Showing papers by "University of Vienna published in 2017"
TL;DR: ModelFinder is presented, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
Abstract: Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.
7,425 citations
TL;DR: UFBoot2 is presented, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations and provides suitable bootstrap resampling strategies for phylogenomic data.
Abstract: The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches. Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 and 8.4 times (median) faster than SBS and RAxML rapid bootstrap on tested datasets, respectively. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
1,742 citations
TL;DR: The number of adults with raised blood pressure increased from 594 million in 1975 to 1·13 billion in 2015, with the increase largely in low-income and middle-income countries, and the contributions of changes in prevalence versus population growth and ageing to the increase.
1,573 citations
University of Vienna1, University of Oldenburg2, Zoological Society of London3, University College London4, International Union for Conservation of Nature and Natural Resources5, Lincoln University (New Zealand)6, Free University of Berlin7, Leibniz Association8, University of Auckland9, Charles University in Prague10, Stellenbosch University11, Academy of Sciences of the Czech Republic12, National and Kapodistrian University of Athens13, University of Fribourg14, University of Sassari15, University of Porto16, Sapienza University of Rome17, University of Konstanz18, Durham University19, University of Concepción20, Charles Darwin Foundation21, CABI22, University of Göttingen23, Martin Luther University of Halle-Wittenberg24, Helmholtz Centre for Environmental Research - UFZ25, United States Forest Service26, Bielefeld University27, Botanical Society of Britain and Ireland28, Environment Agency29, National Museum of Natural History30, Institut national de la recherche agronomique31, University of Silesia in Katowice32
TL;DR: In this paper, the authors used a database of 45,813 first records of 16,926 established alien species and showed that the annual rate of first records worldwide has increased during the last 200 years, with 37% of all first records reported most recently (1970-2014).
Abstract: Although research on human-mediated exchanges of species has substantially intensified during the last centuries, we know surprisingly little about temporal dynamics of alien species accumulations across regions and taxa. Using a novel database of 45,813 first records of 16,926 established alien species, we show that the annual rate of first records worldwide has increased during the last 200 years, with 37% of all first records reported most recently (1970-2014). Inter-continental and inter-taxonomic variation can be largely attributed to the diaspora of European settlers in the nineteenth century and to the acceleration in trade in the twentieth century. For all taxonomic groups, the increase in numbers of alien species does not show any sign of saturation and most taxa even show increases in the rate of first records over time. This highlights that past efforts to mitigate invasions have not been effective enough to keep up with increasing globalization.
1,301 citations
Cornell University1, Paris Descartes University2, University of Massachusetts Medical School3, Spanish National Research Council4, University of Rome Tor Vergata5, Boston Children's Hospital6, University of Pittsburgh7, National Scientific and Technical Research Council8, National University of Cuyo9, Albert Einstein College of Medicine10, University of California, San Francisco11, University of New Mexico12, University of Split13, Goethe University Frankfurt14, University of Helsinki15, University of Salento16, German Cancer Research Center17, Virginia Commonwealth University18, St. Jude Children's Research Hospital19, Discovery Institute20, Harvard University21, University of Tromsø22, Hungarian Academy of Sciences23, Eötvös Loránd University24, New York University25, University of Vienna26, Babraham Institute27, University of South Australia28, Howard Hughes Medical Institute29, University of Texas Southwestern Medical Center30, University of Oviedo31, University of Graz32, National Institutes of Health33, City University of New York34, Queens College35, University of Tokyo36, University of Zurich37, Novartis38, Austrian Academy of Sciences39, University of Groningen40, University of Cambridge41, University of Padua42, University of Oxford43, University of Bern44, University of Oslo45, Foundation for Research & Technology – Hellas46, University of Crete47, Francis Crick Institute48, Osaka University49, Icahn School of Medicine at Mount Sinai50
TL;DR: A panel of leading experts in the field attempts here to define several autophagy‐related terms based on specific biochemical features to formulate recommendations that facilitate the dissemination of knowledge within and outside the field of autophagic research.
Abstract: Over the past two decades, the molecular machinery that underlies autophagic responses has been characterized with ever increasing precision in multiple model organisms. Moreover, it has become clear that autophagy and autophagy-related processes have profound implications for human pathophysiology. However, considerable confusion persists about the use of appropriate terms to indicate specific types of autophagy and some components of the autophagy machinery, which may have detrimental effects on the expansion of the field. Driven by the overt recognition of such a potential obstacle, a panel of leading experts in the field attempts here to define several autophagy-related terms based on specific biochemical features. The ultimate objective of this collaborative exchange is to formulate recommendations that facilitate the dissemination of knowledge within and outside the field of autophagy research.
1,095 citations
Bielefeld University1, BRICS2, University of Düsseldorf3, Oregon State University4, University of California, San Diego5, Roskilde University6, University of Copenhagen7, Aarhus University8, Joint Genome Institute9, Pittsburgh Supercomputing Center10, Saint Petersburg State University11, Max Planck Society12, University of Vienna13, University of Technology, Sydney14, Centre national de la recherche scientifique15, Genome Institute of Singapore16, University of Warwick17, University of Tübingen18, Intel19, French Institute for Research in Computer Science and Automation20, Taipei Medical University21, Joint BioEnergy Institute22, Lawrence Berkeley National Laboratory23, Georgia Institute of Technology24, University of Calgary25, University of Göttingen26, National Health Research Institutes27, San Diego State University28, Boyce Thompson Institute for Plant Research29, Robert Koch Institute30, Coordenadoria de Aperfeiçoamento de Pessoal de Nível Superior31, University of Maryland, College Park32, Newcastle University33, Leibniz Association34, ETH Zurich35
TL;DR: The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups as discussed by the authors.
Abstract: Methods for assembly, taxonomic profiling and binning are key to interpreting metagenome data, but a lack of consensus about benchmarking complicates performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups. Assembly and genome binning programs performed well for species represented by individual genomes but were substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below family level. Parameter settings markedly affected performance, underscoring their importance for program reproducibility. The CAMI results highlight current challenges but also provide a roadmap for software selection to answer specific research questions.
593 citations
TL;DR: In this paper, the authors provide a knowledge of how to design a high quality mixed methods research study, and explain the seven major design dimensions: purpose, theoretical drive, timing (simultaneity and dependency), point of integration, typological versus interactive design approaches, planned versus emergent design, and design complexity.
Abstract: This article provides researchers with knowledge of how to design a high quality mixed methods research study. To design a mixed study, researchers must understand and carefully consider each of the dimensions of mixed methods design, and always keep an eye on the issue of validity. We explain the seven major design dimensions: purpose, theoretical drive, timing (simultaneity and dependency), point of integration, typological versus interactive design approaches, planned versus emergent design, and design complexity. There also are multiple secondary dimensions that need to be considered during the design process. We explain ten secondary dimensions of design to be considered for each research study. We also provide two case studies showing how the mixed designs were constructed.
570 citations
Franco D. Albareti1, Franco D. Albareti2, Carlos Allende Prieto3, Carlos Allende Prieto2 +397 more•Institutions (95)
TL;DR: Data Release 13 (DR13) as discussed by the authors provides the first 1390 spatially resolved integral field unit observations of nearby galaxies from the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2), Mapping Nearby Galaxies at APO (MaNGA), and the Extended Baryon Oscillation Spectroscopic Survey (eBOSS).
Abstract: The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) began observations in 2014 July. It pursues three core programs: the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2), Mapping Nearby Galaxies at APO (MaNGA), and the Extended Baryon Oscillation Spectroscopic Survey (eBOSS). As well as its core program, eBOSS contains two major subprograms: the Time Domain Spectroscopic Survey (TDSS) and the SPectroscopic IDentification of ERosita Sources (SPIDERS). This paper describes the first data release from SDSS-IV, Data Release 13 (DR13). DR13 makes publicly available the first 1390 spatially resolved integral field unit observations of nearby galaxies from MaNGA. It includes new observations from eBOSS, completing the Sloan Extended QUasar, Emission-line galaxy, Luminous red galaxy Survey (SEQUELS), which also targeted variability-selected objects and X-ray-selected objects. DR13 includes new reductions of the SDSS-III BOSS data, improving the spectrophotometric calibration and redshift classification, and new reductions of the SDSS-III APOGEE-1 data, improving stellar parameters for dwarf stars and cooler stars. DR13 provides more robust and precise photometric calibrations. Value-added target catalogs relevant for eBOSS, TDSS, and SPIDERS and an updated red-clump catalog for APOGEE are also available. This paper describes the location and format of the data and provides references to important technical papers. The SDSS web site, http://www.sdss.org, provides links to the data, tutorials, examples of data access, and extensive documentation of the reduction and analysis procedures. DR13 is the first of a scheduled set that will contain new data and analyses from the planned ∼6 yr operations of SDSS-IV.
532 citations
TL;DR: A pure culture of a comammox bacterium is isolated and it is shown that it is adapted to slow growth in oligotrophic and dynamic habitats on the basis of a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers, and genomic potential for alternative metabolisms.
Abstract: A pure culture of the complete nitrifier Nitrospira inopinata shows a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers and genomic potential for alternative metabolisms, probably reflecting an important role in nitrification in oligotrophic environments. Nitrospira inopinata was the first bacterium identified that is capable of catalysing complete ammonia oxidization (referred to as comammox). Holger Daims and colleagues now report a pure culture of this organism, which enabled a characterization of its physiology. The authors find that N. inopinata has a high affinity for ammonia, a low maximum rate of ammonia oxidation, a high growth yield compared to canonical nitrifiers, and the genomic potential for alternative metabolisms. The team compare the nitrification kinetics of N. inopinata to that of four ammonia-oxidizing archaea. The results suggest that N. inopinata is likely to have an important role in nitrification, especially in oligotrophic environments. Nitrification, the oxidation of ammonia (NH3) via nitrite (NO2−) to nitrate (NO3−), is a key process of the biogeochemical nitrogen cycle. For decades, ammonia and nitrite oxidation were thought to be separately catalysed by ammonia-oxidizing bacteria (AOB) and archaea (AOA), and by nitrite-oxidizing bacteria (NOB). The recent discovery of complete ammonia oxidizers (comammox) in the NOB genus Nitrospira1,2, which alone convert ammonia to nitrate, raised questions about the ecological niches in which comammox Nitrospira successfully compete with canonical nitrifiers. Here we isolate a pure culture of a comammox bacterium, Nitrospira inopinata, and show that it is adapted to slow growth in oligotrophic and dynamic habitats on the basis of a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers, and genomic potential for alternative metabolisms. The nitrification kinetics of four AOA from soil and hot springs were determined for comparison. Their surprisingly poor substrate affinities and lower growth yields reveal that, in contrast to earlier assumptions, AOA are not necessarily the most competitive ammonia oxidizers present in strongly oligotrophic environments and that N. inopinata has the highest substrate affinity of all analysed ammonia oxidizer isolates except the marine AOA Nitrosopumilus maritimus SCM1 (ref. 3). These results suggest a role for comammox organisms in nitrification under oligotrophic and dynamic conditions.
495 citations
University of Tartu1, Tartu University Hospital2, McMaster University3, University of Lausanne4, Université catholique de Louvain5, University of Adelaide6, Medical University of Graz7, University of Vienna8, University of Nice Sophia Antipolis9, University of Bern10, Maastricht University11, Université libre de Bruxelles12, Rabin Medical Center13, Tel Aviv University14, Ghent University Hospital15, King's College London16, Karolinska University Hospital17, Queen Elizabeth Hospital Birmingham18, Katholieke Universiteit Leuven19, VU University Medical Center20
TL;DR: EEN reduced infectious complications in unselected critically ill patients, in patients with severe acute pancreatitis, and after GI surgery, and did not detect any evidence of superiority for early PN or delayed EN over EEN.
Abstract: Purpose
To provide evidence-based guidelines for early enteral nutrition (EEN) during critical illness.
493 citations
TL;DR: There was evidence of a non-linear relationship between fruits, vegetables, processed meat, whole grains, and SSB and T2D risk, and selecting specific optimal intakes can lead to a considerable change in risk of T1D.
Abstract: The aim of this systematic review and meta-analysis was to synthesize the knowledge about the relation between intake of 12 major food groups and risk of type 2 diabetes (T2D). We conducted a systematic search in PubMed, Embase, Medline (Ovid), Cochrane Central, and Google Scholar for prospective studies investigating the association between whole grains, refined grains, vegetables, fruits, nuts, legumes, eggs, dairy, fish, red meat, processed meat, and sugar-sweetened beverages (SSB) on risk of T2D. Summary relative risks were estimated using a random effects model by contrasting categories, and for linear and non-linear dose-response relationships. Six out of the 12 food-groups showed a significant relation with risk of T2D, three of them a decrease of risk with increasing consumption (whole grains, fruits, and dairy), and three an increase of risk with increasing consumption (red meat, processed meat, and SSB) in the linear dose-response meta-analysis. There was evidence of a non-linear relationship between fruits, vegetables, processed meat, whole grains, and SSB and T2D risk. Optimal consumption of risk-decreasing foods resulted in a 42% reduction, and consumption of risk-increasing foods was associated with a threefold T2D risk, compared to non-consumption. The meta-evidence was graded "low" for legumes and nuts; "moderate" for refined grains, vegetables, fruit, eggs, dairy, and fish; and "high" for processed meat, red meat, whole grains, and SSB. Among the investigated food groups, selecting specific optimal intakes can lead to a considerable change in risk of T2D.
University of Antwerp1, University of Gothenburg2, Norwegian University of Science and Technology3, University of Zurich4, University of Amsterdam5, University of Vienna6, University of Southern Denmark7, University of Lisbon8, Paris-Sorbonne University9, Adam Mickiewicz University in Poznań10, National and Kapodistrian University of Athens11, King Juan Carlos University12, University of Pavia13, Ludwig Maximilian University of Munich14, Hebrew University of Jerusalem15, Loughborough University16
TL;DR: In this article, the authors review research on key changes and trends in political information environments and assess their democratic implications, focusing on advanced postindustrial democracies and six concerns that are all closely linked to the dissemination and acquisition of political knowledge: (1) declining supply of political information, (2) declining quality of news, (3) increasing media concentration and declining diversity of news.
Abstract: During the last decennia media environments and political communication systems have changed fundamentally. These changes have major ramifications for the political information environments and the extent to which they aid people in becoming informed citizens. Against this background, the purpose of this article is to review research on key changes and trends in political information environments and assess their democratic implications. We will focus on advanced postindustrial democracies and six concerns that are all closely linked to the dissemination and acquisition of political knowledge: (1) declining supply of political information, (2) declining quality of news, (3) increasing media concentration and declining diversity of news, (4) increasing fragmentation and polarization, (5) increasing relativism and (6) increasing inequality in political knowledge.
TL;DR: The genomes of the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus are sequenced and nitrogen fixation genes of both host species are encoded.
Abstract: Chemosynthetic symbioses are partnerships between invertebrate animals and chemosynthetic bacteria. The latter are the primary producers, providing most of the organic carbon needed for the animal host's nutrition. We sequenced genomes of the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus. The symbionts of both host species encoded nitrogen fixation genes. This is remarkable as no marine chemosynthetic symbiont was previously known to be capable of nitrogen fixation. We detected nitrogenase expression by the symbionts of lucinid clams at the transcriptomic and proteomic level. Mean stable nitrogen isotope values of Loripes lucinalis were within the range expected for fixed atmospheric nitrogen, further suggesting active nitrogen fixation by the symbionts. The ability to fix nitrogen may be widespread among chemosynthetic symbioses in oligotrophic habitats, where nitrogen availability often limits primary productivity. The chemosynthetic symbionts of the bivalve Loripes lucinalis and nematode Laxus oneistus are found to encode nitrogen fixation genes, with evidence for active nitrogen fixation.
TL;DR: The approach to peripheral neuropathy in patients with cancer is discussed and the clinical phenotypes and pathomechanisms of specific neurotoxic chemotherapeutic agents are addressed.
Abstract: Chemotherapy-induced peripheral neuropathy (CIPN) is a common dose-limiting side effect experienced by patients receiving treatment for cancer. Approximately 30 to 40% of patients treated with neurotoxic chemotherapy will develop CIPN, and there is considerable variability in its severity between patients. It is often sensory-predominant with pain and can lead to long-term morbidity in survivors. The prevalence and burden of CIPN late effects will likely increase as cancer survival rates continue to improve. In this review, we discuss the approach to peripheral neuropathy in patients with cancer and address the clinical phenotypes and pathomechanisms of specific neurotoxic chemotherapeutic agents. Ann Neurol 2017;81:772-781.
TL;DR: An important inverse association between adherence to a MedD and cancer mortality and risk of several cancer types, especially colorectal cancer is confirmed, and protective effects appear to be most attributable to fruits, vegetables, and whole grains.
Abstract: The aim of the present systematic review and meta-analysis was to gain further insight into the effects of adherence to Mediterranean Diet (MedD) on risk of overall cancer mortality, risk of different types of cancer, and cancer mortality and recurrence risk in cancer survivors Literature search was performed using the electronic databases PubMed, and Scopus until 25 August 2017 We included randomized trials (RCTs), cohort (for specific tumors only incidence cases were used) studies, and case-control studies Study-specific risk ratios, hazard ratios, and odds ratios (RR/HR/OR) were pooled using a random effects model Observational studies (cohort and case-control studies), and intervention trials were meta-analyzed separately The updated review process showed 27 studies that were not included in the previous meta-analysis (total number of studies evaluated: 83 studies) An overall population of 2,130,753 subjects was included in the present update The highest adherence score to a MedD was inversely associated with a lower risk of cancer mortality (RRcohort: 086, 95% CI 081 to 091, I2 = 82%; n = 14 studies), colorectal cancer (RRobservational: 082, 95% CI 075 to 088, I2 = 73%; n = 11 studies), breast cancer (RRRCT: 043, 95% CI 021 to 088, n = 1 study) (RRobservational: 092, 95% CI 087 to 096, I2 = 22%, n = 16 studies), gastric cancer (RRobservational: 072, 95% CI 060 to 086, I2 = 55%; n = 4 studies), liver cancer (RRobservational: 058, 95% CI 046 to 073, I2 = 0%; n = 2 studies), head and neck cancer (RRobservational: 049, 95% CI 037 to 066, I2 = 87%; n = 7 studies), and prostate cancer (RRobservational: 096, 95% CI 092 to 100, I2 = 0%; n = 6 studies) Among cancer survivors, the association between the adherence to the highest MedD category and risk of cancer mortality, and cancer recurrence was not statistically significant Pooled analyses of individual components of the MedD revealed that the protective effects appear to be most attributable to fruits, vegetables, and whole grains The updated meta-analysis confirms an important inverse association between adherence to a MedD and cancer mortality and risk of several cancer types, especially colorectal cancer These observed beneficial effects are mainly driven by higher intakes of fruits, vegetables, and whole grains Moreover, we were able to report for the first time a small decrease in breast cancer risk (6%) by pooling seven cohort studies
TL;DR: Selecting specific optimal intakes of the investigated food groups can lead to a considerable change in the risk of premature death, whereas consumption of risk-increasing foods is associated with a 2-fold increased risk of all-cause mortality.
TL;DR: In this paper, the authors investigated the effectiveness of celebrity endorsements by meta-analyzing 46 studies published until April 2016 involving 10,357 participants and found that celebrity endorsements performed worse compared to endorsements of quality seals, awards, or endorser brands.
Abstract: Celebrities frequently endorse products, brands, political candidates, or health campaigns. We investigated the effectiveness of such endorsements by meta-analyzing 46 studies published until April 2016 involving 10,357 participants. Applying multilevel meta-analysis, we analyzed celebrity endorsements in the context of for-profit and non-profit marketing. Findings revealed strong positive and negative effects when theoretically relevant moderators were included in the analysis. The most positive attitudinal effect appeared for male actors who match well with an implicitly endorsed object (d = .90). The most negative effect was found for female models not matching well with an explicitly endorsed object (d = −.96). Furthermore, celebrity endorsements performed worse compared to endorsements of quality seals, awards, or endorser brands. No publication bias was detected. The study has theoretical and practical implications, and provides an agenda for future research.
TL;DR: Remote quantum entanglement is demonstrated in a micromachined solid-state system comprising two optomechanical oscillators across two chips physically separated by 20 cm and with an optical separation of around 70 m.
Abstract: Entanglement, an essential feature of quantum theory that allows for inseparable quantum correlations to be shared between distant parties, is a crucial resource for quantum networks. Of particular importance is the ability to distribute entanglement between remote objects that can also serve as quantum memories. This has been previously realized using systems such as warm and cold atomic vapours, individual atoms and ions, and defects in solid-state systems. Practical communication applications require a combination of several advantageous features, such as a particular operating wavelength, high bandwidth and long memory lifetimes. Here we introduce a purely micromachined solid-state platform in the form of chip-based optomechanical resonators made of nanostructured silicon beams. We create and demonstrate entanglement between two micromechanical oscillators across two chips that are separated by 20 centimetres. The entangled quantum state is distributed by an optical field at a designed wavelength near 1550 nanometres. Therefore, our system can be directly incorporated in a realistic fibre-optic quantum network operating in the conventional optical telecommunication band. Our results are an important step towards the development of large-area quantum networks based on silicon photonics.
TL;DR: This review article gives a brief overview of the theoretical differences between qubits and higher dimensional systems, qudits, in different quantum information scenarios and describes recent experimental developments in this field over the past three years.
Abstract: Quantum information science and quantum information technology have seen a virtual explosion world-wide. It is all based on the observation that fundamental quantum phenomena on the individual particle or system-level lead to completely novel ways of encoding, processing and transmitting information. Quantum mechanics, a child of the first third of the 20th century, has found numerous realizations and technical applications, much more than was thought at the beginning. Decades later, it became possible to do experiments with individual quantum particles and quantum systems. This was due to technological progress, and for light in particular, the development of the laser. Hitherto, nearly all experiments and also nearly all realizations in the fields have been performed with qubits, which are two-level quantum systems. We suggest that this limitation is again mainly a technological one, because it is very difficult to create, manipulate and measure more complex quantum systems. Here, we provide a specific overview of some recent developments with higher-dimensional quantum systems. We mainly focus on Orbital Angular Momentum (OAM) states of photons and possible applications in quantum information protocols. Such states form discrete higher-dimensional quantum systems, also called qudits. Specifically, we will first address the question what kind of new fundamental properties exist and the quantum information applications which are opened up by such novel systems. Then we give an overview of recent developments in the field by discussing several notable experiments over the past 2-3 years. Finally, we conclude with several important open questions which will be interesting for investigations in the future.
TL;DR: Overall the review reveals significant advances in the understanding of the interactions between IOCs and carbonaceous sorbents, with special attention being given to emerging sorption mechanisms including low-barrier, charge-assisted hydrogen bonds and cation-π assisted π-π interactions.
Durham University1, University of Vienna2, University of Konstanz3, Taizhou University4, University of Göttingen5, Academy of Sciences of the Czech Republic6, Charles University in Prague7, Stellenbosch University8, University College London9, University of Adelaide10, Zoological Society of London11, Okinawa Institute of Science and Technology12, University of Hong Kong13, University of Porto14, Landcare Research15, University of Bern16, University of Girona17, International Rice Research Institute18, University of Toronto19, United States Geological Survey20
TL;DR: Analysis of eight taxonomic groups across 186 islands and 423 mainland regions reveals that those with the greatest gross domestic product per capita, human population density and area have the highest established alien species richness, with the strongest effects on islands.
Abstract: Human-mediated transport beyond biogeographic barriers has led to the introduction and establishment of alien species in new regions worldwide. However, we lack a global picture of established alien species richness for multiple taxonomic groups. Here, we assess global patterns and potential drivers of established alien species richness across eight taxonomic groups (amphibians, ants, birds, freshwater fishes, mammals, vascular plants, reptiles and spiders) for 186 islands and 423 mainland regions. Hotspots of established alien species richness are predominantly island and coastal mainland regions. Regions with greater gross domestic product per capita, human population density, and area have higher established alien richness, with strongest effects emerging for islands. Ants and reptiles, birds and mammals, and vascular plants and spiders form pairs of taxonomic groups with the highest spatial congruence in established alien richness, but drivers explaining richness differ between the taxa in each pair. Across all taxonomic groups, our results highlight the need to prioritize prevention of further alien species introductions to island and coastal mainland regions globally. Analysis of eight taxonomic groups across 186 islands and 423 mainland regions reveals that those with the greatest gross domestic product per capita, human population density and area have the highest established alien species richness, with the strongest effects on islands.
TL;DR: Different methodologies are compared for the measurement of elastic constants and microstructural characterization of CAD/CAM restorative materials, showing to be complementary tools in the characterization of their crystal phases.
TL;DR: In this article, a molecular dipole moment model based on environment dependent neural network charges is proposed for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points.
Abstract: Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects – typically neglected by conventional quantum chemistry approaches – we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n-alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.
International Crops Research Institute for the Semi-Arid Tropics1, Institut de recherche pour le développement2, University of Georgia3, Leibniz Association4, Fort Valley State University5, Cornell University6, University of Florida7, Junagadh Agricultural University8, United States Department of Agriculture9, University of Vienna10, Amity University11, University of Arizona12, Indian Council of Agricultural Research13, University of Montpellier14, University of Lyon15, Oklahoma State University–Stillwater16, DuPont Pioneer17, Aberystwyth University18, Visva-Bharati University19, Agricultural Research Service20
TL;DR: This work resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication, and establishes marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance.
Abstract: Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ~1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.
TL;DR: A meta-analysis of 345 published studies to examine the media's role in the construction of a Muslim and Islamic identity is presented in this article, where a quantitative analysis highlights the geographical focus.
Abstract: This article reports a meta-analysis of 345 published studies to examine the media’s role in construction of a Muslim and Islamic identity. A quantitative analysis highlights the geographical focus...
TL;DR: It is shown that the protein gephyrin is the mammalian target of these antimalarial drugs and that the mechanism of action of these molecules depends on the enhancement of GABAA receptor signaling.
TL;DR: A collection of murine bacterial strains and a modular design approach are used to create a minimal bacterial community that provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium and established a highly versatile experimental system that showed efficacy in an enteric infection model.
Abstract: Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm). Initially, a community of 12 strains, termed Oligo-Mouse-Microbiota (Oligo-MM12), representing members of the major bacterial phyla in the murine gut, was selected. This community was stable over consecutive mouse generations and provided colonization resistance against S. Tm infection, albeit not to the degree of a conventional complex microbiota. Comparative (meta)genome analyses identified functions represented in a conventional microbiome but absent from the Oligo-MM12. By genome-informed design, we created an improved version of the Oligo-MM community harbouring three facultative anaerobic bacteria from the mouse intestinal bacterial collection (miBC) that provided conventional-like colonization resistance. In conclusion, we have established a highly versatile experimental system that showed efficacy in an enteric infection model. Thus, in combination with exhaustive bacterial strain collections and systems-based approaches, genome-guided design can be used to generate insights into microbe–microbe and microbe–host interactions for the investigation of ecological and disease-relevant mechanisms in the intestine. A minimal bacterial community has been defined that provides colonization resistance to Salmonella enterica serovar Typhimurium once established in germ-free mice to a similar extent as a conventional microbial community.
TL;DR: The results suggest that organic P (Porg), rather than available P, is the most important P fraction in predicting phosphatase activity, and that P recycling is driven by a broad scale pattern of ecosystem productivity capacity.
Abstract: Soil phosphatase levels strongly control the biotic pathways of phosphorus (P), an essential element for life, which is often limiting in terrestrial ecosystems. We investigated the influence of climatic and soil traits on phosphatase activity in terrestrial systems using metadata analysis from published studies. This is the first analysis of global measurements of phosphatase in natural soils. Our results suggest that organic P (Porg), rather than available P, is the most important P fraction in predicting phosphatase activity. Structural equation modeling using soil total nitrogen (TN), mean annual precipitation, mean annual temperature, thermal amplitude and total soil carbon as most available predictor variables explained up to 50% of the spatial variance in phosphatase activity. In this analysis, Porg could not be tested and among the rest of available variables, TN was the most important factor explaining the observed spatial gradients in phosphatase activity. On the other hand, phosphatase activity was also found to be associated with climatic conditions and soil type across different biomes worldwide. The close association among different predictors like Porg, TN and precipitation suggest that P recycling is driven by a broad scale pattern of ecosystem productivity capacity.
TL;DR: In this article, the authors developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira.
Abstract: Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers (‘comammox’), which oxidize ammonia to nitrate on their own, were identified in the bacterial genus Nitrospira, previously assumed to contain only canonical nitrite oxidizers. Nitrospira are widespread in nature, but for assessments of the distribution and functional importance of comammox Nitrospira in ecosystems, cultivation-independent tools to distinguish comammox from strictly nitrite-oxidizing Nitrospira are required. Here we developed new PCR primer sets that specifically target the amoA genes coding for subunit A of the distinct ammonia monooxygenase of comammox Nitrospira. While existing primers capture only a fraction of the known comammox amoA diversity, the new primer sets cover as much as 95% of the comammox amoA clade A and 92% of the clade B sequences in a reference database containing 326 comammox amoA genes with sequence information at the primer binding sites. Application of the primers to 13 samples from engineered systems (a groundwater well, drinking water treatment and wastewater treatment plants) and other habitats (rice paddy and forest soils, rice rhizosphere, brackish lake sediment and freshwater biofilm) detected comammox Nitrospira in all samples and revealed a considerable diversity of comammox in most habitats. Excellent primer specificity for comammox amoA was achieved by avoiding the use of highly degenerate primer preparations and by using equimolar mixtures of oligonucleotides that match existing comammox amoA genes. Quantitative PCR with these equimolar primer mixtures was highly sensitive and specific, and enabled the efficient quantification of clade A and clade B comammox amoA gene copy numbers in environmental samples. The measured relative abundances of comammox Nitrospira, compared to canonical ammonia oxidizers, were highly variable across environments. The new comammox amoA-targeted primers enable more encompassing future studies of nitrifying microorganisms in diverse habitats. For example, they may be used to monitor the population dynamics of uncultured comammox organisms under changing environmental conditions and in response to altered treatments in engineered and agricultural ecosystems.
TL;DR: Although the news-finds-me perception is positively associated with news exposure on social media, this behavior doesn't facilitate political learning, and results suggest news continues to enhance political knowledge best when actively sought.
Abstract: With social media at the forefront of today's media context, citizens may perceive they don't need to actively seek news because they will be exposed to news and remain well-informed through their peers and social networks. We label this the “news-finds-me perception,” and test its implications for news seeking and political knowledge: “news-finds-me effects.” U.S. panel-survey data show that individuals who perceive news will find them are less likely to use traditional news sources and are less knowledgeable about politics over time. Although the news-finds-me perception is positively associated with news exposure on social media, this behavior doesn't facilitate political learning. These results suggest news continues to enhance political knowledge best when actively sought.