Showing papers by "University of Costa Rica published in 2020"
TL;DR: The extent of the trait data compiled in TRY is evaluated and emerging patterns of data coverage and representativeness are analyzed to conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements.
Abstract: Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
882 citations
University of Bremen1, Duke University2, Max Planck Society3, University of Bristol4, University of Costa Rica5, Western Washington University6, University of Minnesota7, University of Bonn8, Karlsruhe Institute of Technology9, Free University of Berlin10, Oak Ridge National Laboratory11, Ulsan National Institute of Science and Technology12, University of Regensburg13, University of Warwick14, Los Alamos National Laboratory15, Claude Bernard University Lyon 116, University of Newcastle17, Dassault Systèmes18, Facultad de Ciencias Exactas y Naturales19, Argonne National Laboratory20, University of Luxembourg21
TL;DR: An overview of the recently developed capabilities of the DFTB+ code is given, demonstrating with a few use case examples, and the strengths and weaknesses of the various features are discussed, to discuss on-going developments and possible future perspectives.
Abstract: DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green’s functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.
491 citations
University of Montana1, Oregon State University2, University of California, San Diego3, Wageningen University and Research Centre4, Sookmyung Women's University5, University of Nantes6, Acharya Nagarjuna University7, Ensenada Center for Scientific Research and Higher Education8, Universidad Autónoma de Chiriquí9, University of Costa Rica10, Auburn University11, Victoria University of Wellington12, University of Johannesburg13, University of Münster14, John Innes Centre15
TL;DR: This protocol describes how to use GNPS to explore uploaded metabolomics data, and provides step-by-step instructions for creating reproducible, high-quality molecular networks.
Abstract: Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user's underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking-one of the main analysis tools used within the GNPS platform-creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.
274 citations
University of Tartu1, American Museum of Natural History2, University of Gothenburg3, Swedish University of Agricultural Sciences4, University of Oslo5, University of Hawaii at Manoa6, University of Copenhagen7, Purdue University8, Academy of Sciences of the Czech Republic9, University of Turin10, Harvard University11, Synlab Group12, Universidad Santo Tomás13, Universidad Mayor14, University of Electronic Science and Technology of China15, University of Warsaw16, Swedish Museum of Natural History17, Mae Fah Luang University18, University of Florida19, Laos Ministry of Agriculture and Forestry20, São Paulo Federal Institute of Education, Science and Technology21, Estonian University of Life Sciences22, Federal University of Pernambuco23, United States Department of Energy24, Del Rosario University25, National Autonomous University of Mexico26, Ghent University27, West Bengal State University28, Beijing Forestry University29, Pontifical Catholic University of Chile30, Chinese Academy of Sciences31, Field Museum of Natural History32, University of Potsdam33, Leibniz Association34, University of Gilan35, University of Alaska Fairbanks36, University of Tokyo37, University of Costa Rica38, Forest Research Institute39, Westmead Hospital40, University of Sydney41, Uppsala University42, Landcare Research43, University of Chittagong44, University of Memphis45, United Arab Emirates University46, Ministry of Land and Resources of the People's Republic of China47, University of Pretoria48, Royal Botanic Gardens49, Ocean University of China50, Guizhou University51, Mie University52, Hokkaido University53
TL;DR: Fungal traits and character database FungalTraits operating at genus and species hypothesis levels is presented in this article, which includes 17 lifestyle related traits of fungal and Stramenopila genera.
Abstract: The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental studies. Over the past decades, rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats. Yet, in spite of the progress of molecular methods, knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains challenging. In order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis levels. Combining the information from previous efforts such as FUNGuild and Fun(Fun) together with involvement of expert knowledge, we reannotated 10,210 and 151 fungal and Stramenopila genera, respectively. This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera, designed for rapid functional assignments of environmental studies. In order to assign the trait states to fungal species hypotheses, the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS sequences. On the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1% dissimilarity threshold.
245 citations
Royal Observatory of Belgium1, Imperial College London2, University of Auckland3, Royal Holloway, University of London4, National Autonomous University of Mexico5, Swiss Seismological Service6, University of Helsinki7, United States Geological Survey8, Central Institution for Meteorology and Geodynamics9, University of Costa Rica10, Royal Netherlands Meteorological Institute11, Kandilli Observatory and Earthquake Research Institute12, University of Potsdam13, National Institute of Geophysics and Volcanology14, University of Catania15, University of Cologne16, University of Savoy17, King's College, Aberdeen18, Dublin Institute for Advanced Studies19, Delft University of Technology20, Spanish National Research Council21, Institute for Geosciences and Natural Resources22, Mediterranean University23, Norwegian Geotechnical Institute24, University of Alaska Fairbanks25, University of Strasbourg26, University of Lausanne27, University of Bristol28, Princeton University29, University of Tehran30, Boston College31, California Institute of Technology32, Stanford University33, Search for extraterrestrial intelligence34, University of British Columbia35, Ludwig Maximilian University of Munich36, Australian National University37, McGill University38, University of Maine39, University of California, Riverside40, University of Chile41, University of Oxford42, BBN Technologies43, Institut de Physique du Globe de Paris44, Victoria University of Wellington45, University of Patras46, University of Bergen47, University of California, Berkeley48, Institut d'Estudis Catalans49, University of Michigan50, University of California, Santa Barbara51
TL;DR: The 2020 seismic noise quiet period is the longest and most prominent global anthropogenic seismic noise reduction on record and suggests that seismology provides an absolute, real-time estimate of human activities.
Abstract: Human activity causes vibrations that propagate into the ground as high-frequency seismic waves. Measures to mitigate the coronavirus disease 2019 (COVID-19) pandemic caused widespread changes in human activity, leading to a months-long reduction in seismic noise of up to 50%. The 2020 seismic noise quiet period is the longest and most prominent global anthropogenic seismic noise reduction on record. Although the reduction is strongest at surface seismometers in populated areas, this seismic quiescence extends for many kilometers radially and hundreds of meters in depth. This quiet period provides an opportunity to detect subtle signals from subsurface seismic sources that would have been concealed in noisier times and to benchmark sources of anthropogenic noise. A strong correlation between seismic noise and independent measurements of human mobility suggests that seismology provides an absolute, real-time estimate of human activities.
202 citations
TL;DR: The Random Forest based MErging Procedure (RF-MEP), which combines information from ground-based measurements, state-of-the-art precipitation products, and topography-related features to improve the representation of the spatio-temporal distribution of precipitation, is presented, especially in data-scarce regions.
119 citations
TL;DR: In this paper, the authors developed an analytical framework to enhance understanding of the processes by which local top-down and bottom-up forces enhance sustainable rural development by co-developing bottom-linked governance.
97 citations
TL;DR: In this article, the authors derived systematic relationships between learning outcomes and air quality in classrooms using data from published studies and derived the relationship regardless of whether the change in performance was statistically significant at the examined levels of classroom air quality.
89 citations
TL;DR: A comprehensive review of the state-of-the-art in the assessment of moisture source-sinks and how different approaches can contribute to improving our knowledge of this component of the Earth's Climate System can be found in this article.
83 citations
Aniruddha Deshpande1, Molly K. Miller-Petrie2, Paulina A. Lindstedt2, Mathew M. Baumann2 +702 more•Institutions (292)
TL;DR: High-resolution geospatial estimates of access to drinking water and sanitation facilities in low-income and middle-income countries from 2000 to 2017 identify areas with successful approaches or in need of targeted interventions to enable precision public health to effectively progress towards universal access to safe water and sanitary facilities.
80 citations
TL;DR: This paper examines folk theories of algorithmic recommendations on Spotify to make visible the cultural specificities of data assemblages in the global South and argues that folk theories offer a productive way to broaden understanding of what agency means in relation to algorithms.
Abstract: This paper examines folk theories of algorithmic recommendations on Spotify in order to make visible the cultural specificities of data assemblages in the global South. The study was conducted in C...
TL;DR: The strength of the association between actual motor competence and perceived motor competence/physical self-perception in youth is low to moderate, with current data demonstrating that the strength of association does not differ by age, sex, developmental status, or alignment between measurement instruments.
Abstract: Actual and perceived motor competence are important correlates of various health-related behaviors. As such, numerous studies have examined the association between both constructs in children and adolescents. The first aim of this review and meta-analysis was to systematically examine, analyze and summarize the scientific evidence on the relationship between actual and perceived motor competence (and by extension more general physical self-perception) in children, adolescents and young adults with typical and atypical development. The second aim was to examine several a priori determined potential moderators (i.e., age, sex, and developmental status of study participants, as well as level of alignment between measurement instruments) of the relationship between actual motor competence and perceived motor competence/physical self-perception. This systematic review was conducted in accordance with the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) statement and was registered with PROSPERO on August 21st 2017. A systematic literature search of five electronic databases (i.e., MEDLINE, SPORTDiscus, Web of Science, PsycINFO and EMBASE) with no date restrictions was conducted. Eligibility criteria included (1) a study sample of youth aged 3–24 years, (2) an assessment of actual motor competence and perceived motor competence/physical self-perception, and (3) a report of the association between both, using a cross-sectional, longitudinal, or experimental design. Only original articles published in peer-reviewed journals with at least the title and abstract in English were considered. Meta-analyses were conducted by type of actual motor competence (i.e., overall motor competence, locomotor, object control, stability/balance and sport-specific competence) through univariate and multivariable random-effects meta-regression and clustered random-effects meta-regression models. Of the 1643 articles screened, 87 were included for the qualitative review, while 69 remained for the final meta-analyses. All included studies had some risk of bias with only 15% meeting five of the six examined criteria. Significant (p < 0.001) pooled effects were found for overall motor competence (N = 54; r = 0.25; 95% CI [0.20, 0.29]), locomotor (N = 45; r = 0.19; 95% CI [0.13, 0.25]), object control (N = 50; r = 0.22; 95% CI [0.17, 0.27]), stability/balance (N = 8; r = 0.21; 95% CI [0.12, 0.30]), and sport-specific competence (N = 8; r = 0.46; 95% CI [0.28, 0.61]). None of the hypothesized moderators significantly influenced the relationship between actual motor competence and perceived motor competence/physical self-perception. The strength of the association between actual motor competence and perceived motor competence/physical self-perception in youth is low to moderate, with current data demonstrating that the strength of association does not differ by age, sex, developmental status, or alignment between measurement instruments. However, this review highlights the lack of clarity on the relationship between actual motor competence and perceived motor competence/physical self-perception. Future research should address issues surrounding the design of studies and measurement of actual motor competence and perceived motor competence/physical self-perception as well as explore other potential confounding variables (i.e., product- versus process-oriented assessments, race, culture) that might affect the relationship between these two constructs.
TL;DR: Data demonstrate that Y/T‐TEAD activity controls gastric CSC tumorigenic properties, and suggest that the repositioning of verteporfin targeting YAP1/TAZ‐TEad activity could be a promising CSC‐based strategy for the treatment of GC.
Abstract: Gastric carcinomas (GC) are heterogeneous tumors, composed of a subpopulation of cluster of differentiation-44 (CD44)+ tumorigenic and chemoresistant cancer stem cells (CSC). YAP1 and TAZ oncoproteins (Y/T) interact with TEA domain family member 1 (TEAD) transcription factors to promote cell survival and proliferation in multiple tissues. Their activity and role in GC remain unclear. This work aimed to analyze Y/T-TEAD activity and molecular signature in gastric CSC, and to assess the effect of verteporfin, a Food and Drug Administration-approved drug preventing Y/T-TEAD interaction, on gastric CSC tumorigenic properties. Y/T-TEAD molecular signature was investigated using bioinformatical (KmPlot database), transcriptomic and immunostaining analyses in patient-derived GC and cell lines. Verteporfin effects on Y/T-TEAD transcriptional activity, CSC proliferation and tumorigenic properties were evaluated using in vitro tumorsphere assays and mouse models of patient-derived GC xenografts. High expressions of YAP1, TAZ, TEAD1, TEAD4 and their target genes were associated with low overall survival in nonmetastatic human GC patients (n = 444). This Y/T-TEAD molecular signature was enriched in CD44+ patient-derived GC cells and in cells resistant to conventional chemotherapy. Verteporfin treatment inhibited Y/T-TEAD transcriptional activity, cell proliferation and CD44 expression, and decreased the pool of tumorsphere-forming CD44+ /aldehyde dehydrogenase (ALDH)high gastric CSC. Finally, verteporfin treatment inhibited GC tumor growth in vivo; the residual tumor cells exhibited reduced expressions of CD44 and ALDH1, and more importantly, they were unable to initiate new tumorspheres in vitro. All these data demonstrate that Y/T-TEAD activity controls gastric CSC tumorigenic properties. The repositioning of verteporfin targeting YAP1/TAZ-TEAD activity could be a promising CSC-based strategy for the treatment of GC.
SLAC National Accelerator Laboratory1, Thomas Jefferson National Accelerator Facility2, Nanjing University3, George Washington University4, Heidelberg University5, Louisiana State University6, University of Glasgow7, The Catholic University of America8, University of Connecticut9, Inha University10, Old Dominion University11, Université Paris-Saclay12, University of Huelva13, Pablo de Olavide University14, Indiana University15, University of Costa Rica16
TL;DR: The 2019 Strong QCD from Hadron Structure Experiments Workshop as mentioned in this paper aimed to develop plans and facilitate the future synergistic efforts between experimentalists, phenomenologists, and theorists working on studies of hadron spectroscopy and structure with the goal to connect the properties of hadrons and atomic nuclei available from data to the strong QCD dynamics underlying their emergence from QCD.
Abstract: The topical workshop Strong QCD from Hadron Structure Experiments took place at Jefferson Lab from November 6–9, 2019. Impressive progress in relating hadron structure observables to the strong QCD mechanisms has been achieved from the ab initio QCD description of hadron structure in a diverse array of methods in order to expose emergent phenomena via quasi-particle formation. The wealth of experimental data and the advances in hadron structure theory make it possible to gain insight into strong interaction dynamics in the regime of large quark–gluon coupling (the strong QCD regime), which will address the most challenging problems of the Standard Model on the nature of the dominant part of hadron mass, quark–gluon confinement, and the emergence of the ground and excited state hadrons, as well as atomic nuclei, from QCD. This workshop aimed to develop plans and to facilitate the future synergistic efforts between experimentalists, phenomenologists, and theorists working on studies of hadron spectroscopy and structure with the goal to connect the properties of hadrons and atomic nuclei available from data to the strong QCD dynamics underlying their emergence from QCD. These results pave the way for a future breakthrough extension in the studies of QCD with an Electron–Ion Collider in the U.S.
TL;DR: This work aims to present a comprehensive review that exposes how biosensors work in terms of bacterial and viral detection, and the nanotechnological features that are contributing to achieving a faster yet still efficient COVID-19 diagnosis at the point-of-care.
Abstract: Biosensors are measurement devices that can sense several biomolecules, and are widely used for the detection of relevant clinical pathogens such as bacteria and viruses, showing outstanding results. Because of the latent existing risk of facing another pandemic like the one we are living through due to COVID-19, researchers are constantly looking forward to developing new technologies for diagnosis and treatment of infections caused by different bacteria and viruses. Regarding that, nanotechnology has improved biosensors' design and performance through the development of materials and nanoparticles that enhance their affinity, selectivity, and efficacy in detecting these pathogens, such as employing nanoparticles, graphene quantum dots, and electrospun nanofibers. Therefore, this work aims to present a comprehensive review that exposes how biosensors work in terms of bacterial and viral detection, and the nanotechnological features that are contributing to achieving a faster yet still efficient COVID-19 diagnosis at the point-of-care.
TL;DR: In this paper, the authors argue that a far better strategy revolves around the effect of climate change on functions/services that soils render, since climatologists forecast less frequent but more intense rainfall events in the future, which may lead to food shortages, catastrophic flooding and soil erosion if soils are not able to cope.
Abstract: Over the last two decades, the sequestration of carbon in soils has often been presented as a possible way to mitigate the steady increase in the concentration of CO2 in the atmosphere, one of the most commonly mentioned causes of climate change. A large body of literature, as well as sustained efforts to attract funding for the research on soil organic matter, have focused on the soil carbon sequestration – climate change nexus. However, because CO2 is not the only greenhouse gas released by soils, and given the fact that the feasibility of large-scale carbon sequestration remains controversial, this approach does not appear optimal to convince policy makers. In this perspective article, we argue that a far better strategy revolves around the effect of climate change on functions/services that soils render. In particular, since climatologists forecast less frequent but more intense rainfall events in the future, which may lead to food shortages, catastrophic flooding, and soil erosion if soils are not able to cope, a more suitable focus of the research would be to increase soil organic matter content so as to strengthen the water regulation function of soils. The different conceptual and methodological shifts that this new focus will require are discussed in detail.
Inter-American Development Bank1, University of Los Andes2, Del Rosario University3, University of Maryland, College Park4, United States Department of Energy5, University of Costa Rica6, Royal Institute of Technology7, Imperial College London8, Loughborough University9, University of the Pacific (Peru)10, University of Tennessee11, National Technical University12, Federal University of Rio de Janeiro13
TL;DR: The authors in this paper presented the objectives, approach and cross-cutting results of the Latin American Deep Decarbonization Pathways project (DDP-LAC), which synthesized and compared detailed national and sectoral deep decarbonization pathways to 2050 compatible with the Paris Agreement objectives and domestic development priorities in Argentina, Colombia, Costa Rica, Ecuador, Mexico and Peru.
TL;DR: In this paper, the hazard quotient (HQ) approach coupled with ecotoxicological determinations permitted to identify the hazard posed by specific pharmaceuticals and toxicity of the effluents, respectively.
TL;DR: Several compounds included in this study should be incorporated in future water monitoring programs to help in the development of future regulations, due to their potential risk to the aquatic environment.
TL;DR: Overall, results suggest that the two forms of Varespladib are effective in abrogating, or delaying, neurotoxic manifestations induced by some venoms whose neurotoxicity is mainly dependent on presynaptically acting PLA2s.
Abstract: The phospholipase A2 (PLA2) inhibitor Varespladib (LY315920) and its orally bioavailable prodrug, methyl-Varespladib (LY333013) inhibit PLA2 activity of a wide variety of snake venoms. In this study, the ability of these two forms of Varespladib to halt or delay lethality of potent neurotoxic snake venoms was tested in a mouse model. The venoms of Notechis scutatus, Crotalus durissus terrificus, Bungarus multicinctus, and Oxyuranus scutellatus, all of which have potent presynaptically acting neurotoxic PLA2s of variable quaternary structure, were used to evaluate simple dosing regimens. A supralethal dose of each venom was injected subcutaneously in mice, followed by the bolus intravenous (LY315920) or oral (LY333013) administration of the inhibitors, immediately and at various time intervals after envenoming. Control mice receiving venom alone died within 3 h of envenoming. Mice injected with O. scutellatus venom and treated with LY315920 or LY333013 survived the 24 h observation period, whereas those receiving C. d. terrificus and B. multicinctus venoms survived at 3 h or 6 h with a single dose of either form of Varespladib, but not at 24 h. In contrast, mice receiving N. scutatus venom and then the inhibitors died within 3 h, similarly to the control animals injected with venom alone. LY315920 was able to reverse the severe paralytic manifestations in mice injected with venoms of O. scutellatus, B. multicinctus, and C. d. terrificus. Overall, results suggest that the two forms of Varespladib are effective in abrogating, or delaying, neurotoxic manifestations induced by some venoms whose neurotoxicity is mainly dependent on presynaptically acting PLA2s. LY315920 is able to reverse paralytic manifestations in severely envenomed mice, but further work is needed to understand the significance of species-specific differences in animal models as they compare to clinical syndromes in human and for potential use in veterinary medicine.
University of Toulouse1, Silesian University of Technology2, European Institute of Oncology3, National Physical Laboratory4, Institut de radioprotection et de sûreté nucléaire5, University of Oxford6, University Hospital Heidelberg7, University of Wollongong8, French Institute of Health and Medical Research9, St George's Hospital10, University of Costa Rica11, University of Manchester12, University of Lyon13
TL;DR: The OpenDose collaboration produced SAFs for all source region and target combinations of the 2 International Commission on Radiological Protection Publication 110 adult reference models in good agreement at all energies, with SDs below individual statistical uncertainties.
Abstract: Radiopharmaceutical dosimetry depends on the localization in space and time of radioactive sources and requires the estimation of the amount of energy emitted by the sources deposited within targets. In particular, when computing resources are not accessible, this task can be performed using precomputed tables of specific absorbed fractions (SAFs) or S values based on dosimetric models. The aim of the OpenDose collaboration is to generate and make freely available a range of dosimetric data and tools. Methods: OpenDose brings together resources and expertise from 18 international teams to produce and compare traceable dosimetric data using 6 of the most popular Monte Carlo codes in radiation transport (EGSnrc/EGS++, FLUKA, GATE, Geant4, MCNP/MCNPX, and PENELOPE). SAFs are uploaded, together with their associated statistical uncertainties, in a relational database. S values are then calculated from monoenergetic SAFs on the basis of the radioisotope decay data presented in International Commission on Radiological Protection Publication 107. Results: The OpenDose collaboration produced SAFs for all source region and target combinations of the 2 International Commission on Radiological Protection Publication 110 adult reference models. SAFs computed from the different Monte Carlo codes were in good agreement at all energies, with SDs below individual statistical uncertainties. Calculated S values were in good agreement with OLINDA/EXM 2.0 (commercial) and IDAC-Dose 2.1 (free) software. A dedicated website (www.opendose.org) has been developed to provide easy and open access to all data. Conclusion: The OpenDose website allows the display and downloading of SAFs and the corresponding S values for 1,252 radionuclides. The OpenDose collaboration, open to new research teams, will extend data production to other dosimetric models and implement new free features, such as online dosimetric tools and patient-specific absorbed dose calculation software, together with educational resources.
TL;DR: Confinement had a negative effect on every behavior studied in this survey, except for nutrition, and negative mental state changes were strongly associated with nutrition, sleep, physical activity and alcohol consumption changes.
Abstract: Background: A global pandemic due to COVID-19 emerged in November 2019 and hit France in early March 2020. It not only resulted in a loss of lives, but also in very strict confinement measures. The objective of this study was to understand what the determinants of the changes in participants’ behavior and mental state were during the confinement. Methods: An online survey was launched on 23 April 2020 and closed on 7 May 2020. The final sample included 1454 participants from 24 to 65 years old. Descriptive and multivariate analyses were then performed. Results: In total, 28.7% reported having a more balanced diet, against 17.1% with a less balanced diet, 22.7% of respondents reported an increased alcohol consumption, as opposed to only 12.2% declaring a decrease, and 11.2% of respondents increased their tobacco consumption, while 6.3% decreased it. In total, 50.6% of the participants reported being more depressed, stressed, or irritable since the beginning of the lockdown. Confinement had a negative effect on every behavior studied in this survey, except for nutrition. We also found that negative mental state changes were strongly associated with nutrition, sleep, physical activity and alcohol consumption changes.
Liverpool School of Tropical Medicine1, University of Montana2, Scripps Institution of Oceanography3, University of Queensland4, Leiden University5, Cornell University6, Swansea University7, Bangor University8, Nottingham Trent University9, University of Costa Rica10, University of Bristol11, University of São Paulo12
TL;DR: It is shown that the three spitting lineages of spitting cobras possess venom characterized by an upregulation of PLA2 toxins, which potentiate the action of venom cytotoxins to activate mammalian sensory neurons and cause enhanced pain.
Abstract: Convergent evolution provides unparalleled insights into the selective drivers underlying evolutionary change. While snakes use venom primarily for predation, and venom composition often reflects diet specificity, three lineages of spitting cobras have independently evolved the ability to use venom as a defensive projectile. Using gene, protein and functional analyses, we show that the three spitting lineages possess venom characterized by an upregulation of PLA2 toxins, which potentiate the action of venom cytotoxins to activate mammalian sensory neurons and cause enhanced pain. These repeated independent changes provide a fascinating example of convergent evolution across multiple phenotypic levels driven by exaptations. Notably, the timing of their origins suggests that defensive venom spitting may have evolved in response to the emergence of bipedal hominids in Africa and Asia. One Sentence Summary Venom spitting by snakes coincides with the emergence of hominins and is underpinned by convergent increases in pain-enhancing toxins
International Institute for Applied Systems Analysis1, University of Costa Rica2, University of Antwerp3, National University of Costa Rica4, University of Natural Resources and Life Sciences, Vienna5, University of Vienna6, University of Salamanca7, Nanyang Technological University8, Cardiff University9, National Institute of Amazonian Research10, Technische Universität München11, University of Nottingham12
TL;DR: Investigation of how climatic and edaphic factors affect tropical forest diversity and vegetation carbon storage suggests that local heterogeneity in resource availability and plant functional composition should be considered to improve projections of tropical forest ecosystem functioning under future scenarios.
Abstract: Tropical rainforests harbor exceptionally high biodiversity and store large amounts of carbon in vegetation biomass. However, regional variation in plant species richness and vegetation carbon stock can be substantial, and may be related to the heterogeneity of topoedaphic properties. Therefore, aboveground vegetation carbon storage typically differs between geographic forest regions in association with the locally dominant plant functional group. A better understanding of the underlying factors controlling tropical forest diversity and vegetation carbon storage could be critical for predicting tropical carbon sink strength in response to projected climate change. Based on regionally replicated 1-ha forest inventory plots established in a region of high geomorphological heterogeneity we investigated how climatic and edaphic factors affect tropical forest diversity and vegetation carbon storage. Plant species richness (of all living stems >10 cm in diameter) ranged from 69 to 127 ha−1 and vegetation carbon storage ranged from 114 to 200 t ha−1. While plant species richness was controlled by climate and soil water availability, vegetation carbon storage was strongly related to wood density and soil phosphorus availability. Results suggest that local heterogeneity in resource availability and plant functional composition should be considered to improve projections of tropical forest ecosystem functioning under future scenarios.
TL;DR: H pylori infection engages a number of signaling cascades that alienate mucosa homeostasis, including the Hippo LATS2/YAP1/TEAD pathway, which appears as a protective pathway, limiting the loss of gastric epithelial cell identity that precedes gastric carcinoma development.
Abstract: Background & Aims Gastric carcinoma is related mostly to CagA+-Helicobacter pylori infection, which disrupts the gastric mucosa turnover and elicits an epithelial-mesenchymal transition (EMT) and preneoplastic transdifferentiation. The tumor suppressor Hippo pathway controls stem cell homeostasis; its core, constituted by the large tumor suppressor 2 (LATS2) kinase and its substrate Yes-associated protein 1 (YAP1), was investigated in this context. Methods Hippo, EMT, and intestinal metaplasia marker expression were investigated by transcriptomic and immunostaining analyses in human gastric AGS and MKN74 and nongastric immortalized RPE1 and HMLE epithelial cell lines challenged by H pylori, and on gastric tissues of infected patients and mice. LATS2 and YAP1 were silenced using small interfering RNAs. A transcriptional enhanced associated domain (TEAD) reporter assay was used. Cell proliferation and invasion were evaluated. Results LATS2 and YAP1 appear co-overexpressed in the infected mucosa, especially in gastritis and intestinal metaplasia. H pylori via CagA stimulates LATS2 and YAP1 in a coordinated biphasic pattern, characterized by an early transient YAP1 nuclear accumulation and stimulated YAP1/TEAD transcription, followed by nuclear LATS2 up-regulation leading to YAP1 phosphorylation and targeting for degradation. LATS2 and YAP1 reciprocally positively regulate each other’s expression. Loss-of-function experiments showed that LATS2 restricts H pylori–induced EMT marker expression, invasion, and intestinal metaplasia, supporting a role of LATS2 in maintaining the epithelial phenotype of gastric cells and constraining H pylori–induced preneoplastic changes. Conclusions H pylori infection engages a number of signaling cascades that alienate mucosa homeostasis, including the Hippo LATS2/YAP1/TEAD pathway. In the host–pathogen conflict, which generates an inflammatory environment and perturbations of the epithelial turnover and differentiation, Hippo signaling appears as a protective pathway, limiting the loss of gastric epithelial cell identity that precedes gastric carcinoma development.
TL;DR: In this paper, the suitability of trees impacted by floods and their growth-ring records to provide insights into past flood activity and to allow estimation of their magnitude was analyzed, based on the extreme floods triggered by the passage of tropical storm Nate on October 5, 2017 and investigate whether dendrogeomorphic approaches can be employed to date and quantify floods in the catchment of tropical Rio General (Costa Rica).
University of Salzburg1, University of Ulm2, Aix-Marseille University3, North Carolina State University4, University of Portsmouth5, University of Alaska Fairbanks6, Max Planck Society7, University of Savoy8, University of California, Irvine9, University of Costa Rica10, University of Arizona11, Santa Fe Institute12, Federal University of Rio Grande do Norte13, Spanish National Research Council14, University of Lausanne15, University of Oldenburg16, University of California, Los Angeles17, University of British Columbia18, Vrije Universiteit Brussel19, Estonian University of Life Sciences20, Universidade Federal do Rio Grande do Sul21, Uppsala University22, University of New Brunswick23, University of Granada24, University of Jena25, Leiden University26, University of São Paulo27, Duke University28, University of Marburg29
TL;DR: Intraspecific trait variation either increased or decreased with climate stress and species richness, suggesting that both factors can constrain or enhance ITV, which might foster plant populations’ persistence under stressful conditions.
Abstract: Aim
Intraspecific trait variation (ITV) can be large within natural plant communities, influencing local ecological processes and dynamics. Here, we shed light on how ITV in vegetative and floral traits responds to large-scale abiotic and biotic gradients (i.e. climate and species richness). Specifically, we tested if associations of ITV with temperature, precipitation and species richness reflect the predicted patterns of four hypotheses relating to stress-tolerance and competition. Furthermore, we estimate the degree of correlation between ITV in vegetative and floral traits and how it varies along the gradients.
Location
Global.
Time period
1975-2016.
Major taxa studied
Herbaceous and woody plants.
Methods
We compiled a dataset of 18,112 measurements of the absolute extent of ITV (measured as coefficient of variation) in nine vegetative and seven floral traits from 2,774 herbaceous and woody species at 2,306 locations.
Results
Large-scale associations between the absolute extent of ITV and climate were trait-specific and more prominent for vegetative traits, especially leaf morphology, than for floral traits. Climate showed pronounced associations with ITV, with lower ITV values in colder areas and higher values in drier areas. The associations of species richness with ITV were inconsistent across traits. Species-specific associations across gradients were often idiosyncratic and covariation in ITV was weaker between vegetative and floral traits than within the two trait groups.
Main conclusions
Our results show that, depending on the traits considered, ITV either increased or decreased with climate stress and species richness, suggesting that both factors can constrain or enhance ITV, which might foster plant populations’ persistence under stressful conditions. Given the species-specific responses and covariation in ITV, associations can be hard to predict for traits and species not yet studied. We conclude that considering ITV can improve our understanding of how plants cope with stressful conditions and environmental change across spatial and biological scales.
TL;DR: In this paper, the authors presented the experience of the University of Costa Rica Faculty of Dentistry and evaluated the students' conditions and needs in a form of a survey, in order to understand the extent of the impact and the work needed to contain, as far as the possibilities allowed, negative consequences on students learning process.
Abstract: While countries are facing different stages in their COVID-19 infection rates, worldwide there are millions of students affected by universities’ facilities closures due to the pandemic. Some institutions have enforced strategies to transfer some courses to a virtual modality, but many Dental Schools have been challenged to deal with a situation which requires emergency measures to continue the academic course in the middle of lock-downs and social distancing measures. Despite the fact that the number of online academic programs available, especially graduate programs, has increased in diverse modalities, this pandemic forced e-learning processes to develop abruptly. The likelihood of using e-learning strategies in dentistry was substantiated in the scientific literature and an overview of these opportunities is presented. Additionally, the experience of the University of Costa Rica Faculty of Dentistry is presented, as it was evident that some of the key elements in a e-learning environment needed a quick enhancement and initiation of some processes was required. First, it was necessary to categorize the academic courses depending on their virtualization's possibility (curricula analysis and classification), to better understand the extent of the impact and the work needed to contain, as far as the possibilities allowed, negative consequences on students learning process. Second, teachers needed further training in the application of virtual strategies which they hadn’t used before. do Third, an evaluation of the students’ conditions and needs was conducted in a form of a survey. Finally, teachers and students activated the available virtual platforms. For many Dental Schools, this virtualization process is an ongoing progress although it was abruptly imposed, but this moment indeed represents an enormous opportunity to move forward and get immerse in the virtualization environment as a teaching/learning experience.
TL;DR: The results highlight the urgent need for policies and programs to help smallholder farmers improve their overall food security and resilience to extreme weather shocks, and focus on enhancing farmer education levels, securing land tenure, empowering women, promoting generational knowledge exchange, and providing emergency food support in the lean season or following extreme weather events.
Abstract: To ensure food security among rural communities under a changing climate, policymakers need information on the prevalence and determinants of food insecurity, the role of extreme weather events in exacerbating food insecurity, and the strategies that farmers use to cope with food insecurity. Using household surveys in Guatemala and Honduras, we explore the prevalence of food insecurity among smallholder farmers on both a recurrent (seasonal) and episodic (resulting from extreme weather events) basis, analyze the factors associated with both types of food insecurity, and document farmer coping strategies. Of the 439 households surveyed, 56% experienced recurrent food insecurity, 36% experienced episodic food insecurity due to extreme weather events, and 24% experienced both types. Food insecurity among smallholder farmers was correlated with sociodemographic factors (e.g., age, education, migration) and asset ownership. The factors affecting food insecurity differed between type and prevalence of food insecurity. Our results highlight the urgent need for policies and programs to help smallholder farmers improve their overall food security and resilience to extreme weather shocks. Such policies should focus on enhancing farmer education levels, securing land tenure, empowering women, promoting generational knowledge exchange, and providing emergency food support in the lean season or following extreme weather events.