#1 An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV Link logo PDF logo

Byng, James; Chase, Mark; Christenhusz, Maarten; Fay, Michael; Judd, Walter; Mabberley, David; Sennikov, Alexander Nikolaevich; Soltis, Douglas; Soltis, Pamela; Stevens, Peter; ,

Botanical Journal of the Linnean Society Volume 181, Issue 1, Pages n/a–n/a

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  • 1 news
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  • 2089 Mendeley readers


#2 Food-related Gamification: Literature Review PDF logo

Kaisa Könnölä, Tuomas Ranti, Tapani N. Liukkonen, Tuomas Mäkilä

33rd Hawaii International Conference on System Sciences

  • 19 tweets
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  • 1 news
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  • 1867 Mendeley readers


#3 Exploring Online Self-presentation in Computer-mediated environments - Motives and Reasons for Photo-tagging and untagging Open access logo Link logo PDF logo

Dhir, Amandeep

Journal of Computer-Mediated Communication Volume 11, Issue 2, Pages 415–441

  • 8 tweets
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  • 3 news
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  • 645 Mendeley readers


#4 Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity PDF logo

Zhernakova, Alexandra; Kurilshikov, Alexander; Bonder, Marc Jan; Tigchelaar, Ettje F.; Schirmer, Melanie; Vatanen, Tommi; Mujagic, Zlatan; Vila, Arnau Vich; Falony, Gwen; Vieira-Silva, Sara; Wang, Jun; Imhann, Floris; Brandsma, Eelke; Jankipersadsing, Soesma A.; Joossens, Marie; Cenit, Maria Carmen; Deelen, Patrick; Swertz, Morris A.; Weersma, Rinse K.; Feskens, Edith J M

Science Volume 352, Issue 6285, Pages 565–569

  • 271 tweets
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Deep sequencing of the gut microbiomes of 1135 participants from a Dutch population-based cohort shows relations between the microbiome and 126 exogenous and intrinsic host factors, including 31 intrinsic factors, 12 diseases, 19 drug groups, 4 smoking categories, and 60 dietary factors. These factors collectively explain 18.7% of the variation seen in the interindividual distance of microbial composition. We could associate 110 factors to 125 species and observed that fecal chromogranin A (CgA), a protein secreted by enteroendocrine cells, was exclusively associated with 61 microbial species whose abundance collectively accounted for 53% of microbial composition. Low CgA concentrations were seen in individuals with a more diverse microbiome. These results are an important step toward a better understanding of environment-diet-microbe-host interactions.


#5 Challenging games help students learn: An empirical study on engagement, flow and immersion in game-based learning Link logo

Hamari; Juho; Shernoff; David J.; Rowe; Elizabeth; Coller; Brianno; Asbell-Clarke; Jodi; Edwards; Teon

Computers in Human Behavior

  • 6 tweets
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#6 Wellness Routines with Wearable Activity Trackers: A Systematic Review Link logo PDF logo

Muhammad Usman Warraich

International Journal of Behavioral Nutrition and Physical Activity Volume 12, Issue 1

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Consumer-wearable activity trackers are electronic devices used for monitoring fitness- and other health-related metrics. The purpose of this systematic review was to summarize the evidence for validity and reliability of popular consumer-wearable activity trackers (Fitbit and Jawbone) and their ability to estimate steps, distance, physical activity, energy expenditure, and sleep. Searches included only full-length English language studies published in PubMed, Embase, SPORTDiscus, and Google Scholar through July 31, 2015. Two people reviewed and abstracted each included study. In total, 22 studies were included in the review (20 on adults, 2 on youth). For laboratory-based studies using step counting or accelerometer steps, the correlation with tracker-assessed steps was high for both Fitbit and Jawbone (Pearson or intraclass correlation coefficients (CC) > =0.80). Only one study assessed distance for the Fitbit, finding an over-estimate at slower speeds and under-estimate at faster speeds. Two field-based studies compared accelerometry-assessed physical activity to the trackers, with one study finding higher correlation (Spearman CC 0.86, Fitbit) while another study found a wide range in correlation (intraclass CC 0.36-0.70, Fitbit and Jawbone). Using several different comparison measures (indirect and direct calorimetry, accelerometry, self-report), energy expenditure was more often under-estimated by either tracker. Total sleep time and sleep efficiency were over-estimated and wake after sleep onset was under-estimated comparing metrics from polysomnography to either tracker using a normal mode setting. No studies of intradevice reliability were found. Interdevice reliability was reported on seven studies using the Fitbit, but none for the Jawbone. Walking- and running-based Fitbit trials indicated consistently high interdevice reliability for steps (Pearson and intraclass CC 0.76-1.00), distance (intraclass CC 0.90-0.99), and energy expenditure (Pearson and intraclass CC 0.71-0.97). When wearing two Fitbits while sleeping, consistency between the devices was high. This systematic review indicated higher validity of steps, few studies on distance and physical activity, and lower validity for energy expenditure and sleep. The evidence reviewed indicated high interdevice reliability for steps, distance, energy expenditure, and sleep for certain Fitbit models. As new activity trackers and features are introduced to the market, documentation of the measurement properties can guide their use in research settings.


#7 The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea Open access logo

OLSEN JL, ROUZÉ P, VERHELST B, LIN Y-C, BAYER T, COLLEN J, DATTOLO E, DE PAOLI E, DITTAMI S, MAUMUS F, MICHEL G, KERSTING A, LAURITANO C, LOHAUS R, TÖPEL M, TONON T, VANNESTE K, AMIREBRAHIMI M, BRAKEL J, BOSTRÖM C, CHOVATIA M, GRIMWOOD J, JENKINS JW, JÜTERBOCK A, MRAZ A, STAM WT, TICE H, BORNBERG-BAUER E, GREEN P, PEARSON GA, PROCCACINI G, DUARTE CM, SCHMUTZ J, REUSCH TBH & VAN DE PEER, Y

Nature Volume 530, Issue 7590, Pages 331–335

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Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.


#8 The Halogen Bond Link logo

Milani, Roberto;Resnati, Giuseppe;Metrangolo, Pierangelo;Priimägi, Arri;Pilati, Tullio;Terraneo, Giancarlo;Cavallo, Gabriella;

Chemical Reviews

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The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.


#9 What is the animal doing? Tools for exploring behavioural structure in animal movements Link logo PDF logo

Gurarie, Eliezer; Bracis, Chloe; Delgado, Maria; Meckley, Trevor D.; Kojola, Ilpo; Wagner, C. Michael

Journal of Animal Ecology Volume 85, Issue 1, Pages 69–84

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1.Movement data provide a window - often our only window - into the cognitive, social and biological processes that underlie the behavioral ecology of animals in the wild. Robust methods for identifying and interpreting distinct modes of movement behavior are of great importance, but complicated by the fact that movement data are complex, multivariate, and dependent. Many different approaches to exploratory analysis of movement have been developed to answer similar questions and practitioners are often at a loss for how to choose an appropriate tool for a specific question. 2.We apply and compare four methodological approaches: first passage time (FPT), Bayesian partitioning of Markov models (BPMM), behavioral change point analysis (BCPA), and a fitted multi-state random walk (MRW) to three simulated tracks and two animal trajectories - a sea lamprey (Petromyzon marinus) tracked for 12 hours and a wolf (Canis lupus) tracked for one year. 3.The simulations - in which, respectively, velocity, tortuosity, and spatial bias change - highlight the sensitivity of all methods to model misspecification. Methods that do not account for autocorrelation in the movement variables lead to spurious change points while methods that do not account for spatial bias completely miss changes in orientation. We make suggestions towards unifying directions for methodological advances. 4.When applied to the animal data, the methods broadly agree on the structure of the movement behaviors. Important discrepancies, however, reect differences in the assumptions and nature of the outputs. Important trade-offs are between the strength of the a priori assumptions (low in BCPA, high in MRW), complexity of output (high in the BCPA, low in the BPMM and MRW), and explanatory potential (highest in the MRW). 5.The animal track analysis suggests some general principles for the exploratory analysis of movement data, including ways to exploit the strengths of the various methods. We argue for close and detailed exploratory analysis of movement before fitting complex movement models. This article is protected by copyright. All rights reserved.


#10 The effect of host genetics on the gut microbiome

Bonder, Marc Jan; Kurilshikov, Alexander; Tigchelaar, Ettje F.; Mujagic, Zlatan; Imhann, Floris; Vila, Arnau Vich; Deelen, Patrick; Vatanen, Tommi; Schirmer, Melanie; Smeekens, Sanne P.; Zhernakova, Daria V.; Jankipersadsing, Soesma A.; Jaeger, Martin; Oosting, Marije; Cenit, Maria Carmen; Masclee, Ad A M; Swertz, Morris A.; Li, Yang; Kumar, Vinod; Joosten, Leo

Nature Genetics Volume 48, Issue 11, Pages 1407–1412

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The gut microbiome is affected by multiple factors, including genetics. In this study, we assessed the influence of host genetics on microbial species, pathways and gene ontology categories, on the basis of metagenomic sequencing in 1,514 subjects. In a genome-wide analysis, we identified associations of 9 loci with microbial taxonomies and 33 loci with microbial pathways and gene ontology terms at P < 5 × 10(-8). Additionally, in a targeted analysis of regions involved in complex diseases, innate and adaptive immunity, or food preferences, 32 loci were identified at the suggestive level of P < 5 × 10(-6). Most of our reported associations are new, including genome-wide significance for the C-type lectin molecules CLEC4F-CD207 at 2p13.3 and CLEC4A-FAM90A1 at 12p13. We also identified association of a functional LCT SNP with the Bifidobacterium genus (P = 3.45 × 10(-8)) and provide evidence of a gene-diet interaction in the regulation of Bifidobacterium abundance. Our results demonstrate the importance of understanding host-microbe interactions to gain better insight into human health.


#11 Consistent response of bird populations to climate change on two continents Link logo PDF logo

Stephens, Philip A.; Mason, Lucy R.; Green, Rhys E.; Gregory, Richard D.; Sauer, John R.; Alison, Jamie; Aunins, Ainars; Brotons, Lluis; Butchart, Stuart H. M.; Campedelli, Tommaso; Chodkiewicz, Tomasz; Chylarecki, Przemyslaw; Crowe, Olivia; Elts, Jaanus; Escandell, Virginia; Foppen, Ruud P. B.; Heldbjerg, Henning; Herrando, Sergi; Husby, Magne; Jiguet, Frédéric

Science Volume 352, Issue 6281, Pages 84–87

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Global climate change is a major threat to biodiversity. Large-scale analyses have generally focused on the impacts of climate change on the geographic ranges of species and on phenology, the timing of ecological phenomena. We used long-term monitoring of the abundance of breeding birds across Europe and the United States to produce, for both regions, composite population indices for two groups of species: those for which climate suitability has been either improving or declining since 1980. The ratio of these composite indices, the climate impact indicator (CII), reflects the divergent fates of species favored or disadvantaged by climate change. The trend in CII is positive and similar in the two regions. On both continents, interspecific and spatial variation in population abundance trends are well predicted by climate suitability trends.


#12 Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes? Open access logo Link logo PDF logo

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnauld; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.;

Frontiers in Microbiology

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Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.


#13 Where Is Current Research on Blockchain Technology? - A Systematic Review Open access logo PDF logo

Yli-Huumo, Jesse; Ko, Deokoon; Choi, Sujin; Park, Sooyong; Smolander, Kari

PLoS ONE Volume 11, Issue 10

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Blockchain is a decentralized transaction and data management technology developed first for Bitcoin cryptocurrency. The interest in Blockchain technology has been increasing since the idea was coined in 2008. The reason for the interest in Blockchain is its central attributes that provide security, anonymity and data integrity without any third party organization in control of the transactions, and therefore it creates interesting research areas, especially from the perspective of technical challenges and limitations. In this research, we have conducted a systematic mapping study with the goal of collecting all relevant research on Blockchain technology. Our objective is to understand the current research topics, challenges and future directions regarding Blockchain technology from the technical perspective. We have extracted 41 primary papers from scientific databases. The results show that focus in over 80% of the papers is on Bitcoin system and less than 20% deals with other Blockchain applications including e.g. smart contracts and licensing. The majority of research is focusing on revealing and improving limitations of Blockchain from privacy and security perspectives, but many of the proposed solutions lack concrete evaluation on their effectiveness. Many other Blockchain scalability related challenges including throughput and latency have been left unstudied. On the basis of this study, recommendations on future research directions are provided for researchers.


#14 Timing, rates and spectra of human germline mutation Link logo

Rahbari, Raheleh; Wuster, Arthur; Lindsay, Sarah J.; Hardwick, Robert J.; Alexandrov, Ludmil B.; Al Turki, Saeed; Dominiczak, Anna; Morris, Andrew; Porteous, David; Smith, Blair; Stratton, Michael R.; Hurles, Matthew E.; , ; Paunio, Tiina

Nature Genetics Volume 48, Issue 2, Pages 126–133

  • 115 tweets
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Germline mutations are a driving force behind genome evolution and genetic disease. We investigated genome-wide mutation rates and spectra in multi-sibling families. The mutation rate increased with paternal age in all families, but the number of additional mutations per year differed by more than twofold between families. Meta-analysis of 6,570 mutations showed that germline methylation influences mutation rates. In contrast to somatic mutations, we found remarkable consistency in germline mutation spectra between the sexes and at different paternal ages. In parental germ line, 3.8% of mutations were mosaic, resulting in 1.3% of mutations being shared by siblings. The number of these shared mutations varied significantly between families. Our data suggest that the mutation rate per cell division is higher during both early embryogenesis and differentiation of primordial germ cells but is reduced substantially during post-pubertal spermatogenesis. These findings have important consequences for the recurrence risks of disorders caused by de novo mutations.


#15 Advancing Urban Ecology toward a Science of Cities Link logo PDF logo

McPhearson, Timon; Pickett, Steward T. A.; Grimm, Nancy B.; Niemelä, Jari; Alberti, Marina; Elmqvist, Thomas; Weber, Christiane; Haase, Dagmar; Breuste, Juergen; Qureshi, Salman

BioScience Volume 66, Issue 3, Pages biw002–212

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#16 Projecting Global Biodiversity Indicators under Future Development Scenarios Open access logo Link logo PDF logo

Visconti, Piero; Bakkenes, Michel; Baisero, Daniele; Brooks, Thomas; Butchart, Stuart H. M.; Joppa, Lucas; Alkemade, Rob; Di Marco, Moreno; Santini, Luca; Hoffmann, Michael; Maiorano, Luigi; Pressey, Robert L.; Arponen, Anni; Boitani, Luigi; Reside, April E.; van Vuuren, Detlef P.; Rondinini, Carlo

Conservation Letters Volume 9, Issue 1, Pages 5–13

  • 101 tweets
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#17 Macro- and Microevolution of Languages: Exploring Linguistic Divergence with Approaches from Evolutionary Biology. Open access logo Link logo PDF logo

Honkola. Terhi

Journal of Evolutionary Biology Volume 15, Issue 5, Pages 688–701

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#18 Nutrient enrichment modifies temperature-biodiversity relationships in large-scale field experiments Open access logo Link logo

Wang, Jianjun; Pan, Feiyan; Soininen, Janne Henrik; Heino, Jani; Shen, Ji

Nature Communications

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Pagerank, a network-based diffusion algorithm, has emerged as the leading method to rank web content, ecological species and even scientists. Despite its wide use, it remains unknown how the structure of the network on which it operates affects its performance. Here we show that for random networks the ranking provided by pagerank is sensitive to perturbations in the network topology, making it unreliable for incomplete or noisy systems. In contrast, in scale-free networks we predict analytically the emergence of super-stable nodes whose ranking is exceptionally stable to perturbations. We calculate the dependence of the number of super-stable nodes on network characteristics and demonstrate their presence in real networks, in agreement with the analytical predictions. These results not only deepen our understanding of the interplay between network topology and dynamical processes but also have implications in all areas where ranking has a role, from science to marketing.


#19 Community detection in networks: A user guide Open access logo Link logo PDF logo

Fortunato, Santo; Hric, Darko

Physics Reports

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#20 Opportunities and needs for logged usage data analytics of complex industrial systems Link logo

Väätäjä Heli; Heimonen Tomi; Tiitinen Katariina; Hakulinen Jaakko; Turunen Markku; Nieminen Harri; Paunonen Hannu; Ruotsalainen Jouni; Oksanen Jaakko; Lindborg Iiro

Industrial Management & Data Systems Volume 109, Issue 2, Pages 155–172

  • 1 tweet
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#21 Fine-scale life-history structure in a highly mobile marine fish

Roney, Nancy E.; Hutchings, Jeffrey A.; Olsen, Esben Moland; Knutsen, Halvor; Albretsen, Jon; Kuparinen, Anna

Molecular Ecology Volume 10, Issue 12, Pages 2849–2866

  • 192 Mendeley readers

The identification of incipient ecological species represents an opportunity to investigate current evolutionary process where adaptive divergence and reproductive isolation are associated. In this study we analysed the genetic structure of marine and estuarine populations of the silverside fish Odontesthes argentinensis using nine microsatellite loci and 396 bp of the mitochondrial DNA (mtDNA) control region. Our main objective was to investigate the relationship among estuarine colonization, divergent selection and speciation in silversides. Significant genetic structure was detected among all marine and estuarine populations. Despite the low phylogeographic structure in mtDNA haplotypes, there was clear signal of local radiations of haplotypes in more ancient populations. Divergence among marine populations was interpreted as a combined result of homing behaviour, isolation by distance and drift. On the other hand, ecological shifts due to the colonization of estuarine habitats seem to have promoted rapid adaptive divergence and reproductive isolation in estuarine populations, which were considered as incipient ecological species. This conclusion is supported by the existence of a set of environmental factors required for successful reproduction of estuarine ecotypes. The pattern of genetic structure indicates that phenotypic and reproductive divergence evolved in the face of potential gene flow between populations. We suggest that the 'divergence-with-gene-flow' model of speciation may account for the diversification of estuarine populations. The approach used can potentially identify 'incipient estuarine species', being relevant to the investigation of the evolutionary relationships of silversides in several coastal regions of the world.


#22 A gap analysis of Internet-of-Things platforms Link logo PDF logo

Mineraud, Julien; Mazhelis, Oleksiy; Su, Xiang; Tarkoma, Sasu

Computer Communications

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#23 Succinate Dehydrogenase Supports Metabolic Repurposing of Mitochondria to Drive Inflammatory Macrophages Link logo PDF logo

Mills, Evanna L.; Kelly, Beth; Logan, Angela; Costa, Ana S. H.; Varma, Mukund; Bryant, Clare E.; Tourlomousis, Panagiotis; Dabritz, J. Henry M.; Gottlieb, Eyal; Latorre, Isabel; Corr, Sinead C.; McManus, Gavin; Ryan, Dylan; Jacobs, Howard T.; Szibor, Marten; Xavier, Ramnik J.; Braun, Thomas; Frezza, Christian; Murphy, Michael P.; O'Neill, Luke A.

Cell Volume 167, Issue 2

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Activated macrophages undergo metabolic reprogramming, which drives their pro-inflammatory phenotype, but the mechanistic basis for this remains obscure. Here, we demonstrate that upon lipopolysaccharide (LPS) stimulation, macrophages shift from producing ATP by oxidative phosphorylation to glycolysis while also increasing succinate levels. We show that increased mitochondrial oxidation of succinate via succinate dehydrogenase (SDH) and an elevation of mitochondrial membrane potential combine to drive mitochondrial reactive oxygen species (ROS) production. RNA sequencing reveals that this combination induces a pro-inflammatory gene expression profile, while an inhibitor of succinate oxidation, dimethyl malonate (DMM), promotes an anti-inflammatory outcome. Blocking ROS production with rotenone by uncoupling mitochondria or by expressing the alternative oxidase (AOX) inhibits this inflammatory phenotype, with AOX protecting mice from LPS lethality. The metabolic alterations that occur upon activation of macrophages therefore repurpose mitochondria from ATP synthesis to ROS production in order to promote a pro-inflammatory state.


#24 Banning Trophy Hunting Will Exacerbate Biodiversity Loss Link logo PDF logo

Di Minin, Enrico; Leader-Williams, Nigel; Bradshaw, Corey J. A.

Trends in Ecology & Evolution Volume 31, Issue 2, Pages 99–102

  • 115 tweets
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International pressure to ban trophy hunting is increasing. However, we argue that trophy hunting can be an important conservation tool, provided it can be done in a controlled manner to benefit biodiversity conservation and local people. Where political and governance structures are adequate, trophy hunting can help address the ongoing loss of species.


#25 Global priorities for national carnivore conservation under land use change Open access logo Link logo

Di Minin, Enrico; Slotow, Rob; Hunter, Luke; Montesino-Pouzols, Federico; Toivonen, Tuuli Kaarina; Verburg, Peter; Leader-Williams, Nigel; Petracca, Lisa; Moilanen, Atte Jaakko

Scientific Reports

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Mammalian carnivores have suffered the biggest range contraction among all biodiversity and are particularly vulnerable to habitat loss and fragmentation. Therefore, we identified priority areas for the conservation of mammalian carnivores, while accounting for species-specific requirements for connectivity and expected agricultural and urban expansion. While prioritizing for carnivores only, we were also able to test their effectiveness as surrogates for 23,110 species of amphibians, birds, mammals and reptiles and 867 terrestrial ecoregions. We then assessed the risks to carnivore conservation within each country that makes a contribution to global carnivore conservation. We found that land use change will potentially lead to important range losses, particularly amongst already threatened carnivore species. In addition, the 17% of land targeted for protection under the Aichi Target 11 was found to be inadequate to conserve carnivores under expected land use change. Our results also highlight that land use change will decrease the effectiveness of carnivores to protect other threatened species, especially threatened amphibians. In addition, the risk of human-carnivore conflict is potentially high in countries where we identified spatial priorities for their conservation. As meeting the global biodiversity target will be inadequate for carnivore protection, innovative interventions are needed to conserve carnivores outside protected areas to compliment any proposed expansion of the protected area network.


#26 Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers Link logo

Spencer, Sarah J; Tamminen, Manu V; Preheim, Sarah P; Guo, Mira T; Briggs, Adrian W; Brito, Ilana L; A Weitz, David; Pitkanen, Leena K; Vigneault, Francois; Virta, Marko P. Juhani; Alm, Eric J

ISME Journal: Multidisciplinary Journal of Microbial Ecology Volume 10, Issue 2, Pages 427–436

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Many microbial communities are characterized by high genetic diversity. 16S ribosomal RNA sequencing can determine community members, and metagenomics can determine the functional diversity, but resolving the functional role of individual cells in high throughput remains an unsolved challenge. Here, we describe epicPCR (Emulsion, Paired Isolation and Concatenation PCR), a new technique that links functional genes and phylogenetic markers in uncultured single cells, providing a throughput of hundreds of thousands of cells with costs comparable to one genomic library preparation. We demonstrate the utility of our technique in a natural environment by profiling a sulfate-reducing community in a freshwater lake, revealing both known sulfate reducers and discovering new putative sulfate reducers. Our method is adaptable to any conserved genetic trait and translates genetic associations from diverse microbial samples into a sequencing library that answers targeted ecological questions. Potential applications include identifying functional community members, tracing horizontal gene transfer networks and mapping ecological interactions between microbial cells.The ISME Journal advance online publication, 22 September 2015; doi:10.1038/ismej.2015.124.


#27 Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC PDF logo

Vehtari, Aki; Gelman, Andrew; Gabry, Jonah

Statistics and Computing

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#28 Challenges and success factors for large-scale agile transformations A systematic literature review Open access logo

Dikert, Kim; Paasivaara, Maria; Lassenius, Casper

Journal of Systems & Software

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#29 Back to the future of soil metagenomics Open access logo Link logo

Nesme, Joseph; Achouak, Wafa; Agathos, Spiros N.; Bailey, Mark J.; Baldrian, Petr et al.,

Frontiers in Microbiology

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#30 A global spectral library to characterize the world's soil

Viscarra Rossel, R.A.; Behrens, T.; Ben-Dor, E.; Brown, D.J.; Demattê, J.A.M.; Shepherd, K.D.; Shi, Z.; Stenberg, B.; Stevens, A.; Adamchuk, V.; Aïchi, H.; Barthès, B. G.; Bartholomeus, H. M.; Bayer, A.; D.; Bernoux, M.; Böttcher, Kristin; Brodský, L

Earth-Science Reviews

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#31 Evolutionary signals of selection on cognition from the great tit genome and methylome Open access logo Link logo

Laine V.N., Gossmann T.I., Schachtschneider K.M., Garroway C.J., Madsen O., Verhoeven K.J.F, de Jager V., Megens H.-J., Warren W.C., Minx P., Crooijmans R.P.M.A., Corcoran P., Adriaensen F., Belda E., Bushuev A., Cichon M., Charmantier A., Dingemanse N., Doligez B., Eeva T., Erikstad K.E., Fedorov S., Hau M., Hille S., Hinde C., Kempenaers B., Kerimov A., Krist M., Mänd R., Matthysen E., Nager R., Norte C., Orell M., Richner H., Slagsvold T., Tilgar V., Tinbergen J., Török J., Tschirren B., Yuta T., Sheldon B.C., Slate J., Zeng K., van Oers K., Visser M.E., Groenen M.A.M.

Nature Communications

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For over 50 years, the great tit (Parus major) has been a model species for research in evolutionary, ecological and behavioural research; in particular, learning and cognition have been intensively studied. Here, to provide further insight into the molecular mechanisms behind these important traits, we de novo assemble a great tit reference genome and whole-genome re-sequence another 29 individuals from across Europe. We show an overrepresentation of genes related to neuronal functions, learning and cognition in regions under positive selection, as well as increased CpG methylation in these regions. In addition, great tit neuronal non-CpG methylation patterns are very similar to those observed in mammals, suggesting a universal role in neuronal epigenetic regulation which can affect learning-, memory- and experience-induced plasticity. The high-quality great tit genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species.


#32 Planet Hunters IX. KIC 8462852-where's the flux? Link logo PDF logo

Boyajian, T. S.; LaCourse, D. M.; Rappaport, S. A.; Fabrycky, D.; Fischer, D. A.; Gandolfi, D.; Kennedy, G. M.; Korhonen, H.; Liu, M. C.; Moor, A.; Olah, K.; Vida, K.; Wyatt, M. C.; Best, W. M. J.; Brewer, J.; Ciesla, F.; Csak, B.; Deeg, H. J.; Dupuy, T. J.; Handler, G.

arXiv Volume 457, Issue 4, Pages 3988–4004

  • 517 tweets
  • 81 blog posts
  • 284 news
  • 6 references in Wikipedia
  • 171 Mendeley readers


#33 Viral modulation of host cell anti-apoptotic mechanisms and cellular stress to promote viral pathogenesis

Viiliäinen, Johanna Kaarina

Cell Host & Microbe (Science Direct) Volume 3, Issue 6, Pages 375–387

  • 1 reference in Wikipedia
  • 170 Mendeley readers


#34 Biotic homogenization can decrease landscape-scale forest multifunctionality PDF logo

van der Plas, Fons; Manning, Pete; Soliveres, Santiago; Allan, Eric; Scherer-Lorenzen, Michael; Verheyen, Kris; Wirth, Christian; Zavala, Miguel A.; Ampoorter, Evy; Baeten, Lander; Barbaro, Luc; Bauhus, Jürgen; Benavides, Raquel; Benneter, Adam; Bonal, Da

Proceedings of the National Academy of Sciences of the United States of America Volume 113, Issue 13, Pages 201517903–3562

  • 68 tweets
  • 12 news
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Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystem functions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species (α-diversity) and their turnover between plots (β-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between α-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between β-diversity and landscape-scale multifunctionality were always positive, because a high spatial turnover in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality.


#35 Enhanced seasonal CO2 exchange caused by amplified plant productivity in northern ecosystems Link logo PDF logo

Forkel, Matthias; Carvalhais, Nuno; Rödenbeck, Christian; Keeling, Ralph; Heimann, Martin; Thonicke, Kirsten; Zaehle, Sönke; Reichstein, Markus

Science

  • 105 tweets
  • 2 news
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Atmospheric monitoring of high northern latitudes (> 40°N) has shown an enhanced seasonal cycle of carbon dioxide (CO2) since the 1960s but the underlying mechanisms are not yet fully understood. The much stronger increase in high latitudes compared to low ones suggests that northern ecosystems are experiencing large changes in vegetation and carbon cycle dynamics. Here we show that the latitudinal gradient of the increasing CO2 amplitude is mainly driven by positive trends in photosynthetic carbon uptake caused by recent climate change and mediated by changing vegetation cover in northern ecosystems. Our results emphasize the importance of climate-vegetation-carbon cycle feedbacks at high latitudes, and indicate that during the last decades photosynthetic carbon uptake has reacted much more strongly to warming than carbon release processes.


#36 Framing the concept of satellite remote sensing essential biodiversity variables : challenges and future directions PDF logo

Pettorelli, Nathalie; Wegmann, Martin; Skidmore, Andrew; Mücher, Sander; Dawson, Terence P.; Fernandez, Miguel; Lucas, Richard; Schaepman, Michael E.; Wang, Tiejun; O'Connor, Brian; Jongman, Robert H.G.; Kempeneers, Pieter; Sonnenschein, Ruth; Leidner, A

Remote Sensing in Ecology and Conservation Volume 2, Issue 3, Pages n/a–n/a

  • 120 tweets
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  • 163 Mendeley readers


#37 Understanding the dominant controls on litter decomposition Link logo PDF logo

Bradford, Mark A.; Berg, Björn; Maynard, Daniel S.; Wieder, William R.; Wood, Stephen A.

Journal of Ecology Volume 104, Issue 1, Pages 229–238

  • 34 tweets
  • 1 blog post
  • 162 Mendeley readers


#38 A reference panel of 64,976 haplotypes for genotype imputation Link logo

McCarthy, Shane; Das, Sayantan; Kretzschmar, Warren; Delaneau, Olivier; Wood, Andrew R.; Teumer, Alexander; Kang, Hyun Min; Fuchsberger, Christian; Danecek, Petr; Sharp, Kevin; Luo, Yang; Sidorel, Carlo; Kwong, Alan; Timpson, Nicholas; Koskinen, Seppo; Vrieze, Scott; Scott, Laura J.; Zhang, He; Mahajan, Anubha; Veldink, Jan

Nature Genetics

  • 192 tweets
  • 1 blog post
  • 10 news
  • 157 Mendeley readers

We describe a reference panel of 64,976 human haplotypes at 39,235,157 SNPs constructed using whole-genome sequence data from 20 studies of predominantly European ancestry. Using this resource leads to accurate genotype imputation at minor allele frequencies as low as 0.1% and a large increase in the number of SNPs tested in association studies, and it can help to discover and refine causal loci. We describe remote server resources that allow researchers to carry out imputation and phasing consistently and efficiently.


#39 Extending the Technology Acceptance Model with Personal Innovativeness and Technology Readiness : A Comparison of Three Models Link logo

Koivisto, Kerttuli;Makkonen, Markus;Frank, Lauri;Riekkinen, Janne

Information Technology and Management Volume 50, Issue 4, Pages 154–161

  • 152 Mendeley readers


#40 Green economy and related concepts : An overview

Loiseau, Eleonore; Saikku, Laura; Antikainen, Riina; Droste, Nils; Hansjürgens, Bernd; Pitkänen, Kati; Leskinen, Pekka; Kuikman, Peter; Thomsen , Marianne

Journal of Cleaner Production

  • 151 Mendeley readers


#41 The role of low-volatility organic compounds in initial particle growth in the atmosphere Link logo

Troestl, Jasmin; Chuang, Wayne K.; Gordon, Hamish; Heinritzi, Martin; Yan, Chao; Molteni, Ugo; Ahlm, Lars; Frege, Carla; Bianchi, Federico; Wagner, Robert; Simon, Mario; Lehtipalo, Katrianne; Williamson, Christina; Craven, Jill S.; Duplissy, Jonathan; Adamov, Alexey; Almeida, Joao; Bernhammer, Anne-Kathrin; Breitenlechner, Martin; Brilke, Sophia

Nature Volume 533, Issue 7604, Pages 527–531

  • 39 tweets
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  • 53 news
  • 151 Mendeley readers

About half of present-day cloud condensation nuclei originate from atmospheric nucleation, frequently appearing as a burst of new particles near midday. Atmospheric observations show that the growth rate of new particles often accelerates when the diameter of the particles is between one and ten nanometres. In this critical size range, new particles are most likely to be lost by coagulation with pre-existing particles, thereby failing to form new cloud condensation nuclei that are typically 50 to 100 nanometres across. Sulfuric acid vapour is often involved in nucleation but is too scarce to explain most subsequent growth, leaving organic vapours as the most plausible alternative, at least in the planetary boundary layer. Although recent studies predict that low-volatility organic vapours contribute during initial growth, direct evidence has been lacking. The accelerating growth may result from increased photolytic production of condensable organic species in the afternoon, and the presence of a possible Kelvin (curvature) effect, which inhibits organic vapour condensation on the smallest particles (the nano-Köhler theory), has so far remained ambiguous. Here we present experiments performed in a large chamber under atmospheric conditions that investigate the role of organic vapours in the initial growth of nucleated organic particles in the absence of inorganic acids and bases such as sulfuric acid or ammonia and amines, respectively. Using data from the same set of experiments, it has been shown that organic vapours alone can drive nucleation. We focus on the growth of nucleated particles and find that the organic vapours that drive initial growth have extremely low volatilities (saturation concentration less than 10(-4.5) micrograms per cubic metre). As the particles increase in size and the Kelvin barrier falls, subsequent growth is primarily due to more abundant organic vapours of slightly higher volatility (saturation concentrations of 10(-4.5) to 10(-0.5) micrograms per cubic metre). We present a particle growth model that quantitatively reproduces our measurements. Furthermore, we implement a parameterization of the first steps of growth in a global aerosol model and find that concentrations of atmospheric cloud concentration nuclei can change substantially in response, that is, by up to 50 per cent in comparison with previously assumed growth rate parameterizations.


#42 Ion-induced nucleation of pure biogenic particles Link logo

Kirkby, Jasper; Duplissy, Jonathan; Sengupta, Kamalika; Frege, Carla; Gordon, Hamish; Williamson, Christina; Heinritzi, Martin; Simon, Mario; Yan, Chao; Almeida, Joao; Troestl, Jasmin; Nieminen, Tuomo; Ortega, Ismael K.; Wagner, Robert; Adamov, Alexey; Amorim, Antonio; Bernhammer, Anne-Kathrin; Bianchi, Federico; Breitenlechner, Martin; Brilke, Sophia

Nature Volume 533, Issue 7604, Pages 521–526

  • 84 tweets
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  • 53 news
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Atmospheric aerosols and their effect on clouds are thought to be important for anthropogenic radiative forcing of the climate, yet remain poorly understood. Globally, around half of cloud condensation nuclei originate from nucleation of atmospheric vapours. It is thought that sulfuric acid is essential to initiate most particle formation in the atmosphere, and that ions have a relatively minor role. Some laboratory studies, however, have reported organic particle formation without the intentional addition of sulfuric acid, although contamination could not be excluded. Here we present evidence for the formation of aerosol particles from highly oxidized biogenic vapours in the absence of sulfuric acid in a large chamber under atmospheric conditions. The highly oxygenated molecules (HOMs) are produced by ozonolysis of α-pinene. We find that ions from Galactic cosmic rays increase the nucleation rate by one to two orders of magnitude compared with neutral nucleation. Our experimental findings are supported by quantum chemical calculations of the cluster binding energies of representative HOMs. Ion-induced nucleation of pure organic particles constitutes a potentially widespread source of aerosol particles in terrestrial environments with low sulfuric acid pollution.


#43 Metasurfaces From microwaves to visible

Glybovski, Stanislav B.; Tretiakov, Sergei; Belov, Pavel A.; Kivshar, Yuri S.; Simovski, Constantin R.

Physics Reports

  • 1 tweet
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#44 Jack-of-all-trades effects drive biodiversity-ecosystem multifunctionality relationships in European forests Open access logo Link logo

van der Plas, Fons; Manning, Peter; Allan, Eric; Scherer-Lorenzen, Michael; Verheyen, Kris; Wirth, Christian; Zavala, Miguel A.; Hector, Andy; Ampoorter, Evy; Baeten, Lander; Barbaro, Luc; Bauhus, Jürgen; Benavides, Raquel; Benneter, Adam; Berthold, Felix

Nature Communications

  • 64 tweets
  • 9 news
  • 142 Mendeley readers

There is considerable evidence that biodiversity promotes multiple ecosystem functions (multifunctionality), thus ensuring the delivery of ecosystem services important for human well-being. However, the mechanisms underlying this relationship are poorly understood, especially in natural ecosystems. We develop a novel approach to partition biodiversity effects on multifunctionality into three mechanisms and apply this to European forest data. We show that throughout Europe, tree diversity is positively related with multifunctionality when moderate levels of functioning are required, but negatively when very high function levels are desired. For two well-known mechanisms, 'complementarity' and 'selection', we detect only minor effects on multifunctionality. Instead a third, so far overlooked mechanism, the 'jack-of-all-trades' effect, caused by the averaging of individual species effects on function, drives observed patterns. Simulations demonstrate that jack-of-all-trades effects occur whenever species effects on different functions are not perfectly correlated, meaning they may contribute to diversity-multifunctionality relationships in many of the world's ecosystems.


#45 Plant vascular development:from early specification to differentiation Link logo

De Rybel, Bert; Mähonen, Ari Pekka; Helariutta, Yrjö; Weijers, Dolf

Nature Reviews Molecular Cell Biology Volume 17, Issue 1, Pages 30–40

  • 17 tweets
  • 142 Mendeley readers

Vascular tissues in plants are crucial to provide physical support and to transport water, sugars and hormones and other small signalling molecules throughout the plant. Recent genetic and molecular studies have identified interconnections among some of the major signalling networks that regulate plant vascular development. Using Arabidopsis thaliana as a model system, these studies enable the description of vascular development from the earliest tissue specification events during embryogenesis to the differentiation of phloem and xylem tissues. Moreover, we propose a model for how oriented cell divisions give rise to a three-dimensional vascular bundle within the root meristem.


#46 Uncovering hidden spatial structure in species communities with spatially explicit joint species distribution models Link logo PDF logo

Ovaskainen, Otso; Roy, David B.; Fox, Richard; Anderson, Barbara J.

Methods in Ecology and Evolution Volume 7, Issue 4, Pages 428–436

  • 51 tweets
  • 4 blog posts
  • 140 Mendeley readers


#47 Understanding the ecology and evolution of host-parasite interactions across scales Open access logo Link logo PDF logo

Penczykowski, Rachel M.; Laine, Anna-Liisa; Koskella, Britt

Evolutionary Applications Volume 9, Issue 1, Pages 37–52

  • 46 tweets
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Predicting the emergence, spread and evolution of parasites within and among host populations requires insight to both the spatial and temporal scales of adaptation, including an understanding of within-host up through community-level dynamics. Although there are very few pathosystems for which such extensive data exist, there has been a recent push to integrate studies performed over multiple scales or to simultaneously test for dynamics occurring across scales. Drawing on examples from the literature, with primary emphasis on three diverse host-parasite case studies, we first examine current understanding of the spatial structure of host and parasite populations, including patterns of local adaptation and spatial variation in host resistance and parasite infectivity. We then explore the ways to measure temporal variation and dynamics in host-parasite interactions and discuss the need to examine change over both ecological and evolutionary timescales. Finally, we highlight new approaches and syntheses that allow for simultaneous analysis of dynamics across scales. We argue that there is great value in examining interplay among scales in studies of host-parasite interactions.


#48 Women's reproductive success and the preference for Dark Triad in men's faces PDF logo

Urszula M. Marcinkowska, Minna T. Lyons, Samuli Helle

Evolution & Human Behavior Volume 37, Issue 4, Pages 287–292

  • 31 tweets
  • 4 blog posts
  • 12 news
  • 134 Mendeley readers


#49 Genome-wide analysis identifies 12 loci influencing human reproductive behavior Link logo

Barban, Nicola; Jansen, Rick; de Vlaming, Ronald; Vaez, Ahmad; Mandemakers, Jornt J.; Tropf, Felix C.; Shen, Xia; Wilson, James F.; Chasman, Daniel I.; Nolte, Illa M.; Tragante, Vinicius; van der Laan, Sander W.; Perry, John R. B.; Kong, Augustine; Ahluwalia, Tarunveer S.; Albrecht, Eva; Yerges-Armstrong, Laura; Atzmon, Gil; Auro, Kirsi; Ayers, Kristin

Nature Genetics

  • 187 tweets
  • 5 blog posts
  • 71 news
  • 134 Mendeley readers

The genetic architecture of human reproductive behavior-age at first birth (AFB) and number of children ever born (NEB)-has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified, and the underlying mechanisms of AFB and NEB are poorly understood. We report a large genome-wide association study of both sexes including 251,151 individuals for AFB and 343,072 individuals for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study and 4 additional loci associated in a gene-based effort. These loci harbor genes that are likely to have a role, either directly or by affecting non-local gene expression, in human reproduction and infertility, thereby increasing understanding of these complex traits.


#50 Partial least squares path modeling Time for some serious second thoughts

Rönkkö, Mikko; McIntosh, Cameron N.; Antonakis, John; Edwards, Jeffrey R.

Journal of Operations Management

  • 20 tweets
  • 1 reference in Wikipedia
  • 133 Mendeley readers


#51 Population genomic evidence for adaptive differentiation in the Baltic Sea herring Link logo PDF logo

Guo, Baocheng; Li, Zitong; Merilä, Juha

Molecular Ecology Volume 25, Issue 12, Pages 2833–2852

  • 5 tweets
  • 132 Mendeley readers

Detecting and estimating the degree of genetic differentiation among populations of highly mobile marine fish having pelagic larval stages is challenging because their effective population sizes can be large, and thus, little genetic drift and differentiation is expected in neutral genomic sites. However, genomic sites subject to directional selection stemming from variation in local environmental conditions can still show substantial genetic differentiation, yet these signatures can be hard to detect with low-throughput approaches. Using a pooled RAD-seq approach we investigated genome-wide patterns of genetic variability and differentiation within and among 20 populations of Atlantic herring in the Baltic Sea (and adjacent Atlantic sites), where previous low-throughput studies and/or studies based on few populations have found limited evidence for genetic differentiation. Stringent quality control was applied in the filtering of 1 791 254 SNPs, resulting in a final dataset of 68 182 polymorphic loci. Clear differentiation was identified between Atlantic and Baltic populations in many genomic sites, while differentiation within the Baltic Sea area was weaker and geographically less structured. However, outlier analyses - whether including all populations or only those within the Baltic Sea - uncovered hundreds of directionally selected loci in which variability was associated with either salinity, temperature, or both. Hence, our results support the view that although the degree of genetic differentiation among Baltic Sea herring populations is low, there are many genomic regions showing elevated divergence, apparently as a response to temperature- and salinity-related natural selection. As such, the results add to the increasing evidence of local adaptation in highly mobile marine organisms, and those in the young Baltic Sea in particular. This article is protected by copyright. All rights reserved.


#52 A systematic map of ecosystem services assessments around European agroforestry

Fagerholm N., Plieninger T., Torallaba M., Burgess P. J

Ecological Indicators

  • 3 tweets
  • 131 Mendeley readers


#53 Van der Waals interactions and the limits of isolated atom models at interfaces Open access logo Link logo

Shigeki Kawai, Adam S. Foster, Torbjörn Björkman, Sylwia Nowakowska, Jonas Björk, Filippo Federici Canova, Lutz H. Gade, Thomas A. Jung, Ernst Meyer

Nature Communications

  • 14 tweets
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  • 36 news
  • 130 Mendeley readers

Van der Waals forces are among the weakest, yet most decisive interactions governing condensation and aggregation processes and the phase behaviour of atomic and molecular matter. Understanding the resulting structural motifs and patterns has become increasingly important in studies of the nanoscale regime. Here we measure the paradigmatic van der Waals interactions represented by the noble gas atom pairs Ar-Xe, Kr-Xe and Xe-Xe with a Xe-functionalized tip of an atomic force microscope at low temperature. Individual rare gas atoms were fixed at node sites of a surface-confined two-dimensional metal-organic framework. We found that the magnitude of the measured force increased with the atomic radius, yet detailed simulation by density functional theory revealed that the adsorption induced charge redistribution strengthened the van der Waals forces by a factor of up to two, thus demonstrating the limits of a purely atomic description of the interaction in these representative systems.


#54 Towards understanding the organisation of metacommunities in highly dynamic ecological systems PDF logo

Datry, Thibault; Bonada, Núria; Heino, Jani

Oikos Volume 125, Issue 2, Pages 149–159

  • 15 tweets
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  • 128 Mendeley readers


#55 Impact of bacterial-fungal interactions on the colonization of the endosphere PDF logo

van Overbeek, Leonard S.; Saikkonen, Kari

Trends in Plant Science

  • 12 tweets
  • 128 Mendeley readers

Research on different endophyte taxa and the related scientific disciplines have largely developed separately, and comprehensive community-level studies on bacterial and fungal interactions and their importance are lacking. Here, we discuss the transmission modes of bacteria and fungi and the nature of their interactions in the endosphere at both the molecular and physiological level. Mixed-community biofilms in the endosphere may have a role in protecting endophytes against encountered stresses, such as from plant defense systems. However, transmission from static (in biofilms) to free-living (planktonic) forms may be crucial for the exploration of new habitable spaces in plants. Important features previously recognized as plant-microbe interactions or antagonism in endophyte genomes and metagenomes are proposed to have essential roles in the modulation of endophyte communities.


#56 Epigenetic mutations can both help and hinder adaptive evolution Link logo PDF logo

Kronholm, Ilkka;Collins, Sinéad

Molecular Ecology Volume 25, Issue 8, Pages 1856–1868

  • 6 tweets
  • 128 Mendeley readers

Epigenetic variation is being integrated into our understanding of adaptation, yet we lack models on how epigenetic mutations affect evolution that includes de novo genetic change. We model the effects of epigenetic mutations on the dynamics and endpoints of adaptive walks - a process where a series of beneficial mutations move a population towards a fitness optimum. We use an individual based model of an asexual population, where mutational effects are drawn from Fisher's geometric model. We find cases where epigenetic mutations speed adaptation or result in populations with higher fitness. However, we also find cases where they slow adaptation or result in populations with lower fitness. The effect of epigenetic mutations on adaptive walks depends crucially on their stability and fitness effects relative to genetic mutations, with small-effect epigenetic mutations generally speeding adaptation, and epigenetic mutations with the same fitness effects as genetic mutations slowing adaptation. Our work reveals a complex relationship between epigenetic mutations and natural selection, and highlights the need for empirical data. This article is protected by copyright. All rights reserved.


#57 TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions Link logo PDF logo

Martinez-Reyes Immaculada; Diebold Lauren P; Kong Heywon; Schieber Michael; Huang He; Hensley Christopher T; Mehta Manan M; Wang Tianyuan; Santos Janine H; Woychik Richard; Dufour Eric; Spelbrink Johannes N; Weinberg Samuel E; Zhao Yingming; DeBerardinis Ralph J; Chandel Navdeep S

Molecular Cell Volume 61, Issue 2

  • 15 tweets
  • 1 blog post
  • 125 Mendeley readers

Mitochondrial metabolism is necessary for the maintenance of oxidative TCA cycle function and mitochondrial membrane potential. Previous attempts to decipher whether mitochondria are necessary for biological outcomes have been hampered by genetic and pharmacologic methods that simultaneously disrupt multiple functions linked to mitochondrial metabolism. Here, we report that inducible depletion of mitochondrial DNA (ρ(ο) cells) diminished respiration, oxidative TCA cycle function, and the mitochondrial membrane potential, resulting in diminished cell proliferation, hypoxic activation of HIF-1, and specific histone acetylation marks. Genetic reconstitution only of the oxidative TCA cycle function specifically in these inducible ρ(ο) cells restored metabolites, resulting in re-establishment of histone acetylation. In contrast, genetic reconstitution of the mitochondrial membrane potential restored ROS, which were necessary for hypoxic activation of HIF-1 and cell proliferation. These results indicate that distinct mitochondrial functions associated with respiration are necessary for cell proliferation, epigenetics, and HIF-1 activation.


#58 Delineating probabilistic species pools in ecology and biogeography Open access logo PDF logo

Karger DN, Cord AF, Kessler M, Kreft H, Kuehn I, Pompe S, Sandel B, Cabral JS, Smith AB, Svenning JC, Tuomisto H, Weigelt P, Wesche K

Global Ecology & Biogeography Volume 25, Issue 4, Pages 489–501

  • 18 tweets
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  • 123 Mendeley readers


#59 Gamification in Crowdsourcing: A Review Link logo PDF logo

Morschheuser Benedikt; Hamari Juho; Koivisto Jonna

2016 49th Hawaii International Conference on System Sciences (HICSS)

  • 15 tweets
  • 1 reference in Wikipedia
  • 120 Mendeley readers


#60 Colloquium: Non-Markovian dynamics in open quantum systems PDF logo

Breuer HP, Laine EM, Piilo J, Vacchini B

Reviews of Modern Physics Volume 88, Issue 2

  • 6 tweets
  • 117 Mendeley readers


#61 Mitochondrial ROS produced via reverse electron transport extend animal lifespan Link logo PDF logo

Filippo Scialò, Ashwin Sriram, Daniel Fernández-Ayala, Nina Gubina, Madis Lõhmus, Glyn Nelson, Angela Logan, Helen M. Cooper, Plácido Navas, Jose Antonio Enríquez, Michael P. Murphy, Alberto Sanz

Cell Metabolism (Science Direct) Volume 23, Issue 4, Pages 725–734

  • 55 tweets
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  • 1 news
  • 116 Mendeley readers

Increased production of reactive oxygen species (ROS) has long been considered a cause of aging. However, recent studies have implicated ROS as essential secondary messengers. Here we show that the site of ROS production significantly contributes to their apparent dual nature. We report that ROS increase with age as mitochondrial function deteriorates. However, we also demonstrate that increasing ROS production specifically through respiratory complex I reverse electron transport extends Drosophila lifespan. Reverse electron transport rescued pathogenesis induced by severe oxidative stress, highlighting the importance of the site of ROS production in signaling. Furthermore, preventing ubiquinone reduction, through knockdown of PINK1, shortens lifespan and accelerates aging; phenotypes that are rescued by increasing reverse electron transport. These results illustrate that the source of a ROS signal is vital in determining its effects on cellular physiology and establish that manipulation of ubiquinone redox state is a valid strategy to delay aging.


#62 Cold season emissions dominate the Arctic tundra methane budget Link logo PDF logo

Zona, Donatella; Gioli, Beniamino; Commane, Roisin; Lindaas, Jakob; Wofsy, Steven C.; Miller, Charles E.; Dinardo, Steven J.; Dengel, Sigrid; Sweeney, Colm; Karion, Anna; Chang, Rachel Y. -W.; Henderson, John M.; Murphy, Patrick C.; Goodrich, Jordan P.; Moreaux, Virginie; Liljedahl, Anna; Watts, Jennifer D.; Kimball, John S.; Lipson, David A.; Oechel, Walter C.

Proceedings of the National Academy of Sciences of the United States of America Volume 113, Issue 1, Pages 201516017–45

  • 37 tweets
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Arctic terrestrial ecosystems are major global sources of methane (CH4); hence, it is important to understand the seasonal and climatic controls on CH4 emissions from these systems. Here, we report year-round CH4 emissions from Alaskan Arctic tundra eddy flux sites and regional fluxes derived from aircraft data. We find that emissions during the cold season (September to May) account for ≥50% of the annual CH4 flux, with the highest emissions from noninundated upland tundra. A major fraction of cold season emissions occur during the "zero curtain" period, when subsurface soil temperatures are poised near 0 °C. The zero curtain may persist longer than the growing season, and CH4 emissions are enhanced when the duration is extended by a deep thawed layer as can occur with thick snow cover. Regional scale fluxes of CH4 derived from aircraft data demonstrate the large spatial extent of late season CH4 emissions. Scaled to the circumpolar Arctic, cold season fluxes from tundra total 12 ± 5 (95% confidence interval) Tg CH4 y(-1), ∼25% of global emissions from extratropical wetlands, or ∼6% of total global wetland methane emissions. The dominance of late-season emissions, sensitivity to soil environmental conditions, and importance of dry tundra are not currently simulated in most global climate models. Because Arctic warming disproportionally impacts the cold season, our results suggest that higher cold-season CH4 emissions will result from observed and predicted increases in snow thickness, active layer depth, and soil temperature, representing important positive feedbacks on climate warming.


#63 Exosomal microRNA miR-92a concentration in serum reflects human brown fat activity Open access logo

Yong Chen, Joschka J. Buyel, Mark J. W. Hanssen, Franziska Siegel, Ruping Pan, Jennifer Naumann, Michael Schell, Anouk van der Lans, Christian Schlein, Holger Froehlich, Joerg Heeren, Kirsi A. Virtanen, Wouter van Marken Lichtenbelt, Alexander Pfeifer

Nature Communications

  • 1 tweet
  • 114 Mendeley readers

The time reversal of pulsed signals or propagating wave packets has long been recognized to have profound scientific and technological significance. Until now, all experimentally verified time-reversal mechanisms have been reliant upon nonlinear phenomena such as four-wave mixing. In this paper, we report the experimental realization of all-linear time reversal. The time-reversal mechanism we propose is based on the dynamic control of an artificial crystal structure, and is demonstrated in a spin-wave system using a dynamic magnonic crystal. The crystal is switched from an homogeneous state to one in which its properties vary with spatial period a, while a propagating wave packet is inside. As a result, a linear coupling between wave components with wave vectors k≈π/a and k'=k-2π/a≈-π/a is produced, which leads to spectral inversion, and thus to the formation of a time-reversed wave packet. The reversal mechanism is entirely general and so applicable to artificial crystal systems of any physical nature.


#64 Feeding type affects microplastic ingestion in a coastal invertebrate community Link logo

Setälä, Outi; Norkko, Joanna; Lehtiniemi, Maiju

Marine Pollution Bulletin Volume 102, Issue 1

  • 19 tweets
  • 114 Mendeley readers

Marine litter is one of the problems marine ecosystems face at present, coastal habitats and food webs being the most vulnerable as they are closest to the sources of litter. A range of animals (bivalves, free swimming crustaceans and benthic, deposit-feeding animals), of a coastal community of the northern Baltic Sea were exposed to relatively low concentrations of 10μm microbeads. The experiment was carried out as a small scale mesocosm study to mimic natural habitat. The beads were ingested by all animals in all experimental concentrations (5, 50 and 250beadsmL(-1)). Bivalves (Mytilus trossulus, Macoma balthica) contained significantly higher amounts of beads compared with the other groups. Free-swimming crustaceans ingested more beads compared with the benthic animals that were feeding only on the sediment surface. Ingestion of the beads was concluded to be the result of particle concentration, feeding mode and the encounter rate in a patchy environment.


#65 Assessing the societal benefits of river restoration using the ecosystem services approach

Vermaat, Jan E.; Wagtendonk, Alfred J.; Brouwer, Roy; Sheremet, Oleg; Ansink, Erik; Brockhoff, Tim; Plug, Maarten; Hellsten, Seppo; Aroviita, Jukka; Tylec, Luiza; Gielczewski, Marek; Kohut, Lukas; Brabec, Karel; Haverkamp, Jantine; Poppe, Michaela; Böck,

Hydrobiologia Volume 769, Issue 1, Pages 121–135

  • 2 tweets
  • 113 Mendeley readers


#66 The influence of a short-term gluten-free diet on the human gut microbiome Open access logo PDF logo

Bonder, Marc Jan; Tigchelaar, Ettje F.; Cai, Xianghang; Trynka, Gosia; Cenit, Maria C.; Hrdlickova, Barbara; Zhong, Huanzi; Vatanen, Tommi; Gevers, Dirk; Wijmenga, Cisca; Wang, Yang; Zhernakova, Alexandra

Genome Medicine Volume 8, Issue 1

  • 150 tweets
  • 3 blog posts
  • 113 Mendeley readers

A gluten-free diet (GFD) is the most commonly adopted special diet worldwide. It is an effective treatment for coeliac disease and is also often followed by individuals to alleviate gastrointestinal complaints. It is known there is an important link between diet and the gut microbiome, but it is largely unknown how a switch to a GFD affects the human gut microbiome. We studied changes in the gut microbiomes of 21 healthy volunteers who followed a GFD for four weeks. We collected nine stool samples from each participant: one at baseline, four during the GFD period, and four when they returned to their habitual diet (HD), making a total of 189 samples. We determined microbiome profiles using 16S rRNA sequencing and then processed the samples for taxonomic and imputed functional composition. Additionally, in all 189 samples, six gut health-related biomarkers were measured. Inter-individual variation in the gut microbiota remained stable during this short-term GFD intervention. A number of taxon-specific differences were seen during the GFD: the most striking shift was seen for the family Veillonellaceae (class Clostridia), which was significantly reduced during the intervention (p = 2.81 × 10(-05)). Seven other taxa also showed significant changes; the majority of them are known to play a role in starch metabolism. We saw stronger differences in pathway activities: 21 predicted pathway activity scores showed significant association to the change in diet. We observed strong relations between the predicted activity of pathways and biomarker measurements. A GFD changes the gut microbiome composition and alters the activity of microbial pathways.


#67 Plateau:a new method for ecologically plausible climate envelopes for species distribution modelling Link logo PDF logo

Brewer, Mark J.; O'Hara, Robert B.; Anderson, Barbara J.; Ohlemuller, Ralf

Methods in Ecology and Evolution Volume 7, Issue 12, Pages 1489–1502

  • 39 tweets
  • 2 blog posts
  • 113 Mendeley readers


#68 Do European agroforestry systems enhance biodiversity and ecosystem services? A meta-analysis PDF logo

Torralba M, Fagerholm N, Burgess PJ, Moreno G, Plieninger T

Agriculture, Ecosystems & Environment

  • 10 tweets
  • 112 Mendeley readers


#69 Pedagogy in digital learning in food education Open access logo Link logo

Kautola, H., Pirttijärvi, T., Kullaslahti, J., Laitinen, E.

Technology, Pedagogy and Education Volume 20, Issue 1, Pages 19–39

  • 2 tweets
  • 110 Mendeley readers


#70 Dual-process Accounts of Reasoning in User's Information System Risky Behavior Link logo PDF logo

Li, Ying;Zhang, Nan

Philosophy Compass Volume 5, Issue 10, Pages 914–926

  • 108 Mendeley readers


#71 A new valuation school: Integrating diverse values of nature in resource and land use decisions PDF logo

Jacobs, Sander; Dendoncker, Nicolas; Martín-López, Bertac; Barton, David Nicholas; Gomez-Baggethun, Erik; Boeraeve, Fanny; McGrath, L. Francesca; Vierikko, Kati; Geneletti, David; Sevecke, J. Katharina; Pipart, Nathalie; Primmer, Eeva; Mederly, Peter; S

Ecosystem Services

  • 33 tweets
  • 3 blog posts
  • 106 Mendeley readers



#73 Planck intermediate results XXX.:The angular power spectrum of polarized dust emission at intermediate and high Galactic latitudes Link logo PDF logo

Adam, R.; Ade, P. A. R.; Aghanim, N.; Arnaud, M.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartlett, J. G.; Bartolo, N.; Battaner, E.; Benabed, K.; Benoit-Levy, A.; Bernard, J. -P.; Bersanelli, M.; Bielewicz, P.; Bonaldi, A.; Bonavera, L.; Bond, J. R.; Borrill, J.

Astronomy and Astrophysics

  • 469 tweets
  • 41 blog posts
  • 40 news
  • 6 references in Wikipedia
  • 105 Mendeley readers


#74 Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein Link logo PDF logo

Pande, Kanupriya;Hutchison, Christopher D. M.;Groenhof, Gerrit;Aquila, Andy;Robinson, Josef S.;Tenboer, Jason;Basu, Shibom;Boutet, Sébastien;DePonte, Daniel P.;Liang, Mengning;White, Thomas A.;Zatsepin, Nadia A.;Yefanov, Oleksandr;Morozov, Dmitry;Oberthuer, Dominik;Gati, Cornelius;Subramanian, Ganesh;James, Daniel;Zhao, Yun;Koralek, Jake

Science Volume 352, Issue 6286

  • 14 tweets
  • 4 blog posts
  • 23 news
  • 104 Mendeley readers

A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.


#75 Learning and the transformative potential of citizen science PDF logo

Bela, Györgyi; Peltola, Taru; Young, Juliette C.; Balázs, Bálint; Arpin, Isabelle; Pataki, György; Hauck, Eszter; Kelemen, Jennifer; Kopperoinen, Leena; Herzele, Ann; Keune, Hans; Hecker, Susanne; Suskevics, Monika; Roy, Helen E.; Itkonen, Pekka; Kül

Conservation Biology Volume 30, Issue 5, Pages 990–999

  • 41 tweets
  • 103 Mendeley readers

The number of collaborative initiatives between scientists and volunteers (i.e., citizen science) is increasing across many research fields. The promise of societal transformation together with scientific breakthroughs contributes to the current popularity of citizen science (CS) in the policy domain. We examined the transformative capacity of citizen science in particular learning through environmental CS as conservation tool. We reviewed the CS and social-learning literature and examined 14 conservation projects across Europe that involved collaborative CS. We also developed a template that can be used to explore learning arrangements (i.e., learning events and materials) in CS projects and to explain how the desired outcomes can be achieved through CS learning. We found that recent studies aiming to define CS for analytical purposes often fail to improve the conceptual clarity of CS; CS programs may have transformative potential, especially for the development of individual skills, but such transformation is not necessarily occurring at the organizational and institutional levels; empirical evidence on simple learning outcomes, but the assertion of transformative effects of CS learning is often based on assumptions rather than empirical observation; and it is unanimous that learning in CS is considered important, but in practice it often goes unreported or unevaluated. In conclusion, we point to the need for reliable and transparent measurement of transformative effects for democratization of knowledge production. This article is protected by copyright. All rights reserved.


#76 Integrating plant- and animal-based perspectives for more effective restoration of biodiversity Link logo PDF logo

McAlpine, Clive; Catterall, Carla P.; Mac Nally, Ralph; Lindenmayer, David; Reid, J. Leighton; Holl, Karen D.; Bennett, Andrew F.; Runting, Rebecca K.; Wilson, Kerrie; Hobbs, Richard J.; Seabrook, Leonie; Cunningham, Shaun; Moilanen, Atte; Maron, Martine; Shoo, Luke; Lunt, Ian; Vesk, Peter; Rumpff, Libby; Martin, Tara G.; Thomson, James

Frontiers in Ecology & the Environment Volume 14, Issue 1, Pages 37–45

  • 44 tweets
  • 103 Mendeley readers


#77 Human behaviour can trigger large carnivore attacks in developed countries Open access logo Link logo

Penteriani, Vincenzo; del Mar Delgado, Maria; Pinchera, Francesco; Naves, Javier; Fernandez-Gil, Alberto; Kojola, Ilpo; Härkönen, Sauli; Norberg, Harri; Frank, Jens; Maria Fedriani, Jose; Sahlen, Veronica; Stoen, Ole-Gunnar; Swenson, Jon E.; Wabakken, Petter; Pellegrini, Mario; Herrero, Stephen; Vicente Lopez-Bao, Jose

Scientific Reports

  • 285 tweets
  • 2 blog posts
  • 36 news
  • 103 Mendeley readers

The media and scientific literature are increasingly reporting an escalation of large carnivore attacks on humans in North America and Europe. Although rare compared to human fatalities by other wildlife, the media often overplay large carnivore attacks on humans, causing increased fear and negative attitudes towards coexisting with and conserving these species. Although large carnivore populations are generally increasing in developed countries, increased numbers are not solely responsible for the observed rise in the number of attacks by large carnivores. Here we show that an increasing number of people are involved in outdoor activities and, when doing so, some people engage in risk-enhancing behaviour that can increase the probability of a risky encounter and a potential attack. About half of the well-documented reported attacks have involved risk-enhancing human behaviours, the most common of which is leaving children unattended. Our study provides unique insight into the causes, and as a result the prevention, of large carnivore attacks on people. Prevention and information that can encourage appropriate human behaviour when sharing the landscape with large carnivores are of paramount importance to reduce both potentially fatal human-carnivore encounters and their consequences to large carnivores.


#78 Perspectives to Definition of Big Data: A Mapping Study and Discussion Open access logo PDF logo

Ylijoki Ossi; Porras Jari

Journal of Big Data Volume 2, Issue 1

  • 36 tweets
  • 1 news
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#79 Do projections from bioclimatic envelope models and climate change metrics match? Link logo PDF logo

Garcia, Raquel A.; Cabeza, Mar; Altwegg, Res; Araujo, Miguel B.

Global Ecology & Biogeography Volume 25, Issue 1, Pages 65–74

  • 17 tweets
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#80 Guiding light via geometric phases Link logo

Slussarenko, Sergei;Alberucci, Alessandro;Jisha, Chandroth P.;Piccirillo, Bruno;Santamato, Enrico;Assanto, Gaetano;Marrucci, Lorenzo

Nature Photonics Volume 10, Issue 9, Pages 571–575

  • 3 tweets
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  • 2 news
  • 98 Mendeley readers


#81 Emerging themes in agile software development Introduction to the special section on continuous value delivery Open access logo

Dingsøyr, Torgeir; Lassenius, Casper

Information & Software Technology

  • 17 tweets
  • 98 Mendeley readers


#82 The interaction of PRC2 with RNA or chromatin is mutually antagonistic Link logo PDF logo

Beltran Manuel; Yates Christopher; Skalska Lenka; Dawson Marcus; Reis Filipa; Viiri Keijo; Fisher Cynthia; Sibley Cchristopher; Foster Benjamin; Bartke Till; Ule Jernej; Jenner Richard

Genome Research Volume 26, Issue 7, Pages gr.197632.115–907

  • 22 tweets
  • 97 Mendeley readers

Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain genes in a repressed state during development. PRC2 is primarily associated with CpG islands at repressed genes and also possesses RNA binding activity. However, the RNAs that bind PRC2 in cells, the subunits that mediate these interactions, and the role of RNA in PRC2 recruitment to chromatin all remain unclear. By performing iCLIP for PRC2 in comparison with other RNA binding proteins, we show here that PRC2 binds nascent RNA at essentially all active genes. Although interacting with RNA promiscuously, PRC2 binding is enriched at specific locations within RNAs, primarily exon-intron boundaries and the 3'UTR. Deletion of other PRC2 subunits reveals that SUZ12 is sufficient to establish this RNA binding profile. Contrary to prevailing models, we also demonstrate that the interaction of PRC2 with RNA or chromatin is mutually antagonistic in cells and in vitro. RNA degradation in cells triggers PRC2 recruitment to CpG islands at active genes. Correspondingly, release of PRC2 from chromatin in cells increases RNA binding. Consistent with this, RNA and nucleosomes compete for PRC2 binding in vitro. We propose that RNA prevents PRC2 recruitment to chromatin at active genes and that mutual antagonism between RNA and chromatin underlies the pattern of PRC2 chromatin association across the genome.


#83 Additives for vaccine storage to improve thermal stability of adenoviruses from hours to months Open access logo Link logo

Pelliccia, Maria;Andreozzi, Patrizia;Paulose, Jayson;D’Alicarnasso, Marco;Cagno, Valeria;Donalisio, Manuela;Civra, Andrea;Broeckel, Rebecca M.;Haese, Nicole;Silva, Paulo Jacob;Carney, Randy P.;Marjomäki, Varpu;Streblow, Daniel N.;Lembo, David;Stellacci, Francesco;Vitelli, Vincenzo;Krol, Silke

Nature Communications

  • 7 tweets
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Unveiling the neural codes for intricate behaviours is a major challenge in neuroscience. The neural circuit for the temperature-seeking behaviour of Caenorhabditis elegans is an ideal system to dissect how neurons encode sensory information for the execution of behavioural output. Here we show that the temperature-sensing neuron AFD transmits both stimulatory and inhibitory neural signals to a single interneuron AIY. In this circuit, a calcium concentration threshold in AFD acts as a switch for opposing neural signals that direct the opposite behaviours. Remote control of AFD activity, using a light-driven ion pump and channel, reveals that diverse reduction levels of AFD activity can generate warm- or cold-seeking behaviour. Calcium imaging shows that AFD uses either stimulatory or inhibitory neuronal signalling onto AIY, depending on the calcium concentration threshold in AFD. Thus, dual neural regulation in opposite directions is directly coupled to behavioural inversion in the simple neural circuit.


#84 Biomass offsets little or none of permafrost carbon release from soils, streams, and wildfire:an expert assessment Open access logo Link logo PDF logo

Abbott, Benjamin W.; Jones, Jeremy B.; Schuur, Edward A. G.; Chapin, F. Stuart; Bowden, William B.; Bret-Harte, M. Syndonia; Epstein, Howard E.; Flannigan, Michael D.; Harms, Tamara K.; Hollingsworth, Teresa N.; Mack, Michelle C.; McGuire, A. David; Natali, Susan M.; Rocha, Adrian V.; Tank, Suzanne E.; Turetsky, Merritt R.; Vonk, Jorien E.; Wickland, Kimberly P.; Aiken, George R.; Alexander, Heather D.

Environmental Research Letters (ERL) Volume 11, Issue 3

  • 84 tweets
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  • 20 news
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#85 Planck 2015 results XIV. Dark energy and modified gravity Link logo

Ade, P. A. R.; Aghanim, N.; Arnaud, M.; Ashdown, M.; Aumont, J.; Baccigalupi, C.; Banday, A. J.; Barreiro, R. B.; Bartolo, N.; Battaner, E.; Battye, R.; Benabed, K.; Benoit, A.; Benoit-Levy, A.; Bernard, J. -P.; Bersanelli, M.; Bielewicz, P.; Bock, J. J.; Bonaldi, A.; Bonavera, L.

Astronomy and Astrophysics

  • 95 Mendeley readers


#86 The role of landscape, topography, and geodiversity in explaining vascular plant species richness in a fragmented landscape Open access logo PDF logo

Räsänen, Aleksi; Kuitunen, Markku; Hjort, Jan; Vaso, Asta; Kuitunen, Tuomo; Lensu, Anssi

Landscape Ecology

  • 94 Mendeley readers


#87 Continent-scale global change attribution in European birds - combining annual and decadal time scales Link logo PDF logo

Jorgensen, Peter Sogaard; Boehning-Gaese, Katrin; Thorup, Kasper; Tottrup, Anders P.; Chylarecki, Przemyslaw; Jiguet, Frederic; Lehikoinen, Aleksi; Noble, David G.; Reif, Jiri; Schmid, Hans; van Turnhout, Chris; Burfield, Ian J.; Foppen, Ruud; Vorisek, Petr; van Strien, Arco; Gregory, Richard D.; Rahbek, Carsten

Global Change Biology Volume 22, Issue 2, Pages 530–543

  • 49 tweets
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  • 12 news
  • 94 Mendeley readers

Species attributes are commonly used to infer impacts of environmental change on multiyear species trends, e.g. decadal changes in population size. However, by themselves attributes are of limited value in global change attribution since they do not measure the changing environment. A broader foundation for attributing species responses to global change may be achieved by complementing an attributes-based approach by one estimating the relationship between repeated measures of organismal and environmental changes over short time scales. To assess the benefit of this multiscale perspective, we investigate the recent impact of multiple environmental changes on European farmland birds, here focusing on climate change and land use change. We analyze more than 800 time series from 18 countries spanning the past two decades. Analysis of long-term population growth rates documents simultaneous responses that can be attributed to both climate change and land-use change, including long-term increases in populations of hot-dwelling species and declines in long-distance migrants and farmland specialists. In contrast, analysis of annual growth rates yield novel insights into the potential mechanisms driving long-term climate induced change. In particular, we find that birds are affected by winter, spring, and summer conditions depending on the distinct breeding phenology that corresponds to their migratory strategy. Birds in general benefit from higher temperatures or higher primary productivity early on or in the peak of the breeding season with the largest effect sizes observed in cooler parts of species' climatic ranges. Our results document the potential of combining time scales and integrating both species attributes and environmental variables for global change attribution. We suggest such an approach will be of general use when high-resolution time series are available in large-scale biodiversity surveys.


#88 Biological and Bioelectrochemical Recovery of Critical and Scarce Metals Link logo PDF logo

Nancharaiah, Y. V.;Mohan, S. Venkata;Lens, P. N L

Trends in Biotechnology Volume 34, Issue 2

  • 2 tweets
  • 92 Mendeley readers

Metal-bearing solid and liquid wastes are increasingly considered as secondary sources of critical and scarce metals. Undoubtedly, microorganisms are a cost-effective resource for extracting and concentrating diffuse elements from secondary sources. Microbial biotechnology for extracting base metals from ores and treatment of metal-laden wastewaters has already been applied at full scale. By contrast, microbe-metal interactions in the recovery of scarce metals and a few critical metals have received attention, whereas the recovery of many others has been barely explored. Therefore, this article explores and details the potential application of microbial biotechnologies in the recovery of critical and scarce metals. In the past decade bioelectrochemical systems have emerged as a new technology platform for metal recovery coupled to the removal of organic matter.


#89 Metabolomics enables precision medicine: "A White Paper, Community Perspective" Open access logo PDF logo

Richard D. Beger, Warwick Dunn, Michael A. Schmidt, Steven S. Gross, Jennifer A. Kirwan, Marta Cascante, Lorraine Brennan, David S. Wishart, Matej Oresic, Thomas Hankemeier, David I. Broadhurst, Andrew N. Lane, Karsten Suhre, Gabi Kastenmüller, Susan J. Sumner, Ines Thiele, Oliver Fiehn, Rima Kaddurah-Daouk

Metabolomics Volume 12, Issue 10

  • 141 tweets
  • 92 Mendeley readers

Metabolomics is the comprehensive study of the metabolome, the repertoire of biochemicals (or small molecules) present in cells, tissues, and body fluids. The study of metabolism at the global or "-omics" level is a rapidly growing field that has the potential to have a profound impact upon medical practice. At the center of metabolomics, is the concept that a person's metabolic state provides a close representation of that individual's overall health status. This metabolic state reflects what has been encoded by the genome, and modified by diet, environmental factors, and the gut microbiome. The metabolic profile provides a quantifiable readout of biochemical state from normal physiology to diverse pathophysiologies in a manner that is often not obvious from gene expression analyses. Today, clinicians capture only a very small part of the information contained in the metabolome, as they routinely measure only a narrow set of blood chemistry analytes to assess health and disease states. Examples include measuring glucose to monitor diabetes, measuring cholesterol and high density lipoprotein/low density lipoprotein ratio to assess cardiovascular health, BUN and creatinine for renal disorders, and measuring a panel of metabolites to diagnose potential inborn errors of metabolism in neonates. We anticipate that the narrow range of chemical analyses in current use by the medical community today will be replaced in the future by analyses that reveal a far more comprehensive metabolic signature. This signature is expected to describe global biochemical aberrations that reflect patterns of variance in states of wellness, more accurately describe specific diseases and their progression, and greatly aid in differential diagnosis. Such future metabolic signatures will: (1) provide predictive, prognostic, diagnostic, and surrogate markers of diverse disease states; (2) inform on underlying molecular mechanisms of diseases; (3) allow for sub-classification of diseases, and stratification of patients based on metabolic pathways impacted; (4) reveal biomarkers for drug response phenotypes, providing an effective means to predict variation in a subject's response to treatment (pharmacometabolomics); (5) define a metabotype for each specific genotype, offering a functional read-out for genetic variants: (6) provide a means to monitor response and recurrence of diseases, such as cancers: (7) describe the molecular landscape in human performance applications and extreme environments. Importantly, sophisticated metabolomic analytical platforms and informatics tools have recently been developed that make it possible to measure thousands of metabolites in blood, other body fluids, and tissues. Such tools also enable more robust analysis of response to treatment. New insights have been gained about mechanisms of diseases, including neuropsychiatric disorders, cardiovascular disease, cancers, diabetes and a range of pathologies. A series of ground breaking studies supported by National Institute of Health (NIH) through the Pharmacometabolomics Research Network and its partnership with the Pharmacogenomics Research Network illustrate how a patient's metabotype at baseline, prior to treatment, during treatment, and post-treatment, can inform about treatment outcomes and variations in responsiveness to drugs (e.g., statins, antidepressants, antihypertensives and antiplatelet therapies). These studies along with several others also exemplify how metabolomics data can complement and inform genetic data in defining ethnic, sex, and gender basis for variation in responses to treatment, which illustrates how pharmacometabolomics and pharmacogenomics are complementary and powerful tools for precision medicine. Our metabolomics community believes that inclusion of metabolomics data in precision medicine initiatives is timely and will provide an extremely valuable layer of data that compliments and informs other data obtained by these important initiatives. Our Metabolomics Society, through its "Precision Medicine and Pharmacometabolomics Task Group", with input from our metabolomics community at large, has developed this White Paper where we discuss the value and approaches for including metabolomics data in large precision medicine initiatives. This White Paper offers recommendations for the selection of state of-the-art metabolomics platforms and approaches that offer the widest biochemical coverage, considers critical sample collection and preservation, as well as standardization of measurements, among other important topics. We anticipate that our metabolomics community will have representation in large precision medicine initiatives to provide input with regard to sample acquisition/preservation, selection of optimal omics technologies, and key issues regarding data collection, interpretation, and dissemination. We strongly recommend the collection and biobanking of samples for precision medicine initiatives that will take into consideration needs for large-scale metabolic phenotyping studies.


#90 A simple rule governs the evolution and development of hominin tooth size Link logo

Evans, Alistair R.; Daly, E. Susanne; Catlett, Kierstin K.; Paul, Kathleen S.; King, Stephen J.; Skinner, Matthew M.; Nesse, Hans P.; Hublin, Jean-Jacques; Townsend, Grant C.; Schwartz, Gary T.; Jernvall, Jukka

Nature Volume 530, Issue 7591, Pages 477–480

  • 127 tweets
  • 6 blog posts
  • 40 news
  • 92 Mendeley readers

The variation in molar tooth size in humans and our closest relatives (hominins) has strongly influenced our view of human evolution. The reduction in overall size and disproportionate decrease in third molar size have been noted for over a century, and have been attributed to reduced selection for large dentitions owing to changes in diet or the acquisition of cooking. The systematic pattern of size variation along the tooth row has been described as a 'morphogenetic gradient' in mammal, and more specifically hominin, teeth since Butler and Dahlberg. However, the underlying controls of tooth size have not been well understood, with hypotheses ranging from morphogenetic fields to the clone theory. In this study we address the following question: are there rules that govern how hominin tooth size evolves? Here we propose that the inhibitory cascade, an activator-inhibitor mechanism that affects relative tooth size in mammals, produces the default pattern of tooth sizes for all lower primary postcanine teeth (deciduous premolars and permanent molars) in hominins. This configuration is also equivalent to a morphogenetic gradient, finally pointing to a mechanism that can generate this gradient. The pattern of tooth size remains constant with absolute size in australopiths (including Ardipithecus, Australopithecus and Paranthropus). However, in species of Homo, including modern humans, there is a tight link between tooth proportions and absolute size such that a single developmental parameter can explain both the relative and absolute sizes of primary postcanine teeth. On the basis of the relationship of inhibitory cascade patterning with size, we can use the size at one tooth position to predict the sizes of the remaining four primary postcanine teeth in the row for hominins. Our study provides a development-based expectation to examine the evolution of the unique proportions of human teeth.


#91 Ecosystem services-based land planning for environmental impact avoidance Link logo

Nin, Mariana; Soutullo, Alvaro; Rodriguez-Gallego, Lorena; Di Minin, Enrico

Ecosystem Services

  • 1 tweet
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#92 DopeLearning:A Computational Approach to Rap Lyrics Generation Link logo PDF logo

Malmi, Eric; Takala, Pyry; Toivonen, Hannu; Raiko, Tapani; Gionis, Aristides

arXiv

  • 468 tweets
  • 2 blog posts
  • 9 news
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#93 Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants Open access logo Link logo PDF logo

Morandin, Claire; Tin, Mandy M. Y.; Abril, Silvia; Gomez, Crisanto; Pontieri, Luigi; Schiott, Morten; Sundström, Liselotte; Tsuji, Kazuki; Pedersen, Jes Soe; Helanterä, Heikki; Mikheyev, Alexander S.

Genome Biology (Online Edition) Volume 17, Issue 1

  • 26 tweets
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  • 7 news
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Reproductive division of labor in eusocial insects is a striking example of a shared genetic background giving rise to alternative phenotypes, namely queen and worker castes. Queen and worker phenotypes play major roles in the evolution of eusocial insects. Their behavior, morphology and physiology underpin many ecologically relevant colony-level traits, which evolved in parallel in multiple species. Using queen and worker transcriptomic data from 16 ant species we tested the hypothesis that conserved sets of genes are involved in ant reproductive division of labor. We further hypothesized that such sets of genes should also be involved in the parallel evolution of other key traits. We applied weighted gene co-expression network analysis, which clusters co-expressed genes into modules, whose expression levels can be summarized by their 'eigengenes'. Eigengenes of most modules were correlated with phenotypic differentiation between queens and workers. Furthermore, eigengenes of some modules were correlated with repeated evolution of key phenotypes such as complete worker sterility, the number of queens per colony, and even invasiveness. Finally, connectivity and expression levels of genes within the co-expressed network were strongly associated with the strength of selection. Although caste-associated sets of genes evolve faster than non-caste-associated, we found no evidence for queen- or worker-associated co-expressed genes evolving faster than one another. These results identify conserved functionally important genomic units that likely serve as building blocks of phenotypic innovation, and allow the remarkable breadth of parallel evolution seen in ants, and possibly other eusocial insects as well.


#94 What we use is not what we know:environmental predictors in plant distribution models Link logo PDF logo

Mod, Heidi K.; Scherrer, Daniel; Luoto, Miska; Guisan, Antoine

Journal of Vegetation Science Volume 27, Issue 6, Pages 1308–1322

  • 24 tweets
  • 1 blog post
  • 88 Mendeley readers


#95 Crowdsourcing, Citizen Science or Volunteered Geographic Information? The Current State of Crowdsourced Geographic Information PDF logo

See, L.; Mooney, P.; Foody, G.; Bastin, L.; Comber, A.; Estima, J.; Fritz, S.; Kerle, K.; Jiang, B.; Laakso, Mari; Liu, H.-Y.; Milcinski, G.; Niksic, M.; Painho, M.; Podör, A.; Olteanu-Raimond, A.-M.; Rutzinger, M.

ISPRS International Journal of Geo-Information Volume 5, Issue 5

  • 18 tweets
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#96 The ecosystem service of sense of place:benefits for human well-being and biodiversity conservation Link logo PDF logo

Hausmann, Anna; Slotow, Rob; Burns, Jonathan K.; Di Minin, Enrico

Environmental Conservation

  • 8 tweets
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#97 Governing cities reflexively-The biocultural diversity concept as an alternative to ecosystem services Link logo

Buizer, Marleen; Elands, Birgit; Vierikko, Kati

Environmental Science & Policy

  • 2 tweets
  • 87 Mendeley readers


#98 Voluntary non-monetary approaches for implementing conservation Link logo PDF logo

Santangeli, Andrea; Arroyo, Beatriz; Dicks, Lynn V.; Herzon, Iryna; Kukkala, Aija Sonja Sarita; Sutherland, William J.; Moilanen, Atte Jaakko

Biological Conservation

  • 27 tweets
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#99 Impacts of agricultural intensification on bird communities: New insights from a multi-level and multi-facet approach of biodiversity Link logo

Jeliazkov, Alienor;Mimet, Anne;Charge, Rémi;Jiguet, Frédéric;Devictor, Vincent;Chiron, François

Agriculture, Ecosystems & Environment

  • 2 tweets
  • 86 Mendeley readers


#100 Fast Actuation of Magnetic Shape Memory Material Ni-Mn-Ga Using Pulsed Magnetic Field PDF logo

Saren Andrey; Tellinen Juhani; Musiienko Denys; Ullakko Kari

Advanced Materials Volume 23, Issue 2

  • 1 reference in Wikipedia
  • 83 Mendeley readers


#101 Genetic specificity of a plant-insect food web: Implications for linking genetic variation to network complexity PDF logo

Barbour Matthew A, Fortuna Miguel A, Bascompte Jordi, Nicholson Joshua R, Julkunen-Tiitto Riitta, Jules Erik S, Crutsinger Gregory M

Proceedings of the National Academy of Sciences of the United States of America Volume 113, Issue 8, Pages 201513633–2133

  • 35 tweets
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Theory predicts that intraspecific genetic variation can increase the complexity of an ecological network. To date, however, we are lacking empirical knowledge of the extent to which genetic variation determines the assembly of ecological networks, as well as how the gain or loss of genetic variation will affect network structure. To address this knowledge gap, we used a common garden experiment to quantify the extent to which heritable trait variation in a host plant determines the assembly of its associated insect food web (network of trophic interactions). We then used a resampling procedure to simulate the additive effects of genetic variation on overall food-web complexity. We found that trait variation among host-plant genotypes was associated with resistance to insect herbivores, which indirectly affected interactions between herbivores and their insect parasitoids. Direct and indirect genetic effects resulted in distinct compositions of trophic interactions associated with each host-plant genotype. Moreover, our simulations suggest that food-web complexity would increase by 20% over the range of genetic variation in the experimental population of host plants. Taken together, our results indicate that intraspecific genetic variation can play a key role in structuring ecological networks, which may in turn affect network persistence.


#102 Proximity-Based Differential Single-Cell Analysis of the Niche to Identify Stem/Progenitor Cell Regulators PDF logo

Silberstein L, Goncalves KA, Kharchenko PV, Turcotte R, Kfoury Y, Mercier F, Baryawno N, Severe N, Bachand J, Spencer JA, Papazian A, Lee D, Chitteti BR, Srour EF, Hoggatt J, Tate T, Lo Celso C, Ono N, Nutt S, Heino J, Sipila K, Shioda T, Osawa M, Lin CP, Hu GF, Scadden DT

Cell Stem Cell Volume 19, Issue 4, Pages 530–543

  • 31 tweets
  • 1 news
  • 81 Mendeley readers

Physiological stem cell function is regulated by secreted factors produced by niche cells. In this study, we describe an unbiased approach based on the differential single-cell gene expression analysis of mesenchymal osteolineage cells close to, and further removed from, hematopoietic stem/progenitor cells (HSPCs) to identify candidate niche factors. Mesenchymal cells displayed distinct molecular profiles based on their relative location. We functionally examined, among the genes that were preferentially expressed in proximal cells, three secreted or cell-surface molecules not previously connected to HSPC biology-the secreted RNase angiogenin, the cytokine IL18, and the adhesion molecule Embigin-and discovered that all of these factors are HSPC quiescence regulators. Therefore, our proximity-based differential single-cell approach reveals molecular heterogeneity within niche cells and can be used to identify novel extrinsic stem/progenitor cell regulators. Similar approaches could also be applied to other stem cell/niche pairs to advance the understanding of microenvironmental regulation of stem cell function.


#103 Transition towards Circular Economy in the Food System Open access logo Link logo PDF logo

Jurgilevich, Alexandra; Birge, Traci; Kentala-Lehtonen, Johanna; Korhonen-Kurki, Kaisa; Pietikäinen, Janna; Saikku, Laura; Schösler, Hanna

Sustainability (2071-1050)

  • 7 tweets
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#104 Green Infrastructure Design Based on Spatial Conservation Prioritization and Modeling of Biodiversity Features and Ecosystem Services Link logo PDF logo

Snäll, Tord; Lehtomäki, Joona Aleksi; Arponen, Anni Katri Ilona; Elith, Jane; Moilanen, Atte Jaakko

Environmental Management Volume 57, Issue 2, Pages 251–256

  • 5 tweets
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There is high-level political support for the use of green infrastructure (GI) across Europe, to maintain viable populations and to provide ecosystem services (ES). Even though GI is inherently a spatial concept, the modern tools for spatial planning have not been recognized, such as in the recent European Environment Agency (EEA) report. We outline a toolbox of methods useful for GI design that explicitly accounts for biodiversity and ES. Data on species occurrence, habitats, and environmental variables are increasingly available via open-access internet platforms. Such data can be synthesized by statistical species distribution modeling, producing maps of biodiversity features. These, together with maps of ES, can form the basis for GI design. We argue that spatial conservation prioritization (SCP) methods are effective tools for GI design, as the overall SCP goal is cost-effective allocation of conservation efforts. Corridors are currently promoted by the EEA as the means for implementing GI design, but they typically target the needs of only a subset of the regional species pool. SCP methods would help to ensure that GI provides a balanced solution for the requirements of many biodiversity features (e.g., species, habitat types) and ES simultaneously in a cost-effective manner. Such tools are necessary to make GI into an operational concept for combating biodiversity loss and promoting ES.


#105 Spatial structure in ecological communities - a quantitative analysis Link logo PDF logo

Soininen, Janne

Oikos Volume 125, Issue 2, Pages 160–166

  • 8 tweets
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#106 The evolutionary ecology of deception Link logo PDF logo

Mökkönen, Mikael;Lindstedt, Carita

Biological Reviews Volume 91, Issue 4, Pages 1020–1035

  • 69 tweets
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Through dishonest signals or actions, individuals often misinform others to their own benefit. We review recent literature to explore the evolutionary and ecological conditions for deception to be more likely to evolve and be maintained. We identify four conditions: (1) high misinformation potential through perceptual constraints of perceiver; (2) costs and benefits of responding to deception; (3) asymmetric power relationships between individuals and (4) exploitation of common goods. We discuss behavioural and physiological mechanisms that form a deception continuum from secrecy to overt signals. Deceptive tactics usually succeed by being rare and are often evolving under co-evolutionary arms races, sometimes leading to the evolution of polymorphism. The degree of deception can also vary depending on the environmental conditions. Finally, we suggest a conceptual framework for studying deception and highlight important questions for future studies.


#107 Moving superhydrophobic surfaces toward real-world applications PDF logo

Tian, Xuelin; Verho, Tuukka; Ras, Robin H A

Science Volume 352, Issue 6282

  • 47 tweets
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#108 The PLETHORA gene regulatory network guides growth and cell differentiation in Arabidopsis roots Link logo PDF logo

Santuari, Luca; Sanchez-Perez, Gabino F.; Luijten, Marijn; Rutjens, Bas; Terpstra, Inez; Berke, Lidija; Gorte, Maartje; Prasad, Kalika; Bao, Dongping; Timmermans-Hereijgers, Johanna L.P.M.; Maeo, Kenichiro; Nakamura, Kenzo; Shimotohno, Akie; Pencik, Ales; Novak, Ondrej; Ljung, Karin; van Heesch, Sebastiaan; de Bruijn, Ewart; Cuppen, Edwin; Willemsen, Viola

Plant Cell

  • 49 tweets
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Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated across tissues. PLETHORA (PLT) transcription factor gradients are unique in their ability to guide the progression of cell differentiation at different positions in the growing Arabidopsis root, which contrasts with well-described transcription factor gradients in animals specifying distinct cell fates within an essentially static context. To understand the output of the PLT gradient, we studied the gene set transcriptionally controlled by PLTs. Our work reveals how the PLT gradient can regulate cell state by region-specific induction of cell proliferation genes and repression of differentiation. Moreover, PLT targets include major patterning genes and autoregulatory feedback components, enforcing their role as master regulators of organ development.


#109 Twenty-million-year relationship between mammalian diversity and primary productivity Link logo PDF logo

Fritz, Susanne A.; Eronen, Jussi T.; Schnitzler, Jan; Hof, Christian; Janis, Christine M.; Mulch, Andreas; Boehning-Gaese, Katrin; Graham, Catherine H.

Proceedings of the National Academy of Sciences of the United States of America Volume 113, Issue 39

  • 49 tweets
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  • 79 Mendeley readers

At global and regional scales, primary productivity strongly correlates with richness patterns of extant animals across space, suggesting that resource availability and climatic conditions drive patterns of diversity. However, the existence and consistency of such diversity-productivity relationships through geological history is unclear. Here we provide a comprehensive quantitative test of the diversity-productivity relationship for terrestrial large mammals through time across broad temporal and spatial scales. We combine >14,000 occurrences for 690 fossil genera through the Neogene (23-1.8 Mya) with regional estimates of primary productivity from fossil plant communities in North America and Europe. We show a significant positive diversity-productivity relationship through the 20-million-year record, providing evidence on unprecedented spatial and temporal scales that this relationship is a general pattern in the ecology and paleo-ecology of our planet. Further, we discover that genus richness today does not match the fossil relationship, suggesting that a combination of human impacts and Pleistocene climate variability has modified the 20-million-year ecological relationship by strongly reducing primary productivity and driving many mammalian species into decline or to extinction.


#110 Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly Link logo PDF logo

Fountain, Toby Edward Soames; Nieminen, Marko Juhani; Siren, Jukka Pekka; Wong, Swee Chong; Lehtonen, Rainer Juhani; Hanski, Ilkka Aulis

Proceedings of the National Academy of Sciences of the United States of America Volume 113, Issue 10, Pages 2678–2683

  • 72 tweets
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Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction.


#111 Topography-driven isolation, speciation and a global increase of endemism with elevation Link logo PDF logo

Steinbauer, M.; Field, R.; Grytnes, J.-A.; Trigas, P.; Ah-Peng, C.; Attorre, F.; Birks, J.; Borges, P.A.V.; Cardoso, Pedro; Chou, C.-H.; De Sanctis, M.; Duarte, M.; Elias, R.; Fernandez-Palacios, J.-M.; Gabriel, R.; Gereau, R.; Gillespie, R.; Greimler, J.; Harter, D.; Huang, T.-J.

Global Ecology & Biogeography Volume 25, Issue 9, Pages 1097–1107

  • 78 tweets
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#112 Measurements of the Higgs boson production and decay rates and constraints on its couplings from a combined ATLAS and CMS analysis of the LHC pp collision data at root s=7 and 8 TeV Open access logo Link logo PDF logo

Aad, G.; Eerola, P.; Pekkanen, J.; Voutilainen, M.; Härkönen, J.; Heikkilä, J.K.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Peltola, T.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; ,

Journal of High Energy Physics Volume 2016, Issue 8

  • 184 tweets
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#113 The importance of realistic dispersal models in conservation planning:application of a novel modelling platform to evaluate management scenarios in an Afrotropical biodiversity hotspot Link logo PDF logo

Aben, Job; Bocedi, Greta; Palmer, Stephen C. F.; Pellikka, Petri; Strubbe, Diederik; Hallmann, Caspar; Travis, Justin M. J.; Lens, Luc; Matthysen, Erik

Journal of Applied Ecology Volume 53, Issue 4, Pages 1055–1065

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As biodiversity hotspots are often characterized by high human population densities, implementation of conservation management practices that focus only on the protection and enlargement of pristine habitats is potentially unrealistic. An alternative approach to curb species extinction risk involves improving connectivity among existing habitat patches. However, evaluation of spatially explicit management strategies is challenging, as predictive models must account for the process of dispersal, which is difficult in terms of both empirical data collection and modelling.Here, we use a novel, individual-based modelling platform that couples demographic and mechanistic dispersal models to evaluate the effectiveness of realistic management scenarios tailored to conserve forest birds in a highly fragmented biodiversity hotspot. Scenario performance is evaluated based on the spatial population dynamics of a well-studied forest bird species.The largest population increase was predicted to occur under scenarios increasing habitat area. However, the effectiveness was sensitive to spatial planning. Compared to adding one large patch to the habitat network, adding several small patches yielded mixed benefits: although overall population sizes increased, specific newly created patches acted as dispersal sinks, which compromised population persistence in some existing patches. Increasing matrix connectivity by the creation of stepping stones is likely to result in enhanced dispersal success and occupancy of smaller patches. Synthesis and applications. We show that the effectiveness of spatial management is strongly driven by patterns of individual dispersal across landscapes. For species conservation planning, we advocate the use of models that incorporate adequate realism in demography and, particularly, in dispersal behaviours.


#114 Two roles for ecological surrogacy: Indicator surrogates andmanagement surrogates

Malcolm Hunter Jr., Martin Westgate, Philip Barton, Aram Calhoun, Jennifer Pierson, Ayesha Tulloch, Maria Beger, Cristina Branquinho, Tim Caro, John Gross, Jani Heino, Peter Lane, Catherine Longo, Kathy Martin, William H. McDowell, Camille Mellin, Hanna Salo, David Lindenmayer

Ecological Indicators

  • 6 tweets
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#115 Does pollen-assemblage richness reflect floristic richness?:A review of recent developments and future challenges Link logo

Birks, H.J.B.; Felde, V.A.; Bjune, Anne E.; Grytnes, J.-A. ; Seppä, Heikki; Giesecke, Thomas

Review of Palaeobotany & Palynology

  • 4 tweets
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#116 Centrality Dependence of the Charged-Particle Multiplicity Density at Midrapidity in Pb-Pb Collisions at root(NN)-N-S=5.02 TeV Link logo PDF logo

Adam, J.; Brucken, E. J.; Chang, B.; Kim, D. J.; Mieskolainen, M. M.; Orava, R.; Rak, J.; Räsänen, S. S.; Slupecki, M.; Snellman, T. W.; Trzaska, W. H.; Vargyas, M.; Viinikainen, J.; ,

Physical Review Letters Volume 116, Issue 22

  • 13 tweets
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The pseudorapidity density of charged particles, dN_{ch}/dη, at midrapidity in Pb-Pb collisions has been measured at a center-of-mass energy per nucleon pair of sqrt[s_{NN}]=5.02  TeV. For the 5% most central collisions, we measure a value of 1943±54. The rise in dN_{ch}/dη as a function of sqrt[s_{NN}] is steeper than that observed in proton-proton collisions and follows the trend established by measurements at lower energy. The increase of dN_{ch}/dη as a function of the average number of participant nucleons, ⟨N_{part}⟩, calculated in a Glauber model, is compared with the previous measurement at sqrt[s_{NN}]=2.76  TeV. A constant factor of about 1.2 describes the increase in dN_{ch}/dη from sqrt[s_{NN}]=2.76 to 5.02 TeV for all centrality classes, within the measured range of 0%-80% centrality. The results are also compared to models based on different mechanisms for particle production in nuclear collisions.


#117 Suitability of virtual prototypes to support human factors/ergonomics evaluation during the design Link logo

Aromaa, Susanna;Väänänen, Kaisa

Applied Ergonomics

  • 5 tweets
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In recent years, the use of virtual prototyping has increased in product development processes, especially in the assessment of complex systems targeted at end-users. The purpose of this study was to evaluate the suitability of virtual prototyping to support human factors/ergonomics evaluation (HFE) during the design phase. Two different virtual prototypes were used: augmented reality (AR) and virtual environment (VE) prototypes of a maintenance platform of a rock crushing machine. Nineteen designers and other stakeholders were asked to assess the suitability of the prototype for HFE evaluation. Results indicate that the system model characteristics and user interface affect the experienced suitability. The VE system was valued as being more suitable to support the assessment of visibility, reach, and the use of tools than the AR system. The findings of this study can be used as a guidance for the implementing virtual prototypes in the product development process.


#118 Past climate-driven range shifts and population genetic diversity in arctic plants Link logo PDF logo

Pellissier, Loic; Eidesen, Pernille Bronken; Ehrich, Dorothee; Descombes, Patrice; Schoenswetter, Peter; Tribsch, Andreas; Westergaard, Kristine Bakke; Alvarez, Nadir; Guisan, Antoine; Zimmermann, Niklaus E.; Normand, Signe; Vittoz, Pascal; Luoto, Miska; Damgaard, Christian; Brochmann, Christian; Wisz, Mary S.; Alsos, Inger Greve

Journal of Biogeography Volume 43, Issue 3, Pages 461–470

  • 10 tweets
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#119 A new cost-effective approach to survey ecological communities Link logo PDF logo

Blanchet, F. Guillaume; Legendre, Pierre; He, Fangliang

Oikos Volume 125, Issue 7, Pages 975–987

  • 4 tweets
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#120 Last millenium northern hemisphere summer temperatures from tree rings: Part I: The long term context

Wilson, Rob; Anchukaitis, Kevin; Briffa, Keith R.; Büntgen, Ulf; Cook, Edward; D'Arrigo, Rosanne; Davi, Nicole; Esper, Jan; Frank, Dave; Gunnarson, Björn; Hegerl, Gabi; Helama, Samuli; Klesse, Stefan; Krusic, Paul J.; Linderholm, Hans W.; Myglan, Vladimir

Quaternary Science Reviews

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#121 Light-level geolocators reveal migratory connectivity in European populations of pied flycatchers Ficedula hypoleuca Link logo PDF logo

J. Ouwehand, M. P. Ahola, A. N. M. A Ausems, E. S. Bridge, M. Burgess, S. Hahn, C. M. Hewson, R. H. G. Klaassen, T. Laaksonen, H. M. Lampe, W. Velmala, C. Both

Journal of Avian Biology Volume 47, Issue 1, Pages 69–83

  • 148 tweets
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#122 Global atmospheric particle formation from CERN CLOUD measurements Link logo PDF logo

Dunne, Eimear M.; Gordon, Hamish; Kuerten, Andreas; Almeida, Joao; Duplissy, Jonathan; Williamson, Christina; Ortega, Ismael K.; Pringle, Kirsty J.; Adamov, Alexey; Baltensperger, Urs; Barmet, Peter; Benduhn, Francois; Bianchi, Federico; Breitenlechner, Martin; Clarke, Antony; Curtius, Joachim; Dommen, Josef; Donahue, Neil M.; Ehrhart, Sebastian; Flagan, Richard C.

Science Volume 354, Issue 6316, Pages 1119–1124

  • 112 tweets
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Fundamental questions remain about the origin of newly formed atmospheric aerosol particles because data from laboratory measurements have been insufficient to build global models. In contrast, gas-phase chemistry models have been based on laboratory kinetics measurements for decades. Here we build a global model of aerosol formation using extensive laboratory-measured nucleation rates involving sulfuric acid, ammonia, ions and organic compounds. The simulations and a comparison with atmospheric observations show that nearly all nucleation throughout the present-day atmosphere involves ammonia or biogenic organic compounds in addition to sulfuric acid. A significant fraction of nucleation involves ions, but the relatively weak dependence on ion concentrations indicates that for the processes studied variations in cosmic ray intensity do not significantly affect climate via nucleation in the present-day atmosphere.


#123 Highly functionalized organic nitrates in the southeast United States:Contribution to secondary organic aerosol and reactive nitrogen budgets Link logo

Lee, Ben H.; Mohr, Claudia; Lopez-Hilfiker, Felipe D.; Lutz, Anna; Hallquist, Mattias; Lee, Lance; Romer, Paul; Cohen, Ronald C.; Iyer, Siddharth; Kurten, Theo; Hu, Weiwei; Day, Douglas A.; Campuzano-Jost, Pedro; Jimenez, Jose L.; Xu, Lu; Ng, Nga Lee; Guo, Hongyu; Weber, Rodney J.; Wild, Robert J.; Brown, Steven S.

Proceedings of the National Academy of Sciences of the United States of America Volume 113, Issue 6, Pages 1516–1521

  • 72 Mendeley readers

Speciated particle-phase organic nitrates (pONs) were quantified using online chemical ionization MS during June and July of 2013 in rural Alabama as part of the Southern Oxidant and Aerosol Study. A large fraction of pONs is highly functionalized, possessing between six and eight oxygen atoms within each carbon number group, and is not the common first generation alkyl nitrates previously reported. Using calibrations for isoprene hydroxynitrates and the measured molecular compositions, we estimate that pONs account for 3% and 8% of total submicrometer organic aerosol mass, on average, during the day and night, respectively. Each of the isoprene- and monoterpenes-derived groups exhibited a strong diel trend consistent with the emission patterns of likely biogenic hydrocarbon precursors. An observationally constrained diel box model can replicate the observed pON assuming that pONs (i) are produced in the gas phase and rapidly establish gas-particle equilibrium and (ii) have a short particle-phase lifetime (∼2-4 h). Such dynamic behavior has significant implications for the production and phase partitioning of pONs, organic aerosol mass, and reactive nitrogen speciation in a forested environment.


#124 Using Spectral Chlorophyll Fluorescence and the Photochemical Reflectance Index to Predict Physiological Dynamics Link logo

Atherton, Jonathan Mark; Nichol, C. J.; Porcar Castell, Juan Alberto

Remote Sensing of Environment

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#125 Ghost imaging in the time domain Link logo

Ryczkowski, Piotr;Barbier, Margaux;Friberg, Ari T.;Dudley, John M.;Genty, Goëry

Nature Photonics

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#126 The Social Network Position of Lead Users Open access logo PDF logo

Kratzer, Jan; Lettl, Christopher; Franke, Nikolaus; Gloor, Peter A.

Journal of Product Innovation Management Volume 33, Issue 2, Pages 201–216

  • 9 tweets
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#127 Have ecosystem services been oversold? : A response to Silvertown PDF logo

Potschin, Marion B.; Primmer, Eeva; Furman, Eeva; Haines-Young, Roy H.

Trends in Ecology & Evolution

  • 25 tweets
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#128 Modeling European ruminant production systems: Facing the challenges of climate change

Kipling, Richard P.; Bannink, Andre; Bellocchi, Gianni; Dalgaard, Tommy; Fox, Naomi J.; Hutchings, Nicholas J.; Kjeldsen, Chris; Lacetera, Nicola; Sinabell, Franz; Topp, Cairistiona F. E.; van Oijen, Marcel; Virkajärvi, Perttu; Scollan, Nigel D.

Agricultural Systems

  • 5 tweets
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#129 The tumor suppressor PTEN has a critical role in antiviral innate immunity Link logo

Li, Shun; Zhu, Mingzhu; Pan, Ruangang; Fang, Ting; Cao, Yuan-Yuan; Chen, Shuliang; Zhao, Xiaolu; Lei, Cao-Qi; Guo, Lin; Chen, Yu; Li, Chun-Mei; Jokitalo, Eija; Yin, Yuxin; Shu, Hong-Bing; Guo, Deyin

Nature Immunology Volume 17, Issue 3

  • 8 tweets
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The gene encoding PTEN is one of the most frequently mutated tumor suppressor-encoding genes in human cancer. While PTEN's function in tumor suppression is well established, its relationship to anti-microbial immunity remains unknown. Here we found a pivotal role for PTEN in the induction of type I interferon, the hallmark of antiviral innate immunity, that was independent of the pathway of the kinases PI(3)K and Akt. PTEN controlled the import of IRF3, a master transcription factor responsible for IFN-β production, into the nucleus. We further identified a PTEN-controlled negative phosphorylation site at Ser97 of IRF3 and found that release from this negative regulation via the phosphatase activity of PTEN was essential for the activation of IRF3 and its import into the nucleus. Our study identifies crosstalk between PTEN and IRF3 in tumor suppression and innate immunity.


#130 Bursts of activity in collective cell migration PDF logo

Chepizhko, Oleksandr; Giampietro, Costanza; Mastrapasqua, Eleonora; Nourazar, Mehdi; Ascagni, Miriam; Sugni, Michela; Fascio, Umberto; Leggio, Livio; Malinverno, Chiara; Scita, Giorgio; Santucci, Stéphane; Alava, Mikko; Zapperi, Stefano; La Porta, Caterina A M

Proceedings of the National Academy of Sciences of the United States of America

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Dense monolayers of living cells display intriguing relaxation dynamics, reminiscent of soft and glassy materials close to the jamming transition, and migrate collectively when space is available, as in wound healing or in cancer invasion. Here we show that collective cell migration occurs in bursts that are similar to those recorded in the propagation of cracks, fluid fronts in porous media, and ferromagnetic domain walls. In analogy with these systems, the distribution of activity bursts displays scaling laws that are universal in different cell types and for cells moving on different substrates. The main features of the invasion dynamics are quantitatively captured by a model of interacting active particles moving in a disordered landscape. Our results illustrate that collective motion of living cells is analogous to the corresponding dynamics in driven, but inanimate, systems.


#131 Detection of timescales in evolving complex systems Open access logo

Darst, Richard; Granell, Clara; Arenas, Alex; Gómez, Sergio; Saramäki, Jari; Fortunato, Santo

Scientific Reports

  • 96 tweets
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Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant of time. This is often done by using constant intervals but a better approach would be to define dynamic intervals that match the evolution of the system's configuration. To this end, we propose a method that aims at detecting evolutionary changes in the configuration of a complex system, and generates intervals accordingly. We show that evolutionary timescales can be identified by looking for peaks in the similarity between the sets of events on consecutive time intervals of data. Tests on simple toy models reveal that the technique is able to detect evolutionary timescales of time-varying data both when the evolution is smooth as well as when it changes sharply. This is further corroborated by analyses of several real datasets. Our method is scalable to extremely large datasets and is computationally efficient. This allows a quick, parameter-free detection of multiple timescales in the evolution of a complex system.


#132 Quantitative criteria for choosing targets and indicators for sustainable use of ecosyst

Rossberg, Axel G.; Uusitalo, Laura; Berg, Torsten; Zaiko, Anastasija; Chenuil, Anne; . Uyarra, María C; Borja, Àngel; Lynam, Christopher P.

Ecological Indicators

  • 11 tweets
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Wide-ranging, indicator-based assessments of large, complex ecosystems are playing an increasing role in guiding environmental policy and management. An example is the EU's Marine Strategy Framework Directive, which requires Member States to take measures to reach "good environmental status" (GES) in European marine waters. However, formulation of indicator targets consistent with the Directive's high-level policy goal of sustainable use has proven challenging. We develop a specific, quantitative interpretation of the concepts of GES and sustainable use in terms of indicators and associated targets, by sharply distinguishing between current uses to satisfy current societal needs and preferences, and unknown future uses. We argue that consistent targets to safeguard future uses derive from a requirement that any environmental state indicator should recover within a defined time (e.g. 30 years) to its pressure-free range of variation when all pressures are hypothetically removed. Within these constraints, specific targets for current uses should be set. Routes to implementation of this proposal for indicators of fish-community size structure, population size of selected species, eutrophication, impacts of non-indigenous species, and genetic diversity are discussed. Important policy implications are that (a) indicator target ranges, which may be wider than natural ranges, systematically and rationally derive from our proposal; (b) because relevant state indicators tend to respond slowly, corresponding pressures should also be monitored and assessed;


#133 Socio-economic impacts of community wind power projects in Northern Scotland

Okkonen, Lasse; Lehtonen, Olli

Renewable Energy: An International Journal

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#134 Network Structure, Metadata, and the Prediction of Missing Nodes and Annotations Open access logo PDF logo

Hric, Darko; Peixoto, Tiago P.; Fortunato, Santo

arXiv Volume 6, Issue 3

  • 114 tweets
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#135 Synergistic effects of climate and land-use change on representation of African bats in priority conservation areas Link logo

Smith, Alain; Schoeman, Corrie; Keith, Mark; Erasmus, Barend; Monadjem, Ara; Moilanen, Atte Jaakko; Di Minin, Enrico

Ecological Indicators

  • 4 tweets
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#136 Computational pan-genomics:status, promises and challenges Link logo PDF logo

Marschall, Tobias; , ; Mäkinen, Veli Antti Tapani; Valenzuela, Serra Daniel Alejandro

Briefings in Bioinformatics

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Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.


#137 Population genetics of the Asian tiger mosquito Aedes albopictus, an invasive vector of human diseases Link logo

Goubert, Clement; Minard, Guillaume Emeric; Vieira, Cristina; Boulesteix, Matthieu

Heredity Volume 117, Issue 3, Pages 125–134

  • 12 tweets
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The Asian tiger mosquito Aedes albopictus is currently one of the most threatening invasive species in the world. Native to Southeast Asia, the species has spread throughout the world in the past 30 years and is now present in every continent but Antarctica. Because it was the main vector of recent Dengue and Chikungunya outbreaks, and because of its competency for numerous other viruses and pathogens such as the Zika virus, A. albopictus stands out as a model species for invasive diseases vector studies. A synthesis of the current knowledge about the genetic diversity of A. albopictus is needed, knowing the interplays between the vector, the pathogens, the environment and their epidemiological consequences. Such resources are also valuable for assessing the role of genetic diversity in the invasive success. We review here the large but sometimes dispersed literature about the population genetics of A. albopictus. We first debate about the experimental design of these studies and present an up-to-date assessment of the available molecular markers. We then summarize the main genetic characteristics of natural populations and synthesize the available data regarding the worldwide structuring of the vector. Finally, we pinpoint the gaps that remain to be addressed and suggest possible research directions.Heredity advance online publication, 8 June 2016; doi:10.1038/hdy.2016.35.


#138 Karkali. Metsälaitumesta luonnonpuistoksi

Koponen, Timo Juhani

Methods

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Biological imaging based on light microscopy comes at the core of the methods that let us understanding morphology and its dynamics in synergy to the spatiotemporal distribution of cellular and molecular activities as the organism develops and becomes functional. Non-linear optical tools and superesolution methodologies are under constant development and their applications to live imaging of whole organisms keep improving as we speak. Genetically coded biosensors, multicolor clonal methods and optogenetics in different organisms and, in particular, in Drosophila follow equivalent paths. We anticipate a brilliant future for live imaging providing the roots for the holistic understanding, rather than for individual parts, of development and function at the whole-organism level.


#139 Approaching the affective barriers to information seeking: the viewpoint of appraisal theory Open access logo Link logo

Savolainen Reijo

Library & Information Science Research (07408188) Volume 35, Issue 1, Pages 63–68

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#140 Functionalization mediates heat transport in graphene nanoflakes Open access logo

Han, Haoxue; Zhang, Yong; Wang, Nan; Samani, Majid Kabiri; Ni, Yuxiang; Mijbil, Zainelabideen Y.; Edwards, Michael; Xiong, Shiyun; Sääskilahti, Kimmo; Murugesan, Murali; Fu, Yifeng; Ye, Lilei; Sadeghi, Hatef; Bailey, Steven; Kosevich, Yuriy A.; Lambert, Colin J.; Liu, Johan; Volz, Sebastian

Nature Communications

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The high thermal conductivity of graphene and few-layer graphene undergoes severe degradations through contact with the substrate. Here we show experimentally that the thermal management of a micro heater is substantially improved by introducing alternative heat-escaping channels into a graphene-based film bonded to functionalized graphene oxide through amino-silane molecules. Using a resistance temperature probe for in situ monitoring we demonstrate that the hotspot temperature was lowered by ∼28 °C for a chip operating at 1,300 W cm(-2). Thermal resistance probed by pulsed photothermal reflectance measurements demonstrated an improved thermal coupling due to functionalization on the graphene-graphene oxide interface. Three functionalization molecules manifest distinct interfacial thermal transport behaviour, corroborating our atomistic calculations in unveiling the role of molecular chain length and functional groups. Molecular dynamics simulations reveal that the functionalization constrains the cross-plane phonon scattering, which in turn enhances in-plane heat conduction of the bonded graphene film by recovering the long flexural phonon lifetime.


#141 What you need is what you eat? Prey selection by the bat Myotis daubentonii Link logo PDF logo

Vesterinen, Eero J.; Ruokolainen, Lasse; Wahlberg, Niklas; Pena, Carlos; Roslin, Tomas; Laine, Veronika N.; Vasko, Ville; Sääksjarvi, Ilari E.; Norrdahl, Kai; Lilley, Thomas M.

Molecular Ecology Volume 25, Issue 7, Pages 1581–1594

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Optimal foraging theory predicts that predators are selective when faced with abundant prey, but become less picky when prey gets sparse. Insectivorous bats in temperate regions are faced with the challenge of building up fat reserves vital for hibernation during a period of decreasing arthropod abundances. According to optimal foraging theory, pre-hibernating bats should adopt a less selective feeding behavior - yet empirical studies have revealed many apparently generalized species to be composed of specialist individuals. Targeting the diet of the bat Myotis daubentonii, we used a combination of molecular techniques to test for seasonal changes in prey selectivity and individual-level variation in prey preferences. DNA metabarcoding was used to characterise both the prey contents of bat droppings and the insect community available as prey. To test for dietary differences among M. daubentonii individuals, we used ten microsatellite loci to assign droppings to individual bats. The comparison between consumed and available prey revealed a preference for certain prey items regardless of availability. Non-biting midges (Chironomidae) remained the most highly consumed prey at all times, despite a significant increase in the availability of black-flies (Simuliidae) towards the end of the season. The bats sampled showed no evidence of individual specialization in dietary preferences. Overall, our approach offers little support for optimal foraging theory. Thus, it shows how novel combinations of genetic markers can be used to test general theory, targeting patterns at both the level of prey communities and individual predators. This article is protected by copyright. All rights reserved.


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