Showing papers by "University of Alcalá published in 2016"
TL;DR: In this paper, the authors present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macro-autophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes.
Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes.
For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy.
Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.
5,187 citations
TL;DR: The report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm.
Abstract: In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.
1,258 citations
08 Oct 2016
TL;DR: A novel convolutional neural network solution, named Counting CNN (CCNN), formulated as a regression model where the network learns how to map the appearance of the image patches to their corresponding object density maps, able to estimate object densities in different very crowded scenarios.
Abstract: In this paper we address the problem of counting objects instances in images. Our models are able to precisely estimate the number of vehicles in a traffic congestion, or to count the humans in a very crowded scene. Our first contribution is the proposal of a novel convolutional neural network solution, named Counting CNN (CCNN). Essentially, the CCNN is formulated as a regression model where the network learns how to map the appearance of the image patches to their corresponding object density maps. Our second contribution consists in a scale-aware counting model, the Hydra CNN, able to estimate object densities in different very crowded scenarios where no geometric information of the scene can be provided. Hydra CNN learns a multiscale non-linear regression model which uses a pyramid of image patches extracted at multiple scales to perform the final density prediction. We report an extensive experimental evaluation, using up to three different object counting benchmarks, where we show how our solutions achieve a state-of-the-art performance.
639 citations
University of Grenoble1, Macquarie University2, University of Cambridge3, Australian National University4, Royal Botanic Gardens5, University of Waikato6, Wageningen University and Research Centre7, University of Regina8, Smithsonian Tropical Research Institute9, Tohoku University10, Florida International University11, Institut national de la recherche agronomique12, University of Toronto13, VU University Amsterdam14, University of Freiburg15, Max Planck Society16, Kyoto University17, Spanish National Research Council18, Forschungszentrum Jülich19, Columbia University20, Landcare Research21, University of Alcalá22, University of Stirling23, National Dong Hwa University24, Swedish University of Agricultural Sciences25, University of Maryland, College Park26, University of Puerto Rico27, University of Puerto Rico, Río Piedras28
TL;DR: Traits generate trade-offs between performance with competition versus performance without competition, a fundamental ingredient in the classical hypothesis that the coexistence of plant species is enabled via differentiation in their successional strategies.
Abstract: Phenotypic traits and their associated trade-offs have been shown to have globally consistent effects on individual plant physiological functions, but how these effects scale up to influence competition, a key driver of community assembly in terrestrial vegetation, has remained unclear. Here we use growth data from more than 3 million trees in over 140,000 plots across the world to show how three key functional traits--wood density, specific leaf area and maximum height--consistently influence competitive interactions. Fast maximum growth of a species was correlated negatively with its wood density in all biomes, and positively with its specific leaf area in most biomes. Low wood density was also correlated with a low ability to tolerate competition and a low competitive effect on neighbours, while high specific leaf area was correlated with a low competitive effect. Thus, traits generate trade-offs between performance with competition versus performance without competition, a fundamental ingredient in the classical hypothesis that the coexistence of plant species is enabled via differentiation in their successional strategies. Competition within species was stronger than between species, but an increase in trait dissimilarity between species had little influence in weakening competition. No benefit of dissimilarity was detected for specific leaf area or wood density, and only a weak benefit for maximum height. Our trait-based approach to modelling competition makes generalization possible across the forest ecosystems of the world and their highly diverse species composition.
618 citations
University of Miami1, Icahn School of Medicine at Mount Sinai2, Fourth Military Medical University3, Kyungpook National University Hospital4, University of Verona5, Samsung Medical Center6, Yonsei University7, Taipei Veterans General Hospital8, University of Pittsburgh9, University of Alcalá10, Bayer HealthCare Pharmaceuticals11, Bayer Corporation12, Newbury College13
TL;DR: Sorafenib plus DEB-TACE was technically feasible, but the combination did not improve TTP in a clinically meaningful manner compared with DEB -TACE alone.
509 citations
TL;DR: In this paper, the authors trace the content, scope and relatively short history of modern social innovation research across disciplines by applying network and bibliometric analyses, and explore their relevance to innovation studies.
447 citations
TL;DR: It is indicated that the population divergence between Neanderthals and Denisovans predates 430,000 years ago, and a mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthal turned over later in their history.
Abstract: A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.
389 citations
TL;DR: It is argued that the excessive rates of medical interventions and disrespect towards women during childbirth should be analysed as a consequence of structural violence, and that the concept of obstetric violence, as it is being used in Latin American childbirth activism and legal documents, might prove to be a useful tool for addressing structural violence in maternity care.
268 citations
World Meteorological Organization1, International Centre for Theoretical Physics2, ENEA3, University of Alcalá4, University of Belgrade5, Max Planck Society6, Technical University of Madrid7, Polytechnic University of Catalonia8, Barcelona Supercomputing Center9, École Polytechnique10, Istanbul Technical University11, National and Kapodistrian University of Athens12
TL;DR: The Med-CORDEX initiative aims at coordinating the Mediterranean climate modeling community towards the development of fully coupled regional climate simulations, improving all relevant components of the system, from atmosphere and ocean dynamics to land surface, hydrology and biogeochemical processes as discussed by the authors.
Abstract: The Mediterranean is expected to be one of the most prominent and vulnerable climate change “hot spots” of the 21st century, and the physical mechanisms underlying this finding are still not clear. Furthermore complex interactions and feedbacks involving ocean-atmosphere-land-biogeochemical processes play a prominent role in modulating the climate and environment of the Mediterranean region on a range of spatial and temporal scales. Therefore it is critical to provide robust climate change information for use in Vulnerability/Impact/Adaptation assessment studies considering the Mediterranean as a fully coupled environmental system. The Med-CORDEX initiative aims at coordinating the Mediterranean climate modeling community towards the development of fully coupled regional climate simulations, improving all relevant components of the system, from atmosphere and ocean dynamics to land surface, hydrology and biogeochemical processes. The primary goals of Med-CORDEX are to improve understanding of past climate variability and trends, and to provide more accurate and reliable future projections, assessing in a quantitative and robust way the added value of using high resolution and coupled regional climate models. The coordination activities and the scientific outcomes of Med-CORDEX can produce an important framework to foster the development of regional earth system models in several key regions worldwide.
267 citations
Uniformed Services University of the Health Sciences1, Centers for Disease Control and Prevention2, McGill University Health Centre3, University of Virginia4, University of Alcalá5, Walter Reed National Military Medical Center6, Oswaldo Cruz Foundation7, Federal University of Rio Grande do Norte8, Bill & Melinda Gates Foundation9
TL;DR: It is important to realize that leishmaniasis guidelines cannot always account for individual variation among patients, and that adherence to these guidelines to be voluntary.
Abstract: It is important to realize that leishmaniasis guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. The IDSA and ASTMH consider adherence to these guidelines to be voluntary, with the ultimate determinations regarding their application to be made by the physician in the light of each patient's individual circumstances.
263 citations
TL;DR: It is demonstrated that by acting on the phase profile of the optical pulses, it is possible to introduce important conceptual and practical changes to the traditional ΦOTDR operation, thus opening a door for new possibilities which are yet to be explored.
Abstract: So far, the optical pulses used in phase-sensitive OTDR (ΦOTDR) were typically engineered so as to have a constant phase along the pulse. In this work, it is demonstrated that by acting on the phase profile of the optical pulses, it is possible to introduce important conceptual and practical changes to the traditional ΦOTDR operation, thus opening a door for new possibilities which are yet to be explored. Using a ΦOTDR with linearly chirped pulses and direct detection, the distributed measurement of temperature/strain changes from trace to trace, with 1mK/4ne resolution, is theoreticaly and experimentaly demonstrated. The measurand resolution and sensitivity can be tuned by acting on the pulse chirp profile. The technique does not require a frequency sweep, thus greatly decreasing the measurement time and complexity of the system, while maintaining the potential for metric spatial resolutions over tens of kilometers as in conventional ΦOTDR. The technique allows for measurements at kHz rates, while maintaining reliability over several hours.
TL;DR: Stem cell membrane-coated nanogels can effectively evade clearance of the immune system, enhance the tumor targeting properties and antitumor chemotherapy efficacy of gelatin nanogel loaded doxorubicin in mice.
Abstract: Stem cell membrane-coated nanogels can effectively evade clearance of the immune system, enhance the tumor targeting properties and antitumor chemotherapy efficacy of gelatin nanogels loaded doxorubicin in mice.
TL;DR: In a randomized controlled trial, addition of simvastatin to standard therapy did not reduce rebleeding, but was associated with a survival benefit for patients with Child-Pugh class A or B cirrhosis.
TL;DR: Study of how well-established approaches compare with more novel ones (gamification and social gamification) in terms of learning performance in an undergraduate course suggests that all experimental conditions significantly impact on learning performance, but socialgamification returned better results interms of immediacy and for all types of assessments.
Abstract: Game-like approaches are becoming increasingly popular in education, with educational games and gamification drawing increasing levels of attention. While games specifically designed for educational purposes have been used for decades, gamification is particularly new and contrasting evidence was presented about its effectiveness. The potential of social networks has also been harnessed by educators and institutions either using popular social networking sites or specific educational instances. This paper studies how well-established approaches (educational game and social networking) compare with more novel ones (gamification and social gamification) in terms of learning performance in an undergraduate course. Four experimental conditions were compared in an experiment (N?=?379). Results suggest that all experimental conditions significantly impact on learning performance, but social gamification returned better results in terms of immediacy and for all types of assessments. Educational games, gamification and social networking are compared.Specific instruments are used or designed for each approach.Four experimental groups and one control group (N?=?379) are part of the experiment.All experimental conditions improve learning in practical assessments.Social gamification returns better results initially and across all learning activities.
University of London1, Stanford University2, University of Maryland, Baltimore3, Emory University4, Brown University5, Katholieke Universiteit Leuven6, University of Alcalá7, Federal University of Rio de Janeiro8, University of Granada9, University of Zurich10, University of Paris11, Harvard University12, Médecins Sans Frontières13, Israel Ministry of Health14, Erasmus University Rotterdam15, University of Rome Tor Vergata16, Karolinska Institutet17, University of Modena and Reggio Emilia18, Kaiser Permanente19, Centers for Disease Control and Prevention20, Public Health England21, Robert Koch Institute22, University College London23, Medical Research Council24, IBM25, University of the Free State26, University of Cologne27, Chulalongkorn University28
TL;DR: A global assessment of drug resistance after virological failure with first-line tenofovir-containing ART, defined as presence of K65R/N or K70E/G/Q mutations in the reverse transcriptase ( RT ) gene.
Abstract: Summary Background Antiretroviral therapy (ART) is crucial for controlling HIV-1 infection through wide-scale treatment as prevention and pre-exposure prophylaxis (PrEP). Potent tenofovir disoproxil fumarate-containing regimens are increasingly used to treat and prevent HIV, although few data exist for frequency and risk factors of acquired drug resistance in regions hardest hit by the HIV pandemic. We aimed to do a global assessment of drug resistance after virological failure with first-line tenofovir-containing ART. Methods The TenoRes collaboration comprises adult HIV treatment cohorts and clinical trials of HIV drug resistance testing in Europe, Latin and North America, sub-Saharan Africa, and Asia. We extracted and harmonised data for patients undergoing genotypic resistance testing after virological failure with a first-line regimen containing tenofovir plus a cytosine analogue (lamivudine or emtricitabine) plus a non-nucleotide reverse-transcriptase inhibitor (NNRTI; efavirenz or nevirapine). We used an individual participant-level meta-analysis and multiple logistic regression to identify covariates associated with drug resistance. Our primary outcome was tenofovir resistance, defined as presence of K65R/N or K70E/G/Q mutations in the reverse transcriptase ( RT ) gene. Findings We included 1926 patients from 36 countries with treatment failure between 1998 and 2015. Prevalence of tenofovir resistance was highest in sub-Saharan Africa (370/654 [57%]). Pre-ART CD4 cell count was the covariate most strongly associated with the development of tenofovir resistance (odds ratio [OR] 1·50, 95% CI 1·27–1·77 for CD4 cell count Interpretation We recorded drug resistance in a high proportion of patients after virological failure on a tenofovir-containing first-line regimen across low-income and middle-income regions. Effective surveillance for transmission of drug resistance is crucial. Funding The Wellcome Trust.
TL;DR: A new method to test hadronic interaction models without relying on the absolute energy calibration is introduced, and it is applied to events with primary energy 6-16 EeV (E_{CM}=110-170 TeV), whose longitudinal development and lateral distribution were simultaneously measured by the Pierre Auger Observatory.
Abstract: Ultrahigh energy cosmic ray air showers probe particle physics at energies beyond the reach of accelerators Here we introduce a new method to test hadronic interaction models without relying on the absolute energy calibration, and apply it to events with primary energy 6-16 EeV (E_CM = 110-170 TeV), whose longitudinal development and lateral distribution were simultaneously measured by the Pierre Auger Observatory The average hadronic shower is 133 +- 016 (161 +- 021) times larger than predicted using the leading LHC-tuned models EPOS-LHC (QGSJetII-04), with a corresponding excess of muons
Centraalbureau voor Schimmelcultures1, University of Pretoria2, Murdoch University3, Rovira i Virgili University4, Stellenbosch University5, Laos Ministry of Agriculture and Forestry6, Spanish National Research Council7, Federal University of Rio Grande do Norte8, Universidade Federal de Viçosa9, Chiang Mai University10, Federal University of Pernambuco11, University of Alcalá12, University of Texas Health Science Center at San Antonio13, James Cook University14, Universidade Federal de Santa Maria15, Pennsylvania State University16, University of Tabriz17, University of Angers18, Sao Paulo State University19, State University of Feira de Santana20, University of Geneva21, La Trobe University22, Hosei University23, Universidad Autónoma de Chiriquí24, Slovak National Museum25, University of Ottawa26, Charles University in Prague27, University of Gothenburg28, University of Calicut29, Empresa Brasileira de Pesquisa Agropecuária30, University of Illinois at Urbana–Champaign31, University of the Basque Country32, Goethe University Frankfurt33, University of North Carolina at Greensboro34, University of Sydney35, University of Arkansas System36, University of Turin37, Federal University of Paraíba38, Complutense University of Madrid39
TL;DR: Novel species of fungi described in this study include those from various countries as follows: Apiognomonia lasiopetali on Lasiopetalum sp.
Abstract: Novel species of fungi described in this study include those from various countries as follows: Australia: Apiognomonia lasiopetali on Lasiopetalum sp., Blastacervulus eucalyptorum on Eucalyptus adesmophloia, Bullanockia australis (incl. Bullanockia gen. nov.) on Kingia australis, Caliciopsis eucalypti on Eucalyptus marginata, Celerioriella petrophiles on Petrophile teretifolia, Coleophoma xanthosiae on Xanthosia rotundifolia, Coniothyrium hakeae on Hakea sp., Diatrypella banksiae on Banksia formosa, Disculoides corymbiae on Corymbia calophylla, Elsinoe eelemani on Melaleuca alternifolia, Elsinoe eucalyptigena on Eucalyptus kingsmillii, Elsinoe preissianae on Eucalyptus preissiana, Eucasphaeria rustici on Eucalyptus creta, Hyweljonesia queenslandica (incl. Hyweljonesia gen. nov.) on the cocoon of an unidentified microlepidoptera, Mycodiella eucalypti (incl. Mycodiella gen. nov.) on Eucalyptus diversicolor, Myrtapenidiella sporadicae on Eucalyptus sporadica, Neocrinula xanthorrhoeae (incl. Neocrinula gen. nov.) on Xanthorrhoea sp., Ophiocordyceps nooreniae on dead ant, Phaeosphaeriopsis agavacearum on Agave sp., Phlogicylindrium mokarei on Eucalyptus sp., Phyllosticta acaciigena on Acacia suaveolens, Pleurophoma acaciae on Acacia glaucoptera, Pyrenochaeta hakeae on Hakea sp., Readeriella lehmannii on Eucalyptus lehmannii, Saccharata banksiae on Banksia grandis, Saccharata daviesiae on Daviesia pachyphylla, Saccharata eucalyptorum on Eucalyptus bigalerita, Saccharata hakeae on Hakea baxteri, Saccharata hakeicola on Hakea victoria, Saccharata lambertiae on Lambertia ericifolia, Saccharata petrophiles on Petrophile sp., Saccharata petrophilicola on Petrophile fastigiata, Sphaerellopsis hakeae on Hakea sp., and Teichospora kingiae on Kingia australis. Brazil: Adautomilanezia caesalpiniae (incl. Adautomilanezia gen. nov.) on Caesalpina echinata, Arthrophiala arthrospora (incl. Arthrophiala gen. nov.) on Sagittaria montevidensis, Diaporthe caatingaensis (endophyte from Tacinga inamoena), Geastrum ishikawae on sandy soil, Geastrum pusillipilosum on soil, Gymnopus pygmaeus on dead leaves and sticks, Inonotus hymenonitens on decayed angiosperm trunk, Pyricularia urashimae on Urochloa brizantha, and Synnemellisia aurantia on Passiflora edulis. Chile: Tubulicrinis australis on Lophosoria quadripinnata. France: Cercophora squamulosa from submerged wood, and Scedosporium cereisporum from fluids of a wastewater treatment plant. Hawaii: Beltraniella acaciae, Dactylaria acaciae, Rhexodenticula acaciae, Rubikia evansii and Torula acaciae (all on Acacia koa). India: Lepidoderma echinosporum on dead semi-woody stems, and Rhodocybe rubrobrunnea from soil. Iran: Talaromyces kabodanensis from hypersaline soil. La Reunion: Neocordana musarum from leaves of Musa sp. Malaysia: Anungitea eucalyptigena on Eucalyptus grandis × pellita, Camptomeriphila leucaenae (incl. Camptomeriphila gen. nov.) on Leucaena leucocephala, Castanediella communis on Eucalyptus pellita, Eucalyptostroma eucalypti (incl. Eucalyptostroma gen. nov.) on Eucalyptus pellita, Melanconiella syzygii on Syzygium sp., Mycophilomyces periconiae (incl. Mycophilomyces gen. nov.) as hyperparasite on Periconia on leaves of Albizia falcataria, Synnemadiella eucalypti (incl. Synnemadiella gen. nov.) on Eucalyptus pellita, and Teichospora nephelii on Nephelium lappaceum. Mexico: Aspergillus bicephalus from soil. New Zealand: Aplosporella sophorae on Sophora microphylla, Libertasomyces platani on Platanus sp., Neothyronectria sophorae (incl. Neothyronectria gen. nov.) on Sophora microphylla, Parastagonospora phoenicicola on Phoenix canariensis, Phaeoacremonium pseudopanacis on Pseudopanax crassifolius, Phlyctema phoenicis on Phoenix canariensis, and Pseudoascochyta novae-zelandiae on Cordyline australis. Panama: Chalara panamensis from needle litter of Pinus cf. caribaea. South Africa: Exophiala eucalypti on leaves of Eucalyptus sp., Fantasmomyces hyalinus (incl. Fantasmomyces gen. nov.) on Acacia exuvialis, Paracladophialophora carceris (incl. Paracladophialophora gen. nov.) on Aloe sp., and Umthunziomyces hagahagensis (incl. Umthunziomyces gen. nov.) on Mimusops caffra. Spain: Clavaria griseobrunnea on bare ground in Pteridium aquilinum field, Cyathus ibericus on small fallen branches of Pinus halepensis, Gyroporus pseudolacteus in humus of Pinus pinaster, and Pseudoascochyta pratensis (incl. Pseudoascochyta gen. nov.) from soil. Thailand: Neoascochyta adenii on Adenium obesum, and Ochroconis capsici on Capsicum annuum. UK: Fusicolla melogrammae from dead stromata of Melogramma campylosporum on bark of Carpinus betulus. Uruguay: Myrmecridium pulvericola from house dust. USA: Neoscolecobasidium agapanthi (incl. Neoscolecobasidium gen. nov.) on Agapanthus sp., Polyscytalum purgamentum on leaf litter, Pseudopithomyces diversisporus from human toenail, Saksenaea trapezispora from knee wound of a soldier, and Sirococcus quercus from Quercus sp. Morphological and culture characteristics along with DNA barcodes are provided.
University of Bern1, University of Freiburg2, Ghent University3, Leipzig University4, University of Alcalá5, University of Oxford6, Institut national de la recherche agronomique7, Martin Luther University of Halle-Wittenberg8, Ştefan cel Mare University of Suceava9, University of Florence10, University of Liège11, University of Cambridge12, Spanish National Research Council13, University of Copenhagen14, Katholieke Universiteit Leuven15, Los Alamos National Laboratory16, University of Montpellier17, University of Warsaw18, Royal Holloway, University of London19, Swedish University of Agricultural Sciences20, King Juan Carlos University21
TL;DR: Simulations demonstrate that jack-of-all-trades effects occur whenever species effects on different functions are not perfectly correlated, meaning they may contribute to diversity–multifunctionality relationships in many of the world's ecosystems.
Abstract: There is considerable evidence that biodiversity promotes multiple ecosystem functions (multifunctionality), thus ensuring the delivery of ecosystem services important for human well-being. However, the mechanisms underlying this relationship are poorly understood, especially in natural ecosystems. We develop a novel approach to partition biodiversity effects on multifunctionality into three mechanisms and apply this to European forest data. We show that throughout Europe, tree diversity is positively related with multifunctionality when moderate levels of functioning are required, but negatively when very high function levels are desired. For two well-known mechanisms, ‘complementarity’ and ‘selection’, we detect only minor effects on multifunctionality. Instead a third, so far overlooked mechanism, the ‘jack-of-all-trades’ effect, caused by the averaging of individual species effects on function, drives observed patterns. Simulations demonstrate that jack-of-all-trades effects occur whenever species effects on different functions are not perfectly correlated, meaning they may contribute to diversity–multifunctionality relationships in many of the world’s ecosystems.
TL;DR: In this paper, the chitin nanocrystal surface coating significantly impacted the surface properties of the membranes, producing a super-hydrophilic membrane (contact angle 0°) from the original hydrophobic CA mats.
Centraalbureau voor Schimmelcultures1, University of Pretoria2, Stellenbosch University3, University of La Réunion4, La Trobe University5, Charles University in Prague6, University of Melbourne7, University of Alcalá8, Spanish National Research Council9, University of Texas Health Science Center at San Antonio10, Rovira i Virgili University11, Academy of Sciences of the Czech Republic12, Russian Academy of Sciences13, University of Calcutta14, Moscow State University15, Federal University of Pernambuco16, Federal University of Rio Grande do Norte17, University of Minnesota18, Murdoch University19, Sofia University20, Central University of Ecuador21, Bulgarian Academy of Sciences22, Internal Revenue Service23, Kasetsart University24, University of Calicut25, Thailand National Science and Technology Development Agency26, University of Illinois at Urbana–Champaign27, Council for Scientific and Industrial Research28, Pontificia Universidad Católica del Ecuador29, United States Department of Agriculture30, Nakhon Phanom University31, Korea University32, Universidade Federal de Santa Maria33, University of Antofagasta34
TL;DR: Novel species of fungi described in the present study include the following from Australia: Vermiculariopsiella eucalypti, Mulderomyces natalis, Fusicladium paraamoenum, Neotrimmatostroma paraexcentricum, and Pseudophloeospora eUCalyptorum.
Abstract: Novel species of fungi described in the present study include the following from Australia: Vermiculariopsiella eucalypti, Mulderomyces natalis (incl. Mulderomyces gen. nov.), Fusicladium paraamoenum, Neotrimmatostroma paraexcentricum, and Pseudophloeospora eucalyptorum on leaves of Eucalyptus spp., Anungitea grevilleae (on leaves of Grevillea sp.), Pyrenochaeta acaciae (on leaves of Acacia sp.), and Brunneocarpos banksiae (incl. Brunneocarpos gen. nov.) on cones of Banksia attenuata. Novel foliicolous taxa from South Africa include Neosulcatispora strelitziae (on Strelitzia nicolai), Colletotrichum ledebouriae (on Ledebouria floridunda), Cylindrosympodioides brabejum (incl. Cylindrosympodioides gen. nov.) on Brabejum stellatifolium, Sclerostagonospora ericae (on Erica sp.), Setophoma cyperi (on Cyperus sphaerocephala), and Phaeosphaeria breonadiae (on Breonadia microcephala). Novelties described from Robben Island (South Africa) include Wojnowiciella cissampeli and Diaporthe cissampeli (both on Cissampelos capensis), Phaeotheca salicorniae (on Salicornia meyeriana), Paracylindrocarpon aloicola (incl. Paracylindrocarpon gen. nov.) on Aloe sp., and Libertasomyces myopori (incl. Libertasomyces gen. nov.) on Myoporum serratum. Several novelties are recorded from La Reunion (France), namely Phaeosphaeriopsis agapanthi (on Agapanthus sp.), Roussoella solani (on Solanum mauritianum), Vermiculariopsiella acaciae (on Acacia heterophylla), Dothiorella acacicola (on Acacia mearnsii), Chalara clidemiae (on Clidemia hirta), Cytospora tibouchinae (on Tibouchina semidecandra), Diaporthe ocoteae (on Ocotea obtusata), Castanediella eucalypticola, Phaeophleospora eucalypticola and Fusicladium eucalypticola (on Eucalyptus robusta), Lareunionomyces syzygii (incl. Lareunionomyces gen. nov.) and Parawiesneriomyces syzygii (incl. Parawiesneriomyces gen. nov.) on leaves of Syzygium jambos. Novel taxa from the USA include Meristemomyces arctostaphylos (on Arctostaphylos patula), Ochroconis dracaenae (on Dracaena reflexa), Rasamsonia columbiensis (air of a hotel conference room), Paecilomyces tabacinus (on Nicotiana tabacum), Toxicocladosporium hominis (from human broncoalveolar lavage fluid), Nothophoma macrospora (from respiratory secretion of a patient with pneumonia), and Penidiellopsis radicularis (incl. Penidiellopsis gen. nov.) from a human nail. Novel taxa described from Malaysia include Prosopidicola albizziae (on Albizzia falcataria), Proxipyricularia asari (on Asarum sp.), Diaporthe passifloricola (on Passiflora foetida), Paramycoleptodiscus albizziae (incl. Paramycoleptodiscus gen. nov.) on Albizzia falcataria, and Malaysiasca phaii (incl. Malaysiasca gen. nov.) on Phaius reflexipetalus. Two species are newly described from human patients in the Czech Republic, namely Microascus longicollis (from toenails of patient with suspected onychomycosis), and Chrysosporium echinulatum (from sole skin of patient). Furthermore, Alternaria quercicola is described on leaves of Quercus brantii (Iran), Stemphylium beticola on leaves of Beta vulgaris (The Netherlands), Scleroderma capeverdeanum on soil (Cape Verde Islands), Scleroderma dunensis on soil, and Blastobotrys meliponae from bee honey (Brazil), Ganoderma mbrekobenum on angiosperms (Ghana), Geoglossum raitviirii and Entoloma kruticianum on soil (Russia), Priceomyces vitoshaensis on Pterostichus melas (Carabidae) (Bulgaria) is the only one for which the family is listed, Ganoderma ecuadoriense on decaying wood (Ecuador), Thyrostroma cornicola on Cornus officinalis (Korea), Cercophora vinosa on decorticated branch of Salix sp. (France), Coprinus pinetorum, Coprinus littoralis and Xerocomellus poederi on soil (Spain). Two new genera from Colombia include Helminthosporiella and Uwemyces on leaves of Elaeis oleifera. Two species are described from India, namely Russula intervenosa (ectomycorrhizal with Shorea robusta), and Crinipellis odorata (on bark of Mytragyna parviflora). Novelties from Thailand include Cyphellophora gamsii (on leaf litter), Pisolithus aureosericeus and Corynascus citrinus (on soil). Two species are newly described from Citrus in Italy, namely Dendryphiella paravinosa on Citrus sinensis, and Ramularia citricola on Citrus floridana. Morphological and culture characteristics along with ITS nrDNA barcodes are provided for all taxa.
TL;DR: Analysis of disseminated neoplasia in mussels, cockles, and golden carpet shell clams finds that neoplasias in all three species are attributable to independent transmissible cancer lineages, and shows that transmission of cancer cells in the marine environment is common in multiple species, that it has originated many times, and that while most transmissible cancers are found spreading within the species of origin, cross-species transmission of cancers can occur.
Abstract: Most cancers arise from oncogenic changes in the genomes of somatic cells, and while the cells may migrate by metastasis, they remain within that single individual. Natural transmission of cancer cells from one individual to another has been observed in two distinct cases in mammals (Tasmanian devils and dogs), but these are generally considered to be rare exceptions in nature. The discovery of transmissible cancer in soft-shell clams (Mya arenaria) suggested that this phenomenon might be more widespread. Here we analyse disseminated neoplasia in mussels (Mytilus trossulus), cockles (Cerastoderma edule), and golden carpet shell clams (Polititapes aureus) and find that neoplasias in all three species are attributable to independent transmissible cancer lineages. In mussels and cockles, the cancer lineages are derived from their respective host species; however, unexpectedly, cancer cells in P. aureus are all derived from Venerupis corrugata, a different species living in the same geographical area. No cases of disseminated neoplasia have thus far been found in V. corrugata from the same region. These findings show that transmission of cancer cells in the marine environment is common in multiple species, that it has originated many times, and that while most transmissible cancers are found spreading within the species of origin, cross-species transmission of cancer cells can occur.
Journal Article•
TL;DR: After recent primary total knee replacement, interventions including physiotherapy and exercise show short-term improvements in physical function and future research should target improvements to long-term function, pain and performance outcomes in appropriately powered trials.
Abstract: Rehabilitation, with an emphasis on physiotherapy and exercise, is widely promoted after total knee replacement. However, provision of services varies in content and duration. The aim of this study is to update the review of Minns Lowe and colleagues 2007 using systematic review and meta-analysis to evaluate the effectiveness of post-discharge physiotherapy exercise in patients with primary total knee replacement. Methods We searched MEDLINE, Embase, PsycInfo, CINAHL and Cochrane CENTRAL to October 4th 2013 for randomised evaluations of physiotherapy exercise in adults with recent primary knee replacement. Outcomes were: patient-reported pain and function, knee range of motion, and functional performance. Authors were contacted for missing data and outcomes. Risk of bias and heterogeneity were assessed. Data was combined using random effects meta-analysis and reported as standardised mean differences (SMD) or mean differences (MD). Results Searches identified 18 randomised trials including 1,739 patients with total knee replacement. Interventions compared: physiotherapy exercise and no provision; home and outpatient provision; pool and gym-based provision; walking skills and more general physiotherapy; and general physiotherapy exercise with and without additional balance exercises or ergometer cycling. Compared with controls receiving minimal physiotherapy, patients receiving physiotherapy exercise had improved physical function at 3–4 months, SMD −0.37 (95% CI −0.62, −0.12), and pain, SMD −0.45 (95% CI −0.85, −0.06). Benefit up to 6 months was apparent when considering only higher quality studies. There were no differences for outpatient physiotherapy exercise compared with home-based provision in physical function or pain outcomes. There was a short-term benefit favouring home-based physiotherapy exercise for range of motion flexion. There were no differences in outcomes when the comparator was hydrotherapy, or when additional balancing or cycling components were included. In one study, a walking skills intervention was associated with a long-term improvement in walking performance. However, for all these evaluations studies were under-powered individually and in combination. Conclusion After recent primary total knee replacement, interventions including physiotherapy and exercise show short-term improvements in physical function. However this conclusion is based on meta-analysis of a few small studies and no long-term benefits of physiotherapy exercise interventions were identified. Future research should target improvements to long-term function, pain and performance outcomes in appropriately powered trials. Electronic supplementary material The online version of this article (doi:10.1186/s12891-015-0469-6) contains supplementary material, which is available to authorized users. Keywords: Systematic review, Meta-analysis, Rehabilitation, Physiotherapy, Total knee replacement, Arthroplasty, Exercise, Osteoarthritis, Outcome
TL;DR: The results obtained are promising given the complexity of the task and open the path to future improvements toward fully functional pipeline threat detection systems operating in real conditions.
Abstract: This paper presents the first available report in the literature of a system aimed at the detection and classification of threats in the vicinity of a long gas pipeline. The system is based on phase-sensitive optical time-domain reflectometry technology for signal acquisition and pattern recognition strategies for threat identification. The system operates in two different modes: 1) machine+activity identification, which outputs the activity being carried out by a certain machine; and 2) threat detection, aimed at detecting threats no matter what the real activity being conducted is. Different strategies dealing with position selection and normalization methods are presented and evaluated using a rigorous experimental procedure on realistic field data. Experiments are conducted with $\text{eight}$ machine+activity pairs, which are further labeled as threat or nonthreat for the second mode of the system. The results obtained are promising given the complexity of the task and open the path to future improvements toward fully functional pipeline threat detection systems operating in real conditions.
TL;DR: The most recent advances on the use of cyclodextrins as chiral selectors in capillary electrophoresis for the enantioseparation of drugs are reviewed and the most relevant applications developed to carry out the quantitation of chiral drugs, to assess theEnantiomeric purity of pharmaceutical formulations, to study their metabolism or to achieve criminalistic or forensic investigations are described.
TL;DR: In ascitic cirrhotic rats, obeticholic acid reduces gut bacterial translocation via several complementary mechanisms at the intestinal level and could be used as an alternative to antibiotics to prevent bacterial infection in cirrhosis.
TL;DR: The most important optimization algorithms based on nonlinear physics, how they have been constructed from specific modeling of a real phenomena, and also their novelty in terms of comparison with alternative existing algorithms for optimization are reviewed.
TL;DR: In this paper, a new global burned area (BA) product developed within the framework of the European Space Agency's Climate Change Initiative (CCI) program, along with a first assessment of its potentials for atmospheric and carbon cycle modelling, is presented.
Abstract: Aim This paper presents a new global burned area (BA) product developed within the framework of the European Space Agency's Climate Change Initiative (CCI) programme, along with a first assessment of its potentials for atmospheric and carbon cycle modelling.
Innovation Methods are presented for generating a new global BA product, along with a comparison with existing BA products, in terms of BA extension, fire size and shapes and emissions derived from biomass burnings.
Main conclusions Three years of the global BA product were produced, accounting for a total BA of between 360 and 380 Mha year-1. General omission and commission errors for BA were 0.76 and 0.64, but they decreased to 0.51 and 0.52, respectively, for sites with more than 10% BA. Intercomparison with other existing BA datasets found similar spatial and temporal trends, mainly with the BA included in the Global Fire Emissions Database (GFED4), although regional differences were found (particularly in the 2006 fires of eastern Europe). The simulated carbon emissions from biomass burning averaged 2.1 Pg C year-1
TL;DR: In this article, the authors reported a measurement for ultra-high energy cosmic rays of the correlation between the depth of shower maximum and the signal in the water Cherenkov stations of air-showers registered simultaneously by the fluorescence and the surface detectors of the Pierre Auger Observatory.
TL;DR: The radiation energy provides direct access to the calorimetric energy in the electromagnetic cascade of extensive air showers and allows the direct calibration of any cosmic-ray radio detector against the well-established energy scale of the Pierre Auger Observatory.
Abstract: We measure the energy emitted by extensive air showers in the form of radio emission in the frequency range from 30 to 80 MHz. Exploiting the accurate energy scale of the Pierre Auger Observatory, we obtain a radiation energy of 15.8 \pm 0.7 (stat) \pm 6.7 (sys) MeV for cosmic rays with an energy of 1 EeV arriving perpendicularly to a geomagnetic field of 0.24 G, scaling quadratically with the cosmic-ray energy. A comparison with predictions from state-of-the-art first-principle calculations shows agreement with our measurement. The radiation energy provides direct access to the calorimetric energy in the electromagnetic cascade of extensive air showers. Comparison with our result thus allows the direct calibration of any cosmic-ray radio detector against the well-established energy scale of the Pierre Auger Observatory.
TL;DR: In this paper, the authors summarized the most representative research activities conducted to prevent membrane fouling and highlighted alternative routes to discarded end-of-life-membranes in order to prevent the uncontrolled disposal of fouled membranes in landfills.