald G. Prinn31, Michel Ramonet1, William J. Riley32, Makoto Saito20, Monia Santini, Ronny Schroeder33, Ronny Schroeder23, Isobel J. Simpson11, Renato Spahni21, P. Steele3, Atsushi Takizawa34, Brett F. Thornton, Hanqin Tian35, Yasunori Tohjima20, Nicolas Viovy1, Apostolos Voulgarakis36, Michiel van Weele37, Guido R. van der Werf38, Ray F. Weiss39, Christine Wiedinmyer22, David J. Wilton10, Andy Wiltshire18, Doug Worthy40, Debra Wunch41, Xiyan Xu32, Yukio Yoshida20, Bowen Zhang35, Zhen Zhang2, Qiuan Zhu42 
TL;DR: The Global Carbon Project (GCP) as discussed by the authors is a consortium of multi-disciplinary scientists, including atmospheric physicists and chemists, biogeochemists of surface and marine emissions, and socio-economists who study anthropogenic emissions.
Abstract: . The global methane (CH4) budget is becoming an increasingly important component for managing realistic pathways to mitigate climate change. This relevance, due to a shorter atmospheric lifetime and a stronger warming potential than carbon dioxide, is challenged by the still unexplained changes of atmospheric CH4 over the past decade. Emissions and concentrations of CH4 are continuing to increase, making CH4 the second most important human-induced greenhouse gas after carbon dioxide. Two major difficulties in reducing uncertainties come from the large variety of diffusive CH4 sources that overlap geographically, and from the destruction of CH4 by the very short-lived hydroxyl radical (OH). To address these difficulties, we have established a consortium of multi-disciplinary scientists under the umbrella of the Global Carbon Project to synthesize and stimulate research on the methane cycle, and producing regular (∼ biennial) updates of the global methane budget. This consortium includes atmospheric physicists and chemists, biogeochemists of surface and marine emissions, and socio-economists who study anthropogenic emissions. Following Kirschke et al. (2013), we propose here the first version of a living review paper that integrates results of top-down studies (exploiting atmospheric observations within an atmospheric inverse-modelling framework) and bottom-up models, inventories and data-driven approaches (including process-based models for estimating land surface emissions and atmospheric chemistry, and inventories for anthropogenic emissions, data-driven extrapolations). For the 2003–2012 decade, global methane emissions are estimated by top-down inversions at 558 Tg CH4 yr−1, range 540–568. About 60 % of global emissions are anthropogenic (range 50–65 %). Since 2010, the bottom-up global emission inventories have been closer to methane emissions in the most carbon-intensive Representative Concentrations Pathway (RCP8.5) and higher than all other RCP scenarios. Bottom-up approaches suggest larger global emissions (736 Tg CH4 yr−1, range 596–884) mostly because of larger natural emissions from individual sources such as inland waters, natural wetlands and geological sources. Considering the atmospheric constraints on the top-down budget, it is likely that some of the individual emissions reported by the bottom-up approaches are overestimated, leading to too large global emissions. Latitudinal data from top-down emissions indicate a predominance of tropical emissions (∼ 64 % of the global budget, The most important source of uncertainty on the methane budget is attributable to emissions from wetland and other inland waters. We show that the wetland extent could contribute 30–40 % on the estimated range for wetland emissions. Other priorities for improving the methane budget include the following: (i) the development of process-based models for inland-water emissions, (ii) the intensification of methane observations at local scale (flux measurements) to constrain bottom-up land surface models, and at regional scale (surface networks and satellites) to constrain top-down inversions, (iii) improvements in the estimation of atmospheric loss by OH, and (iv) improvements of the transport models integrated in top-down inversions. The data presented here can be downloaded from the Carbon Dioxide Information Analysis Center ( http://doi.org/10.3334/CDIAC/GLOBAL_METHANE_BUDGET_2016_V1.1 ) and the Global Carbon Project.

771 citations


Journal ArticleDOI
TL;DR: In the diagnosis and assessment of hypertension, automated office blood pressure, taken without patient-health provider interaction, is now recommended as the preferred method of measuring in-office blood pressure as mentioned in this paper.

413 citations


Journal ArticleDOI
TL;DR: In this article, the authors suggest that model structures should reflect real-world processes, parameters should be calibrated to match model outputs with observations, and external forcing variables should accurately prescribe the environmental conditions that soils experience.
Abstract: Soil carbon (C) is a critical component of Earth system models (ESMs), and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the third to fifth assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C projections is of a high priority for Earth system modeling in the future IPCC and other assessments. To achieve this goal, we suggest that (1) model structures should reflect real-world processes, (2) parameters should be calibrated to match model outputs with observations, and (3) external forcing variables should accurately prescribe the environmental conditions that soils experience. First, most soil C cycle models simulate C input from litter production and C release through decomposition. The latter process has traditionally been represented by first-order decay functions, regulated primarily by temperature, moisture, litter quality, and soil texture. While this formulation well captures macroscopic soil organic C (SOC) dynamics, better understanding is needed of their underlying mechanisms as related to microbial processes, depth-dependent environmental controls, and other processes that strongly affect soil C dynamics. Second, incomplete use of observations in model parameterization is a major cause of bias in soil C projections from ESMs. Optimal parameter calibration with both pool- and flux-based data sets through data assimilation is among the highest priorities for near-term research to reduce biases among ESMs. Third, external variables are represented inconsistently among ESMs, leading to differences in modeled soil C dynamics. We recommend the implementation of traceability analyses to identify how external variables and model parameterizations influence SOC dynamics in different ESMs. Overall, projections of the terrestrial C sink can be substantially improved when reliable data sets are available to select the most representative model structure, constrain parameters, and prescribe forcing fields.

348 citations


Journal ArticleDOI
TL;DR: In this article, the authors proposed that a servant leader's attentive focus on employees' development helps fulfill employees' three basic psychological needs, namely for autonomy, competence and relatedness.
Abstract: How can a servant leader focusing primarily on followers' growth and well-being influence the achievement of organizational outcomes? Despite a growing stream of academic studies exploring positive outcomes of servant leadership practice, little is known empirically about the underlying psychological processes that are activated to enhance individual performance at work. Using the autonomous motivational framework of Self-Determination Theory's (SDT) basic psychological needs (Ryan & Deci, 2000), we propose that a servant leader's attentive focus on employees' development helps fulfill employees' three basic psychological needs, namely for autonomy , competence and relatedness . In turn, satisfaction of each of these three needs fuels employees in a distinct way, either producing an increase in task performance, organizational citizenship behaviors (OCBs) or both. We collected information from 247 supervisor–employee dyads from a large Canadian technology design and manufacturing company. Structural equation modeling results indicate that servant leadership strongly predicted all three needs' satisfaction; autonomy need satisfaction mediated servant leadership's effect on task performance, OCB-Individual (OCB-I) and OCB-Organization (OCB-O); competence need satisfaction mediated servant leadership's effect on task performance only; and relatedness need satisfaction mediated servant leadership's effect on both OCB-I and OCB-O.

344 citations


Journal ArticleDOI
TL;DR: Grounded in four theoretical positions, the present review demonstrates the empirical evidence for the incremental validity of narrative identity as a cross-sectional indicator and prospective predictor of well-being, compared with other individual difference and situational variables.
Abstract: Grounded in four theoretical positions-structural, cognitive, phenomenological, and ethical-the present review demonstrates the empirical evidence for the incremental validity of narrative identity as a cross-sectional indicator and prospective predictor of well-being, compared with other individual difference and situational variables. In doing so, we develop an organizational framework of four categories of narrative variables: (a) motivational themes, (b) affective themes, (c) themes of integrative meaning, and (d) structural elements. Using this framework, we detail empirical evidence supporting the incremental association between narrative identity and well-being, a case that is strongest for motivational, affective, and integrative meaning themes. These categories of themes serve as vital complimentary correlates and predictors of well-being, alongside commonly assessed variables such as dispositional personality traits. We then use the theoretically grounded review of the empirical literature to develop concrete areas of future research for the field.

333 citations


Journal ArticleDOI
TL;DR: Control experiments and spectroscopic studies suggest that this C-S cross-coupling reaction does not involve a Ni(0)-species, and Mechanistic investigations indicated that the reaction proceeded through transient Ni(I)-species and thiyl radicals.
Abstract: Ni-catalyzed cross-couplings of aryl, benzyl, and alkyl thiols with aryl and heteroaryl iodides were accomplished in the presence of an Ir-photoredox catalyst. Highly chemoselective C–S cross-coupling was achieved versus competitive C–O and C–N cross-couplings. This C–S cross-coupling method exhibits remarkable functional group tolerance, and the reactions can be carried out in the presence of molecular oxygen. Mechanistic investigations indicated that the reaction proceeded through transient Ni(I)-species and thiyl radicals. Distinct from nickel-catalyzed cross-coupling reactions involving carbon-centered radicals, control experiments and spectroscopic studies suggest that this C–S cross-coupling reaction does not involve a Ni(0)-species.

304 citations


Journal ArticleDOI
TL;DR: This article examined context factors as subjective perceptions made by consumers about aspects of their own situation, specifically the extent to which they perceive having more or less time, money, and power available.

296 citations


Journal ArticleDOI
TL;DR: Sociocultural knowledge and cultural competency can improve the design and delivery of interventions to promote mental health and psychosocial wellbeing of Syrians affected by armed conflict and displacement, both within Syria and in countries hosting refugees from Syria.
Abstract: AIMS: This paper is based on a report commissioned by the United Nations High Commissioner for Refugees, which aims to provide information on cultural aspects of mental health and psychosocial wellbeing relevant to care and support for Syrians affected by the crisis. This paper aims to inform mental health and psychosocial support (MHPSS) staff of the mental health and psychosocial wellbeing issues facing Syrians who are internally displaced and Syrian refugees. METHODS: We conducted a systematic literature search designed to capture clinical, social science and general literature examining the mental health of the Syrian population. The main medical, psychological and social sciences databases (e.g. Medline, PubMed, PsycInfo) were searched (until July 2015) in Arabic, English and French language sources. This search was supplemented with web-based searches in Arabic, English and French media, and in assessment reports and evaluations, by nongovernmental organisations, intergovernmental organisations and agencies of the United Nations. This search strategy should not be taken as a comprehensive review of all issues related to MHPSS of Syrians as some unpublished reports and evaluations were not reviewed. RESULTS: Conflict affected Syrians may experience a wide range of mental health problems including (1) exacerbations of pre-existing mental disorders; (2) new problems caused by conflict related violence, displacement and multiple losses; as well as (3) issues related to adaptation to the post-emergency context, for example living conditions in the countries of refuge. Some populations are particularly vulnerable such as men and women survivors of sexual or gender based violence, children who have experienced violence and exploitation and Syrians who are lesbian, gay, bisexual, transgender or intersex. Several factors influence access to MHPSS services including language barriers, stigma associated with seeking mental health care and the power dynamics of the helping relationship. Trust and collaboration can be maximised by ensuring a culturally safe environment, respectful of diversity and based on mutual respect, in which the perspectives of clients and their families can be carefully explored. CONCLUSIONS: Sociocultural knowledge and cultural competency can improve the design and delivery of interventions to promote mental health and psychosocial wellbeing of Syrians affected by armed conflict and displacement, both within Syria and in countries hosting refugees from Syria. Language: en

Journal ArticleDOI
TL;DR: Wang et al. as mentioned in this paper reported an increasing trend of greenness in the Three North region using the satellite-retrieved normalized difference vegetation index (NDVI) from GIMMS and MODIS datasets in the past 32 years.

Journal ArticleDOI
TL;DR: In this paper, the authors used the Nd isotope data to model the mafic detrital input into sedimentary basins in northern Rodinia and found that flood basalt weathering contributed to both the high average δ 13 C of seawater in the Neoproterozoic and to the initiation of the first Sturtian Snowball Earth.

Journal ArticleDOI
TL;DR: Evidence is reviewed and the biopsychosocial model is used to illustrate risk factors, mediators and moderators underlying associations between maternal depression and child outcomes in low-income and middle-income countries.

Journal ArticleDOI
TL;DR: Early results on the carbon sequestration and pest resistance potential of more diverse plantations are highlighted and suggestions are made for new, innovative experiments in understudied regions to complement the existing network.
Abstract: The area of forest plantations is increasing worldwide helping to meet timber demand and protect natural forests. However, with global change, monospecific plantations are increasingly vulnerable to abiotic and biotic disturbances. As an adaption measure we need to move to plantations that are more diverse in genotypes, species, and structure, with a design underpinned by science. TreeDivNet, a global network of tree diversity experiments, responds to this need by assessing the advantages and disadvantages of mixed species plantations. The network currently consists of 18 experiments, distributed over 36 sites and five ecoregions. With plantations 1-15 years old, TreeDivNet can already provide relevant data for forest policy and management. In this paper, we highlight some early results on the carbon sequestration and pest resistance potential of more diverse plantations. Finally, suggestions are made for new, innovative experiments in understudied regions to complement the existing network.

Journal ArticleDOI
TL;DR: This work uses data from the literature on AP and RP fractions to investigate the potential relationships of climate and growth form with total ray and axial parenchyma fractions and finds a 29‐fold variation in RAP fraction, which was more strongly related to temperature than with precipitation.
Abstract: Summary Parenchyma is an important tissue in secondary xylem of seed plants, with functions ranging from storage to defence and with effects on the physical and mechanical properties of wood. Currently, we lack a large-scale quantitative analysis of ray parenchyma (RP) and axial parenchyma (AP) tissue fractions. Here, we use data from the literature on AP and RP fractions to investigate the potential relationships of climate and growth form with total ray and axial parenchyma fractions (RAP). We found a 29-fold variation in RAP fraction, which was more strongly related to temperature than with precipitation. Stem succulents had the highest RAP values (mean ± SD: 70.2 ± 22.0%), followed by lianas (50.1 ± 16.3%), angiosperm trees and shrubs (26.3 ± 12.4%), and conifers (7.6 ± 2.6%). Differences in RAP fraction between temperate and tropical angiosperm trees (21.1 ± 7.9% vs 36.2 ± 13.4%, respectively) are due to differences in the AP fraction, which is typically three times higher in tropical than in temperate trees, but not in RP fraction. Our results illustrate that both temperature and growth form are important drivers of RAP fractions. These findings should help pave the way to better understand the various functions of RAP in plants.

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TL;DR: It is shown that scientific work is more highly divided in medical disciplines than in mathematics, physics, and disciplines of the social sciences, and that, with the exception of medicine, the writing of the paper is the task most often associated with authorship.
Abstract: Scientific authorship has been increasingly complemented with contributorship statements. While such statements are said to ensure more equitable credit and responsibility attribution, they also provide an opportunity to examine the roles and functions that authors play in the construction of knowledge and the relationship between these roles and authorship order. Drawing on a comprehensive and multidisciplinary dataset of 87,002 documents in which contributorship statements are found, this article examines the forms that division of labor takes across disciplines, the relationships between various types of contributions, as well as the relationships between the contribution types and various indicators of authors’ seniority. It shows that scientific work is more highly divided in medical disciplines than in mathematics, physics, and disciplines of the social sciences, and that, with the exception of medicine, the writing of the paper is the task most often associated with authorship. The results suggest ...

Journal ArticleDOI
TL;DR: The identification of common drivers in this large-scale ecosystem comparison suggests a basis to develop common models across aquatic and terrestrial ecosystems for C and N dynamics during decomposition.
Abstract: Summary Plant leaf litter comprises the major common source of energy and nutrients in forested soil and freshwater ecosystems world-wide. However, despite the similarity of physical and biochemical processes, generalizations across aquatic and terrestrial ecosystems regarding litter decomposition drivers remain elusive. We re-analysed data from a published field decomposition experiment conducted in two ecosystems (forest floors and streams) across five biomes (from the tropics to subarctic) with increasing decomposer community complexity (microbes, microbes and mesofauna, microbes and meso- and macrofauna). Using a wide litter quality gradient (15 litter combinations), we aimed to disentangle the roles of decomposer community complexity from that of leaf litter traits (18 traits encompassing four broad trait categories: nutrients, C quality, physical structure and stoichiometry) on litter C and N loss. Comparisons of decomposition drivers between ecosystems were evaluated across and within biomes. Differences in environmental conditions (e.g. climate, soil/water fertility) and litter nutrients – with a particular focus on Mg and Ca – across biomes were the major drivers of litter C loss in both ecosystems, but decomposer complexity also played a prominent role in streams. Within biomes, we observed consistent effects of litter nutrients and stoichiometry on litter C and N loss between ecosystems, but the effects of decomposer complexity differed between streams and forest floors in the temperate, Mediterranean and tropical biomes. Our results highlight that, beyond the litter traits commonly identified as controlling decomposition (e.g. C, N and lignin), micronutrients (e.g. Mg and Ca) can also play an important, and globally consistent, role in both aquatic and terrestrial ecosystems. In addition, in forest streams the complexity of decomposer communities had similar importance as litter traits for predicting litter C and N turnover across all five biomes. The identification of common drivers in our large-scale ecosystem comparison suggests a basis to develop common models across aquatic and terrestrial ecosystems for C and N dynamics during decomposition. Future modelling efforts should account for the global similarities (litter micronutrient effects) and biome-level differences (contingent decomposer effects) found between ecosystems.

Journal ArticleDOI
TL;DR: Results from the first tree diversity experiment that separated the effect of selection from that of complementarity by varying community composition in high-density plots along a gradient of FD, independent of species richness and testing for the effects of FD and community weighted means of traits on stem biomass increment.
Abstract: Two main effects are proposed to explain biodiversity-ecosystem functioning relationships: niche complementarity and selection effects. Both can be functionally defined using the functional diversity (FD) and functional identity (FI) of the community respectively. Herein, we present results from the first tree diversity experiment that separated the effect of selection from that of complementarity by varying community composition in high-density plots along a gradient of FD, independent of species richness and testing for the effects of FD and community weighted means of traits (a proxy for FI) on stem biomass increment (a proxy for productivity). After 4 years of growth, most mixtures did not differ in productivity from the averages of their respective monocultures, but some did overyield significantly. Those positive diversity effects resulted mostly from selection effects, primarily driven by fast-growing deciduous species and associated traits. Net diversity effect did not increase with time over 4 years.

Journal ArticleDOI
TL;DR: It is demonstrated that host species identity is a stronger driver of temperate tree phyllosphere bacterial communities than site or time.
Abstract: The increasing awareness of the role of phyllosphere microbial communities in plant health calls for a greater understanding of their structure and dynamics in natural ecosystems. Since most knowledge of tree phyllosphere bacterial communities has been gathered in tropical forests, our goal was to characterize the community structure and assembly dynamics of phyllosphere epiphytic bacterial communities in temperate forests in Quebec, Canada. We targeted five dominant tree species: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea, and Picea glauca. We collected 180 samples of phyllosphere communities on these species at four natural forest sites, three times during the growing season. Host functional traits (i.e., wood density, leaf nitrogen content) and climate variables (summer mean temperature and precipitation) were strongly correlated with community structure. We highlight three key findings: (1) temperate tree species share a “core microbiome”; (2) significant evolutionary associations exist between groups of bacteria and host species; and (3) a greater part of the variation in phyllosphere bacterial community assembly is explained by host species identity (27 %) and species-site interaction (14 %), than by site (11 %) or time (1 %). We demonstrated that host species identity is a stronger driver of temperate tree phyllosphere bacterial communities than site or time. Our results suggest avenues for future studies on the influence of host functional traits on phyllosphere community functional biogeography across terrestrial biomes.

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TL;DR: This work investigates the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Québec and shows that both hydrology and local water chemistry interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams toward larger rivers and lakes dominated by fewer taxa.
Abstract: Disentangling the mechanisms shaping bacterioplankton communities across freshwater ecosystems requires considering a hydrologic dimension that can influence both dispersal and local sorting, but how the environment and hydrology interact to shape the biogeography of freshwater bacterioplankton over large spatial scales remains unexplored. Using Illumina sequencing of the 16S ribosomal RNA gene, we investigate the large-scale spatial patterns of bacterioplankton across 386 freshwater systems from seven distinct regions in boreal Quebec. We show that both hydrology and local water chemistry (mostly pH) interact to shape a sequential structuring of communities from highly diverse assemblages in headwater streams toward larger rivers and lakes dominated by fewer taxa. Increases in water residence time along the hydrologic continuum were accompanied by major losses of bacterial richness and by an increased differentiation of communities driven by local conditions (pH and other related variables). This suggests that hydrology and network position modulate the relative role of environmental sorting and mass effects on community assembly by determining both the time frame for bacterial growth and the composition of the immigrant pool. The apparent low dispersal limitation (that is, the lack of influence of geographic distance on the spatial patterns observed at the taxonomic resolution used) suggests that these boreal bacterioplankton communities derive from a shared bacterial pool that enters the networks through the smallest streams, largely dominated by mass effects, and that is increasingly subjected to local sorting of species during transit along the hydrologic continuum.

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TL;DR: The PRISM4 reconstruction of the mid-Piacenzian (∼∼ 3 Ma) is presented in this paper, containing data for paleogeography, land and sea ice, sea-surface temperature, vegetation, soils, and lakes.
Abstract: . The mid-Piacenzian is known as a period of relative warmth when compared to the present day. A comprehensive understanding of conditions during the Piacenzian serves as both a conceptual model and a source for boundary conditions as well as means of verification of global climate model experiments. In this paper we present the PRISM4 reconstruction, a paleoenvironmental reconstruction of the mid-Piacenzian ( ∼ 3 Ma) containing data for paleogeography, land and sea ice, sea-surface temperature, vegetation, soils, and lakes. Our retrodicted paleogeography takes into account glacial isostatic adjustments and changes in dynamic topography. Soils and lakes, both significant as land surface features, are introduced to the PRISM reconstruction for the first time. Sea-surface temperature and vegetation reconstructions are unchanged but now have confidence assessments. The PRISM4 reconstruction is being used as boundary condition data for the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2) experiments.


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TL;DR: The state of knowledge of the main mechanisms, and their associated traits, that underpin the ability of boreal and temperate tree species to persist and (or) shift their distribution in a changing climate are reviewed.
Abstract: The integration of functional traits into vulnerability assessments is a promising approach to quantitatively capture differences in species sensitivity and adaptive capacity to climate change, all...

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Karri Silventoinen1, Karri Silventoinen2, Aline Jelenkovic3, Aline Jelenkovic1, Reijo Sund, Yoon-Mi Hur4, Yoshie Yokoyama5, Chika Honda2, Jacob vB Hjelmborg, Sören Möller, Syuichi Ooki6, Sari Aaltonen1, Fuling Ji7, Feng Ning7, Zengchang Pang7, Esther Rebato3, Andreas Busjahn, Christian Kandler8, Kimberly J. Saudino9, Kerry L. Jang10, Wendy Cozen11, Amie E. Hwang11, Thomas M. Mack11, Wenjing Gao12, Canqing Yu12, Liming Li12, Robin P. Corley, Brooke M. Huibregtse, Kaare Christensen, Axel Skytthe, Kirsten Ohm Kyvik13, Catherine Derom14, Robert F. Vlietinck15, Ruth J. F. Loos16, Kauko Heikkilä1, Jane Wardle17, Clare H. Llewellyn17, Abigail Fisher17, Tom A. McAdams18, Tom A. McAdams17, Thalia C. Eley18, Alice M. Gregory19, Mingguang He20, Mingguang He21, Xiaohu Ding21, Morten Bjerregaard-Andersen22, Henning Beck-Nielsen, Morten Sodemann23, Adam Domonkos Tarnoki24, David Laszlo Tarnoki24, Maria A. Stazi25, Corrado Fagnani25, Cristina D'Ippolito25, Ariel Knafo-Noam26, David Mankuta26, Lior Abramson26, S. Alexandra Burt27, Kelly L. Klump27, Judy L. Silberg, Lindon J. Eaves, Hermine H. Maes28, Robert F. Krueger29, Matt McGue29, Shandell Pahlen29, Margaret Gatz11, David A. Butler30, Meike Bartels31, Toos C. E. M. van Beijsterveldt31, Jeffrey M. Craig32, Jeffrey M. Craig20, Richard Saffery32, Richard Saffery20, Duarte L. Freitas33, José Maia34, Lise Dubois35, Michel Boivin36, Michel Boivin37, Mara Brendgen38, Ginette Dionne37, Frank Vitaro39, Nicholas G. Martin, Sarah E. Medland, Grant W. Montgomery40, Youngsook Chong41, Gary E. Swan42, Ruth Krasnow43, Patrik K. E. Magnusson, Nancy L. Pedersen, Per Tynelius44, Paul Lichtenstein, Claire M. A. Haworth45, Robert Plomin18, Gombojav Bayasgalan, Danshiitsoodol Narandalai46, K. Paige Harden47, Elliot M. Tucker-Drob47, Sevgi Y. Öncel48, Fazil Aliev28, Tim D. Spector18, Massimo Mangino18, Genevieve Lachance18, Laura A. Baker11, Catherine Tuvblad11, Catherine Tuvblad49, Glen E. Duncan50, Dedra Buchwald50, Gonneke Willemsen31, Finn Rasmussen44, Jack H. Goldberg51, Thorkild I. A. Sørensen45, Dorret I. Boomsma31, Jaakko Kaprio1, Jaakko Kaprio52 
University of Helsinki1, Osaka University2, University of the Basque Country3, Mokpo National University4, Osaka City University5, Ishikawa Prefectural Nursing University6, Centers for Disease Control and Prevention7, Bielefeld University8, Boston University9, University of British Columbia10, University of Southern California11, Peking University12, University of Southern Denmark13, Ghent University14, Katholieke Universiteit Leuven15, Icahn School of Medicine at Mount Sinai16, University College London17, King's College London18, Goldsmiths, University of London19, University of Melbourne20, Sun Yat-sen University21, Bandim Health Project22, Odense University Hospital23, Semmelweis University24, Istituto Superiore di Sanità25, Hebrew University of Jerusalem26, Michigan State University27, Virginia Commonwealth University28, University of Minnesota29, National Academy of Sciences30, VU University Amsterdam31, Royal Children's Hospital32, University of Madeira33, University of Porto34, University of Ottawa35, Tomsk State University36, Laval University37, Université du Québec à Montréal38, Université de Montréal39, QIMR Berghofer Medical Research Institute40, Pusan National University41, Stanford University42, Oklahoma State University Center for Health Sciences43, Karolinska Institutet44, University of Bristol45, Hiroshima University46, University of Texas at Austin47, Kırıkkale University48, Örebro University49, Washington State University50, University of Washington51, National Institute for Health and Welfare52
TL;DR: In this article, the authors analyzed the genetic and environmental contributions to BMI variation from infancy to early adulthood and the ways they differ by sex and geographic regions representing high (North America and Australia), moderate (Europe), and low levels (East Asia) of obesogenic environments.

Journal ArticleDOI
Aline Jelenkovic1, Aline Jelenkovic2, Reijo Sund2, Yoon-Mi Hur3, Yoshie Yokoyama4, Jacob v. B. Hjelmborg5, Sören Möller5, Chika Honda6, Patrik K. E. Magnusson7, Nancy L. Pedersen7, Syuichi Ooki8, Sari Aaltonen2, Maria A. Stazi9, Corrado Fagnani9, Cristina D'Ippolito9, Duarte L. Freitas10, José Maia11, Fuling Ji12, Feng Ning12, Zengchang Pang12, Esther Rebato1, Andreas Busjahn, Christian Kandler13, Kimberly J. Saudino14, Kerry L. Jang15, Wendy Cozen16, Amie E. Hwang16, Thomas M. Mack16, Wenjing Gao17, Canqing Yu17, Liming Li17, Robin P. Corley18, Brooke M. Huibregtse18, Catherine Derom19, Catherine Derom20, Robert F. Vlietinck20, Ruth J. F. Loos21, Kauko Heikkilä2, Jane Wardle22, Clare H. Llewellyn22, Abigail Fisher22, Tom A. McAdams23, Thalia C. Eley23, Alice M. Gregory24, Mingguang He25, Xiaohu Ding26, Morten Bjerregaard-Andersen27, Henning Beck-Nielsen5, Morten Sodemann5, Adam Domonkos Tarnoki, David Laszlo Tarnoki, Ariel Knafo-Noam28, David Mankuta28, Lior Abramson28, S. Alexandra Burt29, Kelly L. Klump29, Judy L. Silberg30, Lindon J. Eaves30, Hermine H. Maes30, Robert F. Krueger31, Matt McGue31, Shandell Pahlen31, Margaret Gatz16, David A. Butler32, Meike Bartels33, Toos C. E. M. van Beijsterveldt33, Jeffrey M. Craig25, Richard Saffery25, Lise Dubois34, Michel Boivin35, Michel Boivin36, Mara Brendgen37, Ginette Dionne35, Frank Vitaro38, Nicholas G. Martin39, Sarah E. Medland39, Grant W. Montgomery39, Gary E. Swan40, Ruth Krasnow41, Per Tynelius7, Paul Lichtenstein7, Claire M. A. Haworth42, Robert Plomin23, Gombojav Bayasgalan, Danshiitsoodol Narandalai43, K. Paige Harden44, Elliot M. Tucker-Drob44, Tim D. Spector45, Massimo Mangino45, Genevieve Lachance45, Laura A. Baker16, Catherine Tuvblad16, Catherine Tuvblad46, Glen E. Duncan47, Dedra Buchwald47, Gonneke Willemsen33, Axel Skytthe5, Kirsten Ohm Kyvik5, Kaare Christensen5, Sevgi Y. Öncel48, Fazil Aliev30, Finn Rasmussen7, Jack H. Goldberg49, Thorkild I. A. Sørensen50, Dorret I. Boomsma33, Jaakko Kaprio2, Karri Silventoinen2, Karri Silventoinen6 
TL;DR: Comparing geographic-cultural regions, genetic variance was greatest in North-America and Australia and lowest in East-Asia, but the relative proportion of genetic variation was roughly similar across these regions.
Abstract: Height variation is known to be determined by both genetic and environmental factors, but a systematic description of how their influences differ by sex, age and global regions is lacking. We conducted an individual-based pooled analysis of 45 twin cohorts from 20 countries, including 180,520 paired measurements at ages 1-19 years. The proportion of height variation explained by shared environmental factors was greatest in early childhood, but these effects remained present until early adulthood. Accordingly, the relative genetic contribution increased with age and was greatest in adolescence (up to 0.83 in boys and 0.76 in girls). Comparing geographic-cultural regions (Europe, North-America and Australia, and East-Asia), genetic variance was greatest in North-America and Australia and lowest in East-Asia, but the relative proportion of genetic variation was roughly similar across these regions. Our findings provide further insights into height variation during childhood and adolescence in populations representing different ethnicities and exposed to different environments.

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TL;DR: It is suggested that N addition will increase soil C storage and plant C in both above- and below-ground parts, indicating that terrestrial ecosystems might act to strengthen as a C sink under increasing N deposition.
Abstract: Elevated nitrogen (N) deposition alters the terrestrial carbon (C) cycle, which is likely to feed back to further climate change. However, how the overall terrestrial ecosystem C pools and fluxes respond to N addition remains unclear. By synthesizing data from multiple terrestrial ecosystems, we quantified the response of C pools and fluxes to experimental N addition using a comprehensive meta-analysis method. Our results showed that N addition significantly stimulated soil total C storage by 5.82% ([2.47%, 9.27%], 95% CI, the same below) and increased the C contents of the above- and below-ground parts of plants by 25.65% [11.07%, 42.12%] and 15.93% [6.80%, 25.85%], respectively. Furthermore, N addition significantly increased aboveground net primary production by 52.38% [40.58%, 65.19%] and litterfall by 14.67% [9.24%, 20.38%] at a global scale. However, the C influx from the plant litter to the soil through litter decomposition and the efflux from the soil due to microbial respiration and soil respiration showed insignificant responses to N addition. Overall, our meta-analysis suggested that N addition will increase soil C storage and plant C in both above- and below-ground parts, indicating that terrestrial ecosystems might act to strengthen as a C sink under increasing N deposition.

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TL;DR: In this article, the authors measured metabolism in 14 rivers (discharge range 14-84m3 s−1) in the Western and Midwestern United States (US) and estimated gross primary productivity (GPP) and ecosystem respiration (ER), and gas exchange rates using a Lagrangian, 2-station oxygen model solved in a Bayesian framework.
Abstract: Ecosystem metabolism, that is, gross primary productivity (GPP) and ecosystem respiration (ER), controls organic carbon (OC) cycling in stream and river networks and is expected to vary predictably with network position. However, estimates of metabolism in small streams outnumber those from rivers such that there are limited empirical data comparing metabolism across a range of stream and river sizes. We measured metabolism in 14 rivers (discharge range 14–84 m3 s−1) in the Western and Midwestern United States (US). We estimated GPP, ER, and gas exchange rates using a Lagrangian, 2-station oxygen model solved in a Bayesian framework. GPP ranged from 0.6–22 g O2 m−2 d−1 and ER tracked GPP, suggesting that autotrophic production supports much of riverine ER in summer. Net ecosystem production, the balance between GPP and ER was 0 or greater in 4 rivers showing autotrophy on that day. River velocity and slope predicted gas exchange estimates from these 14 rivers in agreement with empirical models. Carbon turnover lengths (that is, the distance traveled before OC is mineralized to CO2) ranged from 38 to 1190 km, with the longest turnover lengths in high-sediment, arid-land rivers. We also compared estimated turnover lengths with the relative length of the river segment between major tributaries or lakes; the mean ratio of carbon turnover length to river length was 1.6, demonstrating that rivers can mineralize much of the OC load along their length at baseflow. Carbon mineralization velocities ranged from 0.05 to 0.81 m d−1, and were not different than measurements from small streams. Given high GPP relative to ER, combined with generally short OC spiraling lengths, rivers can be highly reactive with regard to OC cycling.

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TL;DR: There is a movement across empirical disciplines, and now within ecology and evolution, to shape editorial policies to better promote transparency, by either requiring more disclosure by scientists or by developing incentives to encourage disclosure.
Abstract: To make progress scientists need to know what other researchers have found and how they found it. However, transparency is often insufficient across much of ecology and evolution. Researchers often fail to report results and methods in detail sufficient to permit interpretation and meta-analysis, and many results go entirely unreported. Further, these unreported results are often a biased subset. Thus the conclusions we can draw from the published literature are themselves often biased and sometimes might be entirely incorrect. Fortunately there is a movement across empirical disciplines, and now within ecology and evolution, to shape editorial policies to better promote transparency. This can be done by either requiring more disclosure by scientists or by developing incentives to encourage disclosure.

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TL;DR: The Roaring compressed bitmap format as mentioned in this paper uses packed arrays for compression instead of RLE, and it has been shown to be faster than RLE-based bitmap compression.
Abstract: Bitmap indexes are commonly used in databases and search engines. By exploiting bit-level parallelism, they can significantly accelerate queries. However, they can use much memory, and thus, we might prefer compressed bitmap indexes. Following Oracle's lead, bitmaps are often compressed using run-length encoding RLE. Building on prior work, we introduce the Roaring compressed bitmap format: it uses packed arrays for compression instead of RLE. We compare it to two high-performance RLE-based bitmap encoding techniques: Word Aligned Hybrid compression scheme and Compressed 'n' Composable Integer Set. On synthetic and real data, we find that Roaring bitmaps 1 often compress significantly better e.g., 2× and 2 are faster than the compressed alternatives up to 900× faster for intersections. Our results challenge the view that RLE-based bitmap compression is best. Copyright © 2015 John Wiley & Sons, Ltd.