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Showing papers by "University of Vienna published in 2014"


Journal ArticleDOI
Bernhard Misof, Shanlin Liu, Karen Meusemann1, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen2, Jessica L. Ware2, Tomas Flouri3, Rolf G. Beutel4, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco3, Torsten Wappler5, Jes Rust5, Andre J. Aberer3, Ulrike Aspöck6, Ulrike Aspöck7, Horst Aspöck6, Daniela Bartel6, Alexander Blanke8, Simon Berger3, Alexander Böhm6, Thomas R. Buckley9, Brett Calcott10, Junqing Chen, Frank Friedrich11, Makiko Fukui12, Mari Fujita8, Carola Greve, Peter Grobe, Shengchang Gu, Ying Huang, Lars S. Jermiin1, Akito Y. Kawahara13, Lars Krogmann14, Martin Kubiak11, Robert Lanfear15, Robert Lanfear16, Robert Lanfear17, Harald Letsch6, Yiyuan Li, Zhenyu Li, Jiguang Li, Haorong Lu, Ryuichiro Machida8, Yuta Mashimo8, Pashalia Kapli18, Pashalia Kapli3, Duane D. McKenna19, Guanliang Meng, Yasutaka Nakagaki8, José Luis Navarrete-Heredia20, Michael Ott21, Yanxiang Ou, Günther Pass6, Lars Podsiadlowski5, Hans Pohl4, Björn M. von Reumont22, Kai Schütte11, Kaoru Sekiya8, Shota Shimizu8, Adam Slipinski1, Alexandros Stamatakis3, Alexandros Stamatakis23, Wenhui Song, Xu Su, Nikolaus U. Szucsich6, Meihua Tan, Xuemei Tan, Min Tang, Jingbo Tang, Gerald Timelthaler6, Shigekazu Tomizuka8, Michelle D. Trautwein24, Xiaoli Tong25, Toshiki Uchifune8, Manfred Walzl6, Brian M. Wiegmann26, Jeanne Wilbrandt, Benjamin Wipfler4, Thomas K. F. Wong1, Qiong Wu, Gengxiong Wu, Yinlong Xie, Shenzhou Yang, Qing Yang, David K. Yeates1, Kazunori Yoshizawa27, Qing Zhang, Rui Zhang, Wenwei Zhang, Yunhui Zhang, Jing Zhao, Chengran Zhou, Lili Zhou, Tanja Ziesmann, Shijie Zou, Yingrui Li, Xun Xu, Yong Zhang, Huanming Yang, Jian Wang, Jun Wang, Karl M. Kjer2, Xin Zhou 
07 Nov 2014-Science
TL;DR: The phylogeny of all major insect lineages reveals how and when insects diversified and provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
Abstract: Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

1,998 citations


Journal ArticleDOI
TL;DR: In this article, the authors address Ronkko and Evermann's criticisms of the Partial Least Squares (PLS) approach to structural equation modeling and conclude that PLS should continue to be used as an important statistical tool for management and organizational research, as well as other social science disciplines.
Abstract: This article addresses Ronkko and Evermann’s criticisms of the partial least squares (PLS) approach to structural equation modeling. We contend that the alleged shortcomings of PLS are not due to problems with the technique, but instead to three problems with Ronkko and Evermann’s study: (a) the adherence to the common factor model, (b) a very limited simulation designs, and (c) overstretched generalizations of their findings. Whereas Ronkko and Evermann claim to be dispelling myths about PLS, they have in reality created new myths that we, in turn, debunk. By examining their claims, our article contributes to reestablishing a constructive discussion of the PLS method and its properties. We show that PLS does offer advantages for exploratory research and that it is a viable estimator for composite factor models. This can pose an interesting alternative if the common factor model does not hold. Therefore, we can conclude that PLS should continue to be used as an important statistical tool for management and organizational research, as well as other social science disciplines.

1,906 citations


Journal ArticleDOI
TL;DR: The theoretical modeling of point defects in crystalline materials by means of electronic-structure calculations, with an emphasis on approaches based on density functional theory (DFT), is reviewed in this paper.
Abstract: Point defects and impurities strongly affect the physical properties of materials and have a decisive impact on their performance in applications. First-principles calculations have emerged as a powerful approach that complements experiments and can serve as a predictive tool in the identification and characterization of defects. The theoretical modeling of point defects in crystalline materials by means of electronic-structure calculations, with an emphasis on approaches based on density functional theory (DFT), is reviewed. A general thermodynamic formalism is laid down to investigate the physical properties of point defects independent of the materials class (semiconductors, insulators, and metals), indicating how the relevant thermodynamic quantities, such as formation energy, entropy, and excess volume, can be obtained from electronic structure calculations. Practical aspects such as the supercell approach and efficient strategies to extrapolate to the isolated-defect or dilute limit are discussed. Recent advances in tractable approximations to the exchange-correlation functional ($\mathrm{DFT}+U$, hybrid functionals) and approaches beyond DFT are highlighted. These advances have largely removed the long-standing uncertainty of defect formation energies in semiconductors and insulators due to the failure of standard DFT to reproduce band gaps. Two case studies illustrate how such calculations provide new insight into the physics and role of point defects in real materials.

1,846 citations


Journal ArticleDOI
Feng Yue1, Feng Yue2, Yong Cheng3, Alessandra Breschi, Jeff Vierstra4, Weisheng Wu5, Weisheng Wu1, Tyrone Ryba6, Tyrone Ryba7, Richard Sandstrom4, Zhihai Ma3, Carrie A. Davis8, Benjamin D. Pope6, Yin Shen2, Dmitri D. Pervouchine, Sarah Djebali, Robert E. Thurman4, Rajinder Kaul4, Eric Rynes4, Anthony Kirilusha9, Georgi K. Marinov9, Brian A. Williams9, Diane Trout9, Henry Amrhein9, Katherine I. Fisher-Aylor9, Igor Antoshechkin9, Gilberto DeSalvo9, Lei Hoon See8, Meagan Fastuca8, Jorg Drenkow8, Chris Zaleski8, Alexander Dobin8, Pablo Prieto, Julien Lagarde, Giovanni Bussotti, Andrea Tanzer10, Olgert Denas11, Kanwei Li11, M. A. Bender4, M. A. Bender12, Miaohua Zhang12, Rachel Byron12, Mark Groudine12, Mark Groudine4, David McCleary2, Long Pham2, Zhen Ye2, Samantha Kuan2, Lee Edsall2, Yi-Chieh Wu13, Matthew D. Rasmussen13, Mukul S. Bansal13, Manolis Kellis13, Manolis Kellis14, Cheryl A. Keller1, Christapher S. Morrissey1, Tejaswini Mishra1, Deepti Jain1, Nergiz Dogan1, Robert S. Harris1, Philip Cayting3, Trupti Kawli3, Alan P. Boyle5, Alan P. Boyle3, Ghia Euskirchen3, Anshul Kundaje3, Shin Lin3, Yiing Lin3, Camden Jansen15, Venkat S. Malladi3, Melissa S. Cline16, Drew T. Erickson3, Vanessa M. Kirkup16, Katrina Learned16, Cricket A. Sloan3, Kate R. Rosenbloom16, Beatriz Lacerda de Sousa17, Kathryn Beal, Miguel Pignatelli, Paul Flicek, Jin Lian18, Tamer Kahveci19, Dongwon Lee20, W. James Kent16, Miguel Santos17, Javier Herrero21, Cedric Notredame, Audra K. Johnson4, Shinny Vong4, Kristen Lee4, Daniel Bates4, Fidencio Neri4, Morgan Diegel4, Theresa K. Canfield4, Peter J. Sabo4, Matthew S. Wilken4, Thomas A. Reh4, Erika Giste4, Anthony Shafer4, Tanya Kutyavin4, Eric Haugen4, Douglas Dunn4, Alex Reynolds4, Shane Neph4, Richard Humbert4, R. Scott Hansen4, Marella F. T. R. de Bruijn22, Licia Selleri23, Alexander Y. Rudensky24, Steven Z. Josefowicz24, Robert M. Samstein24, Evan E. Eichler4, Stuart H. Orkin25, Dana N. Levasseur26, Thalia Papayannopoulou4, Kai Hsin Chang4, Arthur I. Skoultchi27, Srikanta Gosh27, Christine M. Disteche4, Piper M. Treuting4, Yanli Wang1, Mitchell J. Weiss, Gerd A. Blobel28, Xiaoyi Cao2, Sheng Zhong2, Ting Wang29, Peter J. Good30, Rebecca F. Lowdon30, Rebecca F. Lowdon29, Leslie B. Adams31, Leslie B. Adams30, Xiao Qiao Zhou30, Michael J. Pazin30, Elise A. Feingold30, Barbara J. Wold9, James Taylor11, Ali Mortazavi15, Sherman M. Weissman18, John A. Stamatoyannopoulos4, Michael Snyder3, Roderic Guigó, Thomas R. Gingeras8, David M. Gilbert6, Ross C. Hardison1, Michael A. Beer20, Bing Ren2 
20 Nov 2014-Nature
TL;DR: The mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types as mentioned in this paper.
Abstract: The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases

1,335 citations


Journal ArticleDOI
TL;DR: In this article, the authors simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics, construct co-occurrence networks, and evaluate how well networks reveal the underlying interactions, and how experimental and ecological parameters can affect network inference and interpretation.
Abstract: Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics, construct co-occurrence networks, and evaluate how well networks reveal the underlying interactions, and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of “hub” species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.

997 citations


Journal ArticleDOI
10 Oct 2014-Science
TL;DR: A comprehensive mid-term assessment of progress toward 20 biodiversity-related “Aichi Targets” to be achieved within a decade is provided using 55 indicator data sets and pinpoints the problems and areas that will need the most attention in the next few years.
Abstract: In 2010, the international community, under the auspices of the Convention on Biological Diversity, agreed on 20 biodiversity-related “Aichi Targets” to be achieved within a decade. We provide a comprehensive mid-term assessment of progress toward these global targets using 55 indicator data sets. We projected indicator trends to 2020 using an adaptive statistical framework that incorporated the specific properties of individual time series. On current trajectories, results suggest that despite accelerating policy and management responses to the biodiversity crisis, the impacts of these efforts are unlikely to be reflected in improved trends in the state of biodiversity by 2020. We highlight areas of societal endeavor requiring additional efforts to achieve the Aichi Targets, and provide a baseline against which to assess future progress.

970 citations


Journal ArticleDOI
Heike Rauer1, Heike Rauer2, C. Catala3, Conny Aerts4  +164 moreInstitutions (51)
TL;DR: The PLATO 2.0 mission as discussed by the authors has been selected for ESA's M3 launch opportunity (2022/24) to provide accurate key planet parameters (radius, mass, density and age) in statistical numbers.
Abstract: PLATO 2.0 has recently been selected for ESA’s M3 launch opportunity (2022/24). Providing accurate key planet parameters (radius, mass, density and age) in statistical numbers, it addresses fundamental questions such as: How do planetary systems form and evolve? Are there other systems with planets like ours, including potentially habitable planets? The PLATO 2.0 instrument consists of 34 small aperture telescopes (32 with 25 s readout cadence and 2 with 2.5 s candence) providing a wide field-of-view (2232 deg 2) and a large photometric magnitude range (4–16 mag). It focusses on bright (4–11 mag) stars in wide fields to detect and characterize planets down to Earth-size by photometric transits, whose masses can then be determined by ground-based radial-velocity follow-up measurements. Asteroseismology will be performed for these bright stars to obtain highly accurate stellar parameters, including masses and ages. The combination of bright targets and asteroseismology results in high accuracy for the bulk planet parameters: 2 %, 4–10 % and 10 % for planet radii, masses and ages, respectively. The planned baseline observing strategy includes two long pointings (2–3 years) to detect and bulk characterize planets reaching into the habitable zone (HZ) of solar-like stars and an additional step-and-stare phase to cover in total about 50 % of the sky. PLATO 2.0 will observe up to 1,000,000 stars and detect and characterize hundreds of small planets, and thousands of planets in the Neptune to gas giant regime out to the HZ. It will therefore provide the first large-scale catalogue of bulk characterized planets with accurate radii, masses, mean densities and ages. This catalogue will include terrestrial planets at intermediate orbital distances, where surface temperatures are moderate. Coverage of this parameter range with statistical numbers of bulk characterized planets is unique to PLATO 2.0. The PLATO 2.0 catalogue allows us to e.g.: - complete our knowledge of planet diversity for low-mass objects, - correlate the planet mean density-orbital distance distribution with predictions from planet formation theories,- constrain the influence of planet migration and scattering on the architecture of multiple systems, and - specify how planet and system parameters change with host star characteristics, such as type, metallicity and age. The catalogue will allow us to study planets and planetary systems at different evolutionary phases. It will further provide a census for small, low-mass planets. This will serve to identify objects which retained their primordial hydrogen atmosphere and in general the typical characteristics of planets in such low-mass, low-density range. Planets detected by PLATO 2.0 will orbit bright stars and many of them will be targets for future atmosphere spectroscopy exploring their atmosphere. Furthermore, the mission has the potential to detect exomoons, planetary rings, binary and Trojan planets. The planetary science possible with PLATO 2.0 is complemented by its impact on stellar and galactic science via asteroseismology as well as light curves of all kinds of variable stars, together with observations of stellar clusters of different ages. This will allow us to improve stellar models and study stellar activity. A large number of well-known ages from red giant stars will probe the structure and evolution of our Galaxy. Asteroseismic ages of bright stars for different phases of stellar evolution allow calibrating stellar age-rotation relationships. Together with the results of ESA’s Gaia mission, the results of PLATO 2.0 will provide a huge legacy to planetary, stellar and galactic science.

965 citations


Journal ArticleDOI
TL;DR: This work demonstrates simultaneous functional imaging of neuronal activity at single-neuron resolution in an entire Caenorhabditis elegans and in larval zebrafish brain with high-speed volumetric calcium imaging.
Abstract: High-speed, large-scale three-dimensional (3D) imaging of neuronal activity poses a major challenge in neuroscience. Here we demonstrate simultaneous functional imaging of neuronal activity at single-neuron resolution in an entire Caenorhabditis elegans and in larval zebrafish brain. Our technique captures the dynamics of spiking neurons in volumes of ∼700 μm × 700 μm × 200 μm at 20 Hz. Its simplicity makes it an attractive tool for high-speed volumetric calcium imaging.

714 citations


Journal ArticleDOI
09 Oct 2014-Nature
TL;DR: This synthesis maintains that important drivers of evolution, ones that cannot be reduced to genes, must be woven into the very fabric of evolutionary theory, and believes that the EES will shed new light on how Point Yes, urgently is shed.
Abstract: Nobel physicist talks plants with a waiter, then what? p.168 ENERGY Don't assume that renewable energies are problem-free p.168 AGEING Atul Gawande's call to action on end-of-life medical care p.167 HEALTH Lasting legacy of wartime battle against malaria p.166 Does evolutionary theory need a rethink? Researchers are divided over what processes should be considered fundamental. I n October 1881, just six months before he died, Charles Darwin published his final book. The Formation of Vegetable Mould, Through the Actions of Worms 11 sold briskly: Darwin's earlier publications had secured his reputation. He devoted an entire book to these humble creatures in part because they exemplify an interesting feedback process: earthworms are adapted to thrive in an environment that they modify through their own activities. Darwin learned about earthworms from conversations with gardeners and his own simple experiments. He had a genius for distilling penetrating insights about evolutionary processes — often after amassing years of observational and experimental data — and he drew on such disparate topics as agriculture, geology, embryol-ogy and behaviour. Evolutionary thinking ever since has followed Darwin's lead in its emphasis on evidence and in synthesizing information from other fields. A profound shift in evolutionary thinking began C harles Darwin conceived of evolution by natural selection without knowing that genes exist. Now mainstream evolutionary theory has come to focus almost exclusively on genetic inheritance and processes that change gene frequencies. Yet new data pouring out of adjacent fields are starting to undermine this narrow stance. An alternative vision of evolution is beginning to crystallize, in which the processes by which organisms grow and develop are recognized as causes of evolution. Some of us first met to discuss these advances six years ago. In the time since, as members of an interdisciplinary team, we have worked intensively to develop a broader framework, termed the extended evolutionary synthesis 1 (EES), and to flesh out its structure, assumptions and predictions. In essence, this synthesis maintains that important drivers of evolution, ones that cannot be reduced to genes, must be woven into the very fabric of evolutionary theory. We believe that the EES will shed new light on how POINT Yes, urgently Without an extended evolutionary framework, the theory neglects key processes, say Kevin Laland and colleagues.

709 citations


Journal ArticleDOI
TL;DR: In this article, a feature article reviews the various nanocellulose re-feedback reinforcement for the production of high performance biocomposites. But this feature article focuses on the nanocellular reinforcement.

665 citations


Journal ArticleDOI
TL;DR: A two year survey using stationary driftnets detected mean plastic abundance and mass in the Austrian Danube to be higher than those of drifting larval fish and industrial raw material accounted for substantial parts of the plastic debris.

Journal ArticleDOI
13 Mar 2014-Nature
TL;DR: X-ray diffraction, Raman and infrared spectroscopic data are reported that provide the first evidence for the terrestrial occurrence of any higher-pressure polymorph of olivine: ringwoodite is included in a diamond from Juína, Brazil, providing direct evidence that, at least locally, the transition zone is hydrous.
Abstract: X-ray diffraction, Raman and infrared spectroscopic evidence for the inclusion of water-rich ringwoodite in diamond from Juina, Brazil, indicates that, at least locally, the Earth’s transition zone is hydrous to about 1 weight per cent. It is not clear just how much water resides within the solid Earth, and where it is to be found, with many indirect measurements yielding conflicting results. Here Graham Pearson and co-authors present evidence from a diamond inclusion from Juina, Brazil, for the first known terrestrial occurrence of ringwoodite — a high-pressure polymorph of olivine first identified in meteorites and thought to be a major constituent of the Earth's mantle transition zone. The water-rich nature of this inclusion provides direct evidence that, at least locally, the transition zone is hydrous, to about 1 weight per cent. The ultimate origin of water in the Earth’s hydrosphere is in the deep Earth—the mantle. Theory1 and experiments2,3,4 have shown that although the water storage capacity of olivine-dominated shallow mantle is limited, the Earth’s transition zone, at depths between 410 and 660 kilometres, could be a major repository for water, owing to the ability of the higher-pressure polymorphs of olivine—wadsleyite and ringwoodite—to host enough water to comprise up to around 2.5 per cent of their weight. A hydrous transition zone may have a key role in terrestrial magmatism and plate tectonics5,6,7, yet despite experimental demonstration of the water-bearing capacity of these phases, geophysical probes such as electrical conductivity have provided conflicting results8,9,10, and the issue of whether the transition zone contains abundant water remains highly controversial11. Here we report X-ray diffraction, Raman and infrared spectroscopic data that provide, to our knowledge, the first evidence for the terrestrial occurrence of any higher-pressure polymorph of olivine: we find ringwoodite included in a diamond from Juina, Brazil. The water-rich nature of this inclusion, indicated by infrared absorption, along with the preservation of the ringwoodite, is direct evidence that, at least locally, the transition zone is hydrous, to about 1 weight per cent. The finding also indicates that some kimberlites must have their primary sources in this deep mantle region.

Journal ArticleDOI
26 Feb 2014-PLOS ONE
TL;DR: Occupation, occupational status, age, gender, and wealth are identified as the main socio-demographic factors associated with musical sophistication.
Abstract: Musical skills and expertise vary greatly in Western societies. Individuals can differ in their repertoire of musical behaviours as well as in the level of skill they display for any single musical behaviour. The types of musical behaviours we refer to here are broad, ranging from performance on an instrument and listening expertise, to the ability to employ music in functional settings or to communicate about music. In this paper, we first describe the concept of ‘musical sophistication’ which can be used to describe the multi-faceted nature of musical expertise. Next, we develop a novel measurement instrument, the Goldsmiths Musical Sophistication Index (Gold-MSI) to assess self-reported musical skills and behaviours on multiple dimensions in the general population using a large Internet sample (n = 147,636). Thirdly, we report results from several lab studies, demonstrating that the Gold-MSI possesses good psychometric properties, and that self-reported musical sophistication is associated with performance on two listening tasks. Finally, we identify occupation, occupational status, age, gender, and wealth as the main socio-demographic factors associated with musical sophistication. Results are discussed in terms of theoretical accounts of implicit and statistical music learning and with regard to social conditions of sophisticated musical engagement.

Journal ArticleDOI
TL;DR: It is found that microbes retain most immobilized organic N when they are N limited, resulting in low N mineralization, however, when the metabolic control of microbial decomposers switches from N to C limitation, they release an increasing fraction of organic N as ammonium (low NUE).
Abstract: Microbial nitrogen use efficiency (NUE) describes the partitioning of organic N taken up between growth and the release of inorganic N to the environment (that is, N mineralization), and is thus central to our understanding of N cycling. Here we report empirical evidence that microbial decomposer communities in soil and plant litter regulate their NUE. We find that microbes retain most immobilized organic N (high NUE), when they are N limited, resulting in low N mineralization. However, when the metabolic control of microbial decomposers switches from N to C limitation, they release an increasing fraction of organic N as ammonium (low NUE). We conclude that the regulation of NUE is an essential strategy of microbial communities to cope with resource imbalances, independent of the regulation of microbial carbon use efficiency, with significant effects on terrestrial N cycling.

Journal ArticleDOI
TL;DR: A method for categorising and comparing alien or invasive species in terms of how damaging they are to the environment, that can be applied across all taxa, scales, and impact metrics is presented.
Abstract: Species moved by human activities beyond the limits of their native geographic ranges into areas in which they do not naturally occur (termed aliens) can cause a broad range of significant changes to recipient ecosystems; however, their impacts vary greatly across species and the ecosystems into which they are introduced. There is therefore a critical need for a standardised method to evaluate, compare, and eventually predict the magnitudes of these different impacts. Here, we propose a straightforward system for classifying alien species according to the magnitude of their environmental impacts, based on the mechanisms of impact used to code species in the International Union for Conservation of Nature (IUCN) Global Invasive Species Database, which are presented here for the first time. The classification system uses five semi-quantitative scenarios describing impacts under each mechanism to assign species to different levels of impact-ranging from Minimal to Massive-with assignment corresponding to the highest level of deleterious impact associated with any of the mechanisms. The scheme also includes categories for species that are Not Evaluated, have No Alien Population, or are Data Deficient, and a method for assigning uncertainty to all the classifications. We show how this classification system is applicable at different levels of ecological complexity and different spatial and temporal scales, and embraces existing impact metrics. In fact, the scheme is analogous to the already widely adopted and accepted Red List approach to categorising extinction risk, and so could conceivably be readily integrated with existing practices and policies in many regions.

Journal ArticleDOI
TL;DR: A great deal of research will be required over the coming years into the development of experimental protocols to generate reliable fate properties, investigations into the bioavailability and durability of nanopesticides, and evaluation of current environmental risk assessment approaches, and their refinement where appropriate.

Journal ArticleDOI
TL;DR: It is concluded that a HF diet markedly affects the gut bacterial ecosystem at the functional level.
Abstract: The intestinal microbiota is known to regulate host energy homeostasis and can be influenced by high-calorie diets. However, changes affecting the ecosystem at the functional level are still not well characterized. We measured shifts in cecal bacterial communities in mice fed a carbohydrate or high-fat (HF) diet for 12 weeks at the level of the following: (i) diversity and taxa distribution by high-throughput 16S ribosomal RNA gene sequencing; (ii) bulk and single-cell chemical composition by Fourier-transform infrared- (FT-IR) and Raman micro-spectroscopy and (iii) metaproteome and metabolome via high-resolution mass spectrometry. High-fat diet caused shifts in the diversity of dominant gut bacteria and altered the proportion of Ruminococcaceae (decrease) and Rikenellaceae (increase). FT-IR spectroscopy revealed that the impact of the diet on cecal chemical fingerprints is greater than the impact of microbiota composition. Diet-driven changes in biochemical fingerprints of members of the Bacteroidales and Lachnospiraceae were also observed at the level of single cells, indicating that there were distinct differences in cellular composition of dominant phylotypes under different diets. Metaproteome and metabolome analyses based on the occurrence of 1760 bacterial proteins and 86 annotated metabolites revealed distinct HF diet-specific profiles. Alteration of hormonal and anti-microbial networks, bile acid and bilirubin metabolism and shifts towards amino acid and simple sugars metabolism were observed. We conclude that a HF diet markedly affects the gut bacterial ecosystem at the functional level.

Journal ArticleDOI
TL;DR: Taken together, KP1019 and NKP-1339 are promising drug candidates, and especially the very limited side effects observed so far in clinical phase I trials seem to be a major advantage of this class of ruthenium drugs as compared to other chemotherapeutics and targeted anticancer compounds.
Abstract: NKP-1339 is the first-in-class ruthenium-based anticancer drug in clinical development against solid cancer and has recently been studied successfully in a phase I clinical trial. Ruthenium compounds such as KP1019 (indazolium trans-[tetrachloridobis(1H-indazole)ruthenate(III)]) and NKP-1339 (the sodium salt analogue of KP1019, sodium trans-[tetrachloridobis(1H-indazole)ruthenate(III)]) have a high tumour targeting potential based (1) on their strong binding to serum proteins such as albumin and transferrin as well as (2) on their activation in the reductive tumour milieu. The redox activity of ruthenium compounds is believed to represent one major mode of action leading to disturbance of the cellular redox balance and, consequently, induction of G2/M cell cycle arrest, blockage of DNA synthesis, and induction of apoptosis via the mitochondrial pathway. Moreover, potent synergistic activities of NKP-1339 with the clinically approved tyrosine kinase inhibitor sorafenib were recently reported in vitro and in vivo. Taken together, KP1019 and NKP-1339 are promising drug candidates, and especially the very limited side effects observed so far in clinical phase I trials seem to be a major advantage of this class of ruthenium drugs as compared to other chemotherapeutics and targeted anticancer compounds.

Journal ArticleDOI
TL;DR: A significant research effort has recently been undertaken to explore the PPARγ-activating potential of a wide range of natural products originating from traditionally used medicinal plants or dietary sources.

Journal ArticleDOI
TL;DR: In this paper, the role of social media as a sphere for political expression and its effects on political participation was examined and it was shown that social media use for social interaction does not have direct influence in people's political engagement, but rather an indirect effect by means of citizens expressing themselves politically.
Abstract: This article relies on U.S. 2-wave panel data to examine the role of social media as a sphere for political expression and its effects on political participation. Informational uses of social media are expected to explain political expression on social media and to promote political participation. This study clarifies the effect of using social media for social interaction in fostering political expression and participation processes. Results indicate that social media news use has direct effects on offline political participation and indirect effects on offline and online political participation mediated via political expression. Furthermore, social media use for social interaction does not have direct influence in people’s political engagement, but rather an indirect effect by means of citizens expressing themselves politically.

Journal ArticleDOI
01 Jul 2014-Genetics
TL;DR: It is proposed that the domestication syndrome results predominantly from mild neural crest cell deficits during embryonic development, which can be readily explained as direct consequences of such deficiencies, while other traits are explicable as indirect consequences.
Abstract: Charles Darwin, while trying to devise a general theory of heredity from the observations of animal and plant breeders, discovered that domesticated mammals possess a distinctive and unusual suite of heritable traits not seen in their wild progenitors. Some of these traits also appear in domesticated birds and fish. The origin of Darwin's "domestication syndrome" has remained a conundrum for more than 140 years. Most explanations focus on particular traits, while neglecting others, or on the possible selective factors involved in domestication rather than the underlying developmental and genetic causes of these traits. Here, we propose that the domestication syndrome results predominantly from mild neural crest cell deficits during embryonic development. Most of the modified traits, both morphological and physiological, can be readily explained as direct consequences of such deficiencies, while other traits are explicable as indirect consequences. We first show how the hypothesis can account for the multiple, apparently unrelated traits of the syndrome and then explore its genetic dimensions and predictions, reviewing the available genetic evidence. The article concludes with a brief discussion of some genetic and developmental questions raised by the idea, along with specific predictions and experimental tests.

Journal ArticleDOI
TL;DR: This review summarizes different views on how microbes cope with imbalanced supply of C, N and P, thereby providing a framework for integrating and linking microbial adaptation to resource imbalances to ecosystem scale fluxes across scales and ecosystems.
Abstract: Terrestrial microbial decomposer communities thrive on a wide range of organic matter types that rarely ever meet their elemental demands. In this review we synthesize the current state-of-the-art of microbial adaptations to resource stoichiometry, in order to gain a deeper understanding of the interactions between heterotrophic microbial communities and their chemical environment. The stoichiometric imbalance between microbial communities and their organic substrates generally decreases from wood to leaf litter and further to topsoil and subsoil organic matter. Microbial communities can respond to these imbalances in four ways: first, they adapt their biomass composition toward their resource in a non-homeostatic behavior. Such changes are, however, only moderate, and occur mainly because of changes in microbial community structure and less so due to cellular storage of elements in excess. Second, microbial communities can mobilize resources that meet their elemental demand by producing specific extracellular enzymes, which, in turn, is restricted by the C and N requirement for enzyme production itself. Third, microbes can regulate their element use efficiencies (ratio of element invested in growth over total element uptake), such that they release elements in excess depending on their demand (e.g., respiration and N mineralization). Fourth, diazotrophic bacteria and saprotrophic fungi may trigger the input of external N and P to decomposer communities. Theoretical considerations show that adjustments in element use efficiencies may be the most important mechanism by which microbes regulate their biomass stoichiometry. This review summarizes different views on how microbes cope with imbalanced supply of C, N and P, thereby providing a framework for integrating and linking microbial adaptation to resource imbalances to ecosystem scale fluxes across scales and ecosystems.

Journal ArticleDOI
16 May 2014-Science
TL;DR: It is shown, in experiments performed with the CLOUD (Cosmics Leaving Outdoor Droplets) chamber at CERN, that sulfuric acid and oxidized organic vapors at atmospheric concentrations reproduce particle nucleation rates observed in the lower atmosphere.
Abstract: Atmospheric new-particle formation affects climate and is one of the least understood atmospheric aerosol processes. The complexity and variability of the atmosphere has hindered elucidation of the fundamental mechanism of new-particle formation from gaseous precursors. We show, in experiments performed with the CLOUD (Cosmics Leaving Outdoor Droplets) chamber at CERN, that sulfuric acid and oxidized organic vapors at atmospheric concentrations reproduce particle nucleation rates observed in the lower atmosphere. The experiments reveal a nucleation mechanism involving the formation of clusters containing sulfuric acid and oxidized organic molecules from the very first step. Inclusion of this mechanism in a global aerosol model yields a photochemically and biologically driven seasonal cycle of particle concentrations in the continental boundary layer, in good agreement with observations.

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TL;DR: In this paper, the binding energy and Van der Waals (vdW) interlayer spacing between the two layers of bilayer transition metal dichalcogenides were investigated for five different stacking patterns, and examined the stacking-induced modifications on the electronic and optical/excitonic properties within the GW approximation with a priori inclusion of spin-orbit coupling and by solving the twoparticle Bethe-Salpeter equation.
Abstract: Employing the random phase approximation we investigate the binding energy and Van der Waals (vdW) interlayer spacing between the two layers of bilayer transition metal dichalcogenides ${\mathrm{MoS}}_{2}$, ${\mathrm{MoSe}}_{2}$, ${\mathrm{WS}}_{2}$, and ${\mathrm{WSe}}_{2}$ for five different stacking patterns, and examine the stacking-induced modifications on the electronic and optical/excitonic properties within the GW approximation with a priori inclusion of spin-orbit coupling and by solving the two-particle Bethe-Salpeter equation. Our results show that for all cases, the most stable stacking order is the high symmetry $A{A}^{\ensuremath{'}}$ type, distinctive of the bulklike $2H$ symmetry, followed by the $AB$ stacking fault, typical of the $3R$ polytypism, which is by only 5 meV/formula unit less stable. The conduction band minimum is always located in the midpoint between K and $\ensuremath{\Gamma}$, regardless of the stacking and chemical composition. All $M{X}_{2}$ undergo an direct-to-indirect optical gap transition going from the monolayer to the bilayer regime. The stacking and the characteristic vdW interlayer distance mainly influence the valence band splitting at K and its relative energy with respect to $\ensuremath{\Gamma}$, as well as, the electron-hole binding energy and the values of the optical excitations.

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TL;DR: In this paper, the progress, current status, and open challenges of QCD-driven physics, in theory and in experiment, are highlighted, highlighting how the strong interaction is intimately connected to a broad sweep of physical problems, in settings ranging from astrophysics and cosmology to strongly coupled, complex systems in particle and condensed-matter physics, as well as searches for physics beyond the Standard Model.
Abstract: We highlight the progress, current status, and open challenges of QCD-driven physics, in theory and in experiment. We discuss how the strong interaction is intimately connected to a broad sweep of physical problems, in settings ranging from astrophysics and cosmology to strongly coupled, complex systems in particle and condensed-matter physics, as well as to searches for physics beyond the Standard Model. We also discuss how success in describing the strong interaction impacts other fields, and, in turn, how such subjects can impact studies of the strong interaction. In the course of the work we offer a perspective on the many research streams which flow into and out of QCD, as well as a vision for future developments.

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TL;DR: Ass associations between belief in conspiracy theories and a range of measures of thinking dispositions and an alternative method of eliciting analytic thinking, which related to cognitive disfluency, was effective at reducing conspiracist ideation in a student sample.

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TL;DR: Evidence is provided that an MD decreases inflammation and improves endothelial function and that high adherence to a Mediterranean diet is associated with reduced all-cause and cardiovascular mortality risk.
Abstract: Background High adherence to a Mediterranean diet (MD) is associated with reduced all-cause and cardiovascular mortality risk. To our knowledge, there is no systematic review and meta-analysis of randomized controlled trials that has compared the effects of an MD on outcomes of endothelial function and inflammation. Methods and results Literature search was performed using the electronic databases MEDLINE, EMBASE, and the Cochrane Trial Register. Inclusion criteria were: randomized controlled trials, 19 + years of age, and minimum intervention period of 12 weeks. Study specific weighted mean differences (WMD) were pooled using a random effect model. Seventeen trials including 2300 subjects met the objectives. MD regimens resulted in a significantly more pronounced increase in flow mediated dilatation [WMD: 1.86%, 95% CI 0.23 to 3.48, p = 0.02; I 2 = 43%], and adiponectin [WMD: 1.69 μg/ml, 95% CI 0.27 to 3.11, p = 0.02; I 2 = 78%], while high-sensitive C reactive protein [WMD: −0.98 mg/l, 95% CI −1.48 to −0.49, p I 2 = 91%], interleukin-6 [WMD: −0.42 pg/ml, 95% CI −0.73 to −0.11, p = 0.008; I 2 = 81%], and intracellular adhesion molecule-1 [WMD: −23.73 ng/ml, 95% CI −41.24 to −6.22 p = 0.008; I 2 = 34%] turned out to be significantly more decreased. Conclusion The results of the present meta-analysis provide evidence that an MD decreases inflammation and improves endothelial function.

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TL;DR: Newton‐X can perform nonadiabatic dynamics using Columbus, Turbomole, Gaussian, and Gamess program packages with multireference configuration interaction, multiconfigurational self‐consistent field, time‐dependent density functional theory, and other methods.
Abstract: The Newton-X program is a general-purpose program package for excited-state molecular dynamics, including nonadiabatic methods. Its modular design allows Newton-X to be easily linked to any quantum-chemistry package that can provide excited-state energy gradients. At the current version, Newton-X can perform nonadiabatic dynamics using Columbus, Turbomole, Gaussian, and Gamess program packages with multireference configuration interaction, multiconfigurational self-consistent field, time-dependent density functional theory, and other methods. Nonadiabatic dynamics simulations with a hybrid combination of methods, such as Quantum-Mechanics/Molecular-Mechanics, are also possible. Moreover, Newton-X can be used for the simulation of absorption and emission spectra. The code is distributed free of charge for noncommercial and nonprofit uses at www.newtonx.org. WIREs Comput Mol Sci 2014, 4:26–33. doi: 10.1002/wcms.1158 The authors have declared no conflicts of interest in relation to this article. For further resources related to this article, please visit the WIREs website.

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TL;DR: This paper used meta-regression analysis to reconcile the empirical findings of the literature by quantitatively analyzing a sample of 578 estimates collected from 68 studies for the 1983-2008 period.
Abstract: The last three decades have witnessed a great deal of research effort devoted to measuring the private output elasticity of public capital. The wide range of available estimates have precluded any consensus so far, however. This paper reconciles the empirical findings of the literature by quantitatively analyzing a sample of 578 estimates collected from 68 studies for the 1983–2008 period. Using meta-regression analysis, we show how study design characteristics and publication bias can explain a large fraction of the variation across estimates. We find a short-run output elasticity of public capital supplied at the central government level of 0.083, which increases to 0.122 in the long run. If, in addition, only core infrastructure at a regional/local level of government is considered, these estimates are almost doubled. The average output elasticity of public capital amounts to 0.106. Our results suggest that public capital is undersupplied in OECD economies.

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TL;DR: The Coordinated Synoptic Investigation of NGC 2264 (CSI 2264) as discussed by the authors was a 30-day multi-wavelength photometric monitoring campaign on more than 1000 young star members using 16 telescopes.
Abstract: We present the Coordinated Synoptic Investigation of NGC 2264, a continuous 30 day multi-wavelength photometric monitoring campaign on more than 1000 young cluster members using 16 telescopes. The unprecedented combination of multi-wavelength, high-precision, high-cadence, and long-duration data opens a new window into the time domain behavior of young stellar objects. Here we provide an overview of the observations, focusing on results from Spitzer and CoRoT. The highlight of this work is detailed analysis of 162 classical T Tauri stars for which we can probe optical and mid-infrared flux variations to 1% amplitudes and sub-hour timescales. We present a morphological variability census and then use metrics of periodicity, stochasticity, and symmetry to statistically separate the light curves into seven distinct classes, which we suggest represent different physical processes and geometric effects. We provide distributions of the characteristic timescales and amplitudes and assess the fractional representation within each class. The largest category (>20%) are optical "dippers" with discrete fading events lasting ~1-5 days. The degree of correlation between the optical and infrared light curves is positive but weak; notably, the independently assigned optical and infrared morphology classes tend to be different for the same object. Assessment of flux variation behavior with respect to (circum)stellar properties reveals correlations of variability parameters with Hα emission and with effective temperature. Overall, our results point to multiple origins of young star variability, including circumstellar obscuration events, hot spots on the star and/or disk, accretion bursts, and rapid structural changes in the inner disk.