Showing papers by "University of Lisbon published in 2017"

2016 update of the ASAS-EULAR management recommendations for axial spondyloarthritis

Abstract: To update and integrate the recommendations for ankylosing spondylitis and the recommendations for the use of tumour necrosis factor inhibitors (TNFi) in axial spondyloarthritis (axSpA) into one set applicable to the full spectrum of patients with axSpA. Following the latest version of the European League Against Rheumatism (EULAR) Standardised Operating Procedures, two systematic literature reviews first collected the evidence regarding all treatment options (pharmacological and non-pharmacological) that were published since 2009. After a discussion of the results in the steering group and presentation to the task force, overarching principles and recommendations were formulated, and consensus was obtained by informal voting. A total of 5 overarching principles and 13 recommendations were agreed on. The first three recommendations deal with personalised medicine including treatment target and monitoring. Recommendation 4 covers non-pharmacological management. Recommendation 5 describes the central role of non-steroidal anti-inflammatory drugs (NSAIDs) as first-choice drug treatment. Recommendations 6-8 define the rather modest role of analgesics, and disprove glucocorticoids and conventional synthetic disease-modifying antirheumatic drugs (DMARDs) for axSpA patents with predominant axial involvement. Recommendation 9 refers to biological DMARDs (bDMARDs) including TNFi and IL-17 inhibitors (IL-17i) for patients with high disease activity despite the use (or intolerance/contraindication) of at least two NSAIDs. In addition, they should either have an elevated C reactive protein and/or definite inflammation on MRI and/or radiographic evidence of sacroiliitis. Current practice is to start with a TNFi. Switching to another TNFi or an IL-17i is recommended in case TNFi fails (recommendation 10). Tapering, but not stopping a bDMARD, can be considered in patients in sustained remission (recommendation 11). The final two recommendations (12, 13) deal with surgery and spinal fractures. The 2016 Assessment of SpondyloArthritis international Society-EULAR recommendations provide up-to-date guidance on the management of patients with axSpA.

antiSMASH 4.0-improvements in chemistry prediction and gene cluster boundary identification.

Abstract: Many antibiotics, chemotherapeutics, crop protection agents and food preservatives originate from molecules produced by bacteria, fungi or plants. In recent years, genome mining methodologies have been widely adopted to identify and characterize the biosynthetic gene clusters encoding the production of such compounds. Since 2011, the â € antibiotics and secondary metabolite analysis shell - antiSMASH' has assisted researchers in efficiently performing this, both as a web server and a standalone tool. Here, we present the thoroughly updated antiSMASH version 4, which adds several novel features, including prediction of gene cluster boundaries using the ClusterFinder method or the newly integrated CASSIS algorithm, improved substrate specificity prediction for non-ribosomal peptide synthetase adenylation domains based on the new SANDPUMA algorithm, improved predictions for terpene and ribosomally synthesized and post-translationally modified peptides cluster products, reporting of sequence similarity to proteins encoded in experimentally characterized gene clusters on a per-protein basis and a domain-level alignment tool for comparative analysis of trans-AT polyketide synthase assembly line architectures. Additionally, several usability features have been updated and improved. Together, these improvements make antiSMASH up-to-date with the latest developments in natural product research and will further facilitate computational genome mining for the discovery of novel bioactive molecules.

Histopathological Findings in Brain Tissue Obtained during Epilepsy Surgery.

Abstract: BackgroundDetailed neuropathological information on the structural brain lesions underlying seizures is valuable for understanding drug-resistant focal epilepsy. MethodsWe report the diagnoses made on the basis of resected brain specimens from 9523 patients who underwent epilepsy surgery for drug-resistant seizures in 36 centers from 12 European countries over 25 years. Histopathological diagnoses were determined through examination of the specimens in local hospitals (41%) or at the German Neuropathology Reference Center for Epilepsy Surgery (59%). ResultsThe onset of seizures occurred before 18 years of age in 75.9% of patients overall, and 72.5% of the patients underwent surgery as adults. The mean duration of epilepsy before surgical resection was 20.1 years among adults and 5.3 years among children. The temporal lobe was involved in 71.9% of operations. There were 36 histopathological diagnoses in seven major disease categories. The most common categories were hippocampal sclerosis, found in 36.4% of...

Performance of the ATLAS trigger system in 2015

Abstract: During 2015 the ATLAS experiment recorded 3.8 fb(-1) of proton-proton collision data at a centre-of-mass energy of 13 TeV. The ATLAS trigger system is a crucial component of the experiment, respons ...

Political communication in a high-choice media environment: a challenge for democracy?

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.

Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia

Abstract: Background: Over the past decade genome-wide association studies (GWAS) have been applied to aid in the understanding of the biology of traits. The success of this approach is governed by the underlying effect sizes carried by the true risk variants and the corresponding statistical power to observe such effects given the study design and sample size under investigation. Previous ASD GWAS have identified genome-wide significant (GWS) risk loci; however, these studies were of only of low statistical power to identify GWS loci at the lower effect sizes (odds ratio (OR) <1.15). Methods: We conducted a large-scale coordinated international collaboration to combine independent genotyping data to improve the statistical power and aid in robust discovery of GWS loci. This study uses genome-wide genotyping data from a discovery sample (7387 ASD cases and 8567 controls) followed by meta-analysis of summary statistics from two replication sets (7783 ASD cases and 11359 controls; and 1369 ASD cases and 137308 controls). Results: We observe a GWS locus at 10q24.32 that overlaps several genes including PITX3, which encodes a transcription factor identified as playing a role in neuronal differentiation and CUEDC2 previously reported to be associated with social skills in an independent population cohort. We also observe overlap with regions previously implicated in schizophrenia which was further supported by a strong genetic correlation between these disorders (Rg = 0.23; P=9 ×10−6). We further combined these Psychiatric Genomics Consortium (PGC) ASD GWAS data with the recent PGC schizophrenia GWAS to identify additional regions which may be important in a common neurodevelopmental phenotype and identified 12 novel GWS loci. These include loci previously implicated in ASD such as FOXP1 at 3p13, ATP2B2 at 3p25.3, and a ‘neurodevelopmental hub’ on chromosome 8p11.23. Conclusions: This study is an important step in the ongoing endeavour to identify the loci which underpin the common variant signal in ASD. In addition to novel GWS loci, we have identified a significant genetic correlation with schizophrenia and association of ASD with several neurodevelopmental-related genes such as EXT1, ASTN2, MACROD2, and HDAC4.

Variations in the Prevalence of Obesity Among European Countries, and a Consideration of Possible Causes

Abstract: Over the last 10 years the prevalence of obesity across the European continent has in general been rising. With the exception of a few countries where a levelling-off can be perceived, albeit at a high level, this upward trend seems likely to continue. However, considerable country to country variation is noticeable, with the proportion of people with obesity varying by 10% or more. This variation is intriguing and suggests the existence of different profiles of risk or protection factors operating in different countries. The identification of such protection factors could indicate suitable targets for interventions to help manage the obesity epidemic in Europe. This report is the output of a 2-day workshop on the ‘Diversity of Obesity in Europe'. The workshop included 14 delegates from 12 different European countries. This report contains the contributions and discussions of the materials and viewpoints provided by these 14 experts; it is not the output of a single mind. However, such is the nature of scientific analysis regarding obesity that it is possible that a different set of 14 experts may have come to a different set of conclusions. Therefore the report should not be seen as a definitive statement of a stable situation. Rather it is a focus for discussion and comment, and a vehicle to drive forward further understanding and management of obesity in Europe.

European Stroke Organization guideline for the diagnosis and treatment of cerebral venous thrombosis - endorsed by the European Academy of Neurology

Abstract: The current proposal for cerebral venous thrombosis guideline followed the Grading of Recommendations, Assessment, Development, and Evaluation system, formulating relevant diagnostic and treatment questions, performing systematic reviews of all available evidence and writing recommendations and deciding on their strength on an explicit and transparent manner, based on the quality of available scientific evidence. The guideline addresses both diagnostic and therapeutic topics. We suggest using magnetic resonance or computed tomography angiography for confirming the diagnosis of cerebral venous thrombosis and not screening patients with cerebral venous thrombosis routinely for thrombophilia or cancer. We recommend parenteral anticoagulation in acute cerebral venous thrombosis and decompressive surgery to prevent death due to brain herniation. We suggest to use preferentially low-molecular weight heparin in the acute phase and not using direct oral anticoagulants. We suggest not using steroids and acetazolamide to reduce death or dependency. We suggest using antiepileptics in patients with an early seizure and supratentorial lesions to prevent further early seizures. We could not make recommendations due to very poor quality of evidence concerning duration of anticoagulation after the acute phase, thrombolysis and/or thrombectomy, therapeutic lumbar puncture, and prevention of remote seizures with antiepileptic drugs. We suggest that in women who suffered a previous cerebral venous thrombosis, contraceptives containing oestrogens should be avoided. We suggest that subsequent pregnancies are safe, but use of prophylactic low-molecular weight heparin should be considered throughout pregnancy and puerperium. Multicentre observational and experimental studies are needed to increase the level of evidence supporting recommendations on the diagnosis and management of cerebral venous thrombosis.

A critical review of traditional and emerging techniques and fluids for electronics cooling

Abstract: Continued miniaturization and demand for high-end performance of electronic devices and appliances have led to dramatic increase in their heat flux generation. Consequently, conventional coolants and cooling approaches are increasingly falling short in meeting the ever-increasing cooling needs and challenges of those high heat generating electronic devices. This study provides a critical review of traditional and emerging cooling methods as well as coolants for electronics. In addition to summarizing traditional coolants, heat transfer properties and performances of potential new coolants such as nanofluids are also reviewed and analyzed. With superior thermal properties and numerous benefits nanofluids show great promises in fulfilling the cooling demands of high heat generating electronic devices. It is believed that applications of such novel coolants in emerging techniques like micro-channels and micro-heat pipes can revolutionize cooling technologies for electronics in the future.

Topological cell clustering in the ATLAS calorimeters and its performance in LHC Run 1

Abstract: The reconstruction of the signal from hadrons and jets emerging from the proton–proton collisions at the Large Hadron Collider (LHC) and entering the ATLAS calorimeters is based on a three-dimensional topological clustering of individual calorimeter cell signals. The cluster formation follows cell signal-significance patterns generated by electromagnetic and hadronic showers. In this, the clustering algorithm implicitly performs a topological noise suppression by removing cells with insignificant signals which are not in close proximity to cells with significant signals. The resulting topological cell clusters have shape and location information, which is exploited to apply a local energy calibration and corrections depending on the nature of the cluster. Topological cell clustering is established as a well-performing calorimeter signal definition for jet and missing transverse momentum reconstruction in ATLAS.

Use of essential oils in active food packaging: Recent advances and future trends

Abstract: Background Essential oils (EOs) extracted from plants have been the focus of numerous researches due to their potential in the food and pharmaceutical industries and aromatherapy. Scope and approach The effectiveness of EO may be observed in antimicrobial and antioxidant tests. Volatile compounds are present in EOs and are responsible by their biological activities, namely antimicrobial and antioxidant capacity. Several manuscripts and patents have emerged with applications of EOs and their constituents, and their incorporation into food packaging. These packages with EOs have shown efficiency against microorganisms and oxidants in vitro, in tests with food and/or food simulants evaluation tests. In line with this, chromatographic techniques can be used to identify the main volatile compounds present in EOs or to determine the compounds that migrated from packaging to food or food simulants. This review provides a concise and critical insight in the use of EOs with emphasis in food applications. The innovative food packaging applications are highlighted and future trends are discussed. Key findings and conclusions In general, EOs extend food stability during storage, inhibiting the growth of spoilage or pathogenic microorganisms and protecting against oxidation. Moreover, in spite of the potential of EOs, more studies should evaluate their safety and possible side effects before considering their use for food purposes.

A synthesis of radial growth patterns preceding tree mortality

Abstract: Tree mortality is a key factor influencing forest functions and dynamics, but our understanding of the mechanisms leading to mortality and the associated changes in tree growth rates are still limited. We compiled a new pan-conti- nental tree-ring width database from sites where both dead and living trees were sampled (2970 dead and 4224 living trees from 190 sites, including 36 species), and compared early and recent growth rates between trees that died and those that survived a given mortality event. We observed a decrease in radial growth before death in ca. 84% of the mortality events. The extent and duration of these reductions were highly variable (1–100 years in 96% of events) due to the complex interactions among study species and the source(s) of mortality. Strong and long-lasting declines were found for gymnosperms, shade- and drought-tolerant species, and trees that died from competition. Angiosperms and trees that died due to biotic attacks (especially bark-beetles) typically showed relatively small and short-term growth reductions. Our analysis did not highlight any universal trade-off between early growth and tree longevity within a species, although this result may also reflect high variability in sampling design among sites. The intersite and interspecific variability in growth patterns before mortality provides valuable information on the nature of the mortality process, which is consistent with our understanding of the physiological mechanisms leading to mortality. Abrupt changes in growth immediately before death can be associated with generalized hydraulic failure and/or bark-beetle attack, while long-term decrease in growth may be associated with a gradual decline in hydraulic performance coupled with depletion in carbon reserves. Our results imply that growth-based mortality algorithms may be a powerful tool for predicting gymnosperm mortality induced by chronic stress, but not necessarily so for angiosperms and in case of intense drought or bark-beetle outbreaks.

First light for GRAVITY: Phase referencing optical interferometry for the Very Large Telescope Interferometer

Abstract: GRAVITY is a new instrument to coherently combine the light of the European Southern Observatory Very Large Telescope Interferometer to form a telescope with an equivalent 130 m diameter angular resolution and a collecting area of 200 m2. The instrument comprises fiber fed integrated optics beam combination, high resolution spectroscopy, built-in beam analysis and control, near-infrared wavefront sensing, phase-tracking, dual-beam operation, and laser metrology. GRAVITY opens up to optical/infrared interferometry the techniques of phase referenced imaging and narrow angle astrometry, in many aspects following the concepts of radio interferometry. This article gives an overview of GRAVITY and reports on the performance and the first astronomical observations during commissioning in 2015/16. We demonstrate phase-tracking on stars as faint as mK ≈ 10 mag, phase-referenced interferometry of objects fainter than mK ≈ 15 mag with a limiting magnitude of mK ≈ 17 mag, minute long coherent integrations, a visibility accuracy of better than 0.25%, and spectro-differential phase and closure phase accuracy better than 0.5°, corresponding to a differential astrometric precision of better than ten microarcseconds (μas). The dual-beam astrometry, measuring the phase difference of two objects with laser metrology, is still under commissioning. First observations show residuals as low as 50 μas when following objects over several months. We illustrate the instrument performance with the observations of archetypical objects for the different instrument modes. Examples include the Galactic center supermassive black hole and its fast orbiting star S2 for phase referenced dual-beam observations and infrared wavefront sensing, the high mass X-ray binary BP Cru and the active galactic nucleus of PDS 456 for a few μas spectro-differential astrometry, the T Tauri star S CrA for a spectro-differential visibility analysis, ξ Tel and 24 Cap for high accuracy visibility observations, and η Car for interferometric imaging with GRAVITY.

Towards process-informed bias correction of climate change simulations

Abstract: Biases in climate model simulations introduce biases in subsequent impact simulations. Therefore, bias correction methods are operationally used to post-process regional climate projections. However, many problems have been identified, and some researchers question the very basis of the approach. Here we demonstrate that a typical cross-validation is unable to identify improper use of bias correction. Several examples show the limited ability of bias correction to correct and to downscale variability, and demonstrate that bias correction can cause implausible climate change signals. Bias correction cannot overcome major model errors, and naive application might result in ill-informed adaptation decisions. We conclude with a list of recommendations and suggestions for future research to reduce, post-process, and cope with climate model biases. Bias correction methods aim to remove introduced bias for climate model simulations; however, improper use can result in spurious climate signals. This Perspective considers the issues of bias correction and makes recommendations for research to overcome model biases.

Search for new high-mass phenomena in the dilepton final state using 36 fb−1 of proton-proton collision data at √s=13 TeV with the ATLAS detector

Abstract: A search is conducted for new resonant and non-resonant high-mass phenomena in dielectron and dimuon fi nal states. The search uses 36 : 1 fb(-1) of proton-proton collision data, collected at root ...

A state of the art review on viscosity of nanofluids

Abstract: A comprehensive review of research and development on rheological characteristics of nanofluids for their advanced heat transfer applications is performed and reported in this paper. It identifies the research anomaly and importance on this topic besides analysing rheology of nanofluids. Various classical and recently developed viscosity models for nanofluids are presented and discussed. Nanofluids are classified as metallic and nonmetallic types and research findings on this key property of available nanofluids are analyzed. Effects of several important factors such as concentration of nanoparticles and temperature on viscosity of each type of nanofluids have been explicitly reviewed. Results from various research groups and predictions from viscosity models are also compared and discussed in detail. Role and importance of the viscosity in connection with other thermal properties and parameters for their thermal management applications are highlighted. Furthermore, the research challenges and needs in this important area of nanofluids are also revealed.

Deep intronic mutations and human disease.

Abstract: Next-generation sequencing has revolutionized clinical diagnostic testing. Yet, for a substantial proportion of patients, sequence information restricted to exons and exon-intron boundaries fails to identify the genetic cause of the disease. Here we review evidence from mRNA analysis and entire genomic sequencing indicating that pathogenic mutations can occur deep within the introns of over 75 disease-associated genes. Deleterious DNA variants located more than 100 base pairs away from exon-intron junctions most commonly lead to pseudo-exon inclusion due to activation of non-canonical splice sites or changes in splicing regulatory elements. Additionally, deep intronic mutations can disrupt transcription regulatory motifs and non-coding RNA genes. This review aims to highlight the importance of studying variation in deep intronic sequence as a cause of monogenic disorders as well as hereditary cancer syndromes.

Handbook of protocols for standardized measurement of terrestrial invertebrate functional traits

Abstract: Summary 1. Trait-based approaches are increasingly being used to test mechanisms underlying species assemblages and biotic interactions across a wide range of organisms including terrestrial arthropods and to investigate consequences for ecosystem processes. Such an approach relies on the standardized measurement of functional traits that can be applied across taxa and regions. Currently, however, unified methods of trait measurements are lacking for terrestrial arthropods and related macroinvertebrates (terrestrial invertebrates hereafter). 2. Here, we present a comprehensive review and detailed protocol for a set of 29 traits known to be sensitive to global stressors and to affect ecosystem processes and services. We give rec- ommendations how to measure these traits under standardized conditions across various ter- restrial invertebrate taxonomic groups. 3. We provide considerations and approaches that apply to almost all traits described, such as the selection of species and individuals needed for the measurements, the importance of intraspecific trait variability, how many populations or communities to sample and over which spatial scales. 4. The approaches outlined here provide a means to improve the reliability and predictive power of functional traits to explain community assembly, species diversity patterns and ecosystem processes and services within and across taxa and trophic levels, allowing compar- ison of studies and running meta-analyses across regions and ecosystems. 5. This handbook is a crucial first step towards standardizing trait methodology across the most studied terrestrial invertebrate groups, and the protocols are aimed to balance general applicability and requirements for special cases or particular taxa. Therefore, we envision this handbook as a common platform to which researchers can further provide methodological input for additional special cases.

Search for new phenomena in dijet events using 37 fb-1 of pp collision data collected at √s=13 TeV with the ATLAS detector

Abstract: Dijet events are studied in the proton-proton collision dataset recorded at root s = 13 TeV with the ATLAS detector at the Large Hadron Collider in 2015 and 2016, corresponding to integrated lumino ...

European contribution to the study of ROS : a summary of the findings and prospects for the future from the COST action BM1203 (EU-ROS)

Abstract: The European Cooperation in Science and Technology (COST) provides an ideal framework to establish multi-disciplinary research networks COST Action BM1203 (EU-ROS) represents a consortium of researchers from different disciplines who are dedicated to providing new insights and tools for better understanding redox biology and medicine and, in the long run, to finding new therapeutic strategies to target dysregulated redox processes in various diseases This report highlights the major achievements of EU-ROS as well as research updates and new perspectives arising from its members The EU-ROS consortium comprised more than 140 active members who worked together for four years on the topics briefly described below The formation of reactive oxygen and nitrogen species (RONS) is an established hallmark of our aerobic environment and metabolism but RONS also act as messengers via redox regulation of essential cellular processes The fact that many diseases have been found to be associated with oxidative stress established the theory of oxidative stress as a trigger of diseases that can be corrected by antioxidant therapy However, while experimental studies support this thesis, clinical studies still generate controversial results, due to complex pathophysiology of oxidative stress in humans For future improvement of antioxidant therapy and better understanding of redox-associated disease progression detailed knowledge on the sources and targets of RONS formation and discrimination of their detrimental or beneficial roles is required In order to advance this important area of biology and medicine, highly synergistic approaches combining a variety of diverse and contrasting disciplines are needed

A global synthesis of the effects of diversified farming systems on arthropod diversity within fields and across agricultural landscapes.

Abstract: Agricultural intensification is a leading cause of global biodiversity loss, which can reduce the provisioning of ecosystem services in managed ecosystems. Organic farming and plant diversification are farm management schemes that may mitigate potential ecological harm by increasing species richness and boosting related ecosystem services to agroecosystems. What remains unclear is the extent to which farm management schemes affect biodiversity components other than species richness, and whether impacts differ across spatial scales and landscape contexts. Using a global metadataset, we quantified the effects of organic farming and plant diversification on abundance, local diversity (communities within fields), and regional diversity (communities across fields) of arthropod pollinators, predators, herbivores, and detritivores. Both organic farming and higher in-field plant diversity enhanced arthropod abundance, particularly for rare taxa. This resulted in increased richness but decreased evenness. While these responses were stronger at local relative to regional scales, richness and abundance increased at both scales, and richness on farms embedded in complex relative to simple landscapes. Overall, both organic farming and in-field plant diversification exerted the strongest effects on pollinators and predators, suggesting these management schemes can facilitate ecosystem service providers without augmenting herbivore (pest) populations. Our results suggest that organic farming and plant diversification promote diverse arthropod metacommunities that may provide temporal and spatial stability of ecosystem service provisioning. Conserving diverse plant and arthropod communities in farming systems therefore requires sustainable practices that operate both within fields and across landscapes.

The ancestral flower of angiosperms and its early diversification

Abstract: Recent advances in molecular phylogenetics and a series of important palaeobotanical discoveries have revolutionized our understanding of angiosperm diversification. Yet, the origin and early evolution of their most characteristic feature, the flower, remains poorly understood. In particular, the structure of the ancestral flower of all living angiosperms is still uncertain. Here we report model-based reconstructions for ancestral flowers at the deepest nodes in the phylogeny of angiosperms, using the largest data set of floral traits ever assembled. We reconstruct the ancestral angiosperm flower as bisexual and radially symmetric, with more than two whorls of three separate perianth organs each (undifferentiated tepals), more than two whorls of three separate stamens each, and more than five spirally arranged separate carpels. Although uncertainty remains for some of the characters, our reconstruction allows us to propose a new plausible scenario for the early diversification of flowers, leading to new testable hypotheses for future research on angiosperms.