Long-term Ecological Research: Chasing fashions or being prepared for fashion changes?

Long-term-ecological-research (LTER) faces many challenges, including the difficulty of obtaining long-term funding, changes in research questions and sampling designs, keeping researchers collecting standardized data for many years, impediments to interactions with local people, and the difficulty of integrating the needs of local decision makers with "big science". These issues result in a lack of universally accepted guidelines as to how research should be done and integrated among LTER sites. Here we discuss how the RAPELD (standardized field infrastructure system), can help deal with these issues as a complementary technique in LTER studies, allowing comparisons across landscapes and ecosystems and reducing sampling costs. RAPELD uses local surveys to understand broad spatial and temporal patterns while enhancing decision-making and training of researchers, local indigenous groups and traditional communities. Sampling of ecological data can be carried out by different researchers through standardized protocols, resulting in spatial data that can be used to answer temporal questions, and allow new questions to be investigated. Results can also be integrated into existing biodiversity networks. Integrated systems are the most efficient way to save resources, maximize results, and accumulate information that can be used in the face of the unknown unknowns upon which our future depends.

Analysis and implementation of the DynDiff tool when comparing versions of ontology.

BACKGROUND: Ontologies play a key role in the management of medical knowledge because they have the properties to support a wide range of knowledge-intensive tasks. The dynamic nature of knowledge requires frequent changes to the ontologies to keep them up-to-date. The challenge is to understand and manage these changes and their impact on depending systems well in order to handle the growing volume of data annotated with ontologies and the limited documentation describing the changes. METHODS: We present a method to detect and characterize the changes occurring between different versions of an ontology together with an ontology of changes entitled DynDiffOnto, designed according to Semantic Web best practices and FAIR principles. We further describe the implementation of the method and the evaluation of the tool with different ontologies from the biomedical domain (i.e. ICD9-CM, MeSH, NCIt, SNOMEDCT, GO, IOBC and CIDO), showing its performance in terms of time execution and capacity to classify ontological changes, compared with other state-of-the-art approaches. RESULTS: The experiments show a top-level performance of DynDiff for large ontologies and a good performance for smaller ones, with respect to execution time and capability to identify complex changes. In this paper, we further highlight the impact of ontology matchers on the diff computation and the possibility to parameterize the matcher in DynDiff, enabling the possibility of benefits from state-of-the-art matchers. CONCLUSION: DynDiff is an efficient tool to compute differences between ontology versions and classify these differences according to DynDiffOnto concepts. This work also contributes to a better understanding of ontological changes through DynDiffOnto, which was designed to express the semantics of the changes between versions of an ontology and can be used to document the evolution of an ontology.

P2Y12 inhibitor monotherapy versus dual antiplatelet therapy in patients with acute coronary syndromes undergoing coronary stenting: rationale and design of the NEOMINDSET Trial.

Dual antiplatelet therapy (DAPT) is currently the standard of care after percutaneous coronary intervention (PCI). Recent studies suggest that reducing DAPT to 1-3 months followed by an aspirin-free single antiplatelet therapy (SAPT) strategy with a potent P2Y12 inhibitor is safe and associated with less bleeding. However, to date, no randomised trial has tested the impact of initiating SAPT immediately after PCI, particularly in patients with acute coronary syndromes (ACS). NEOMINDSET is a multicentre, randomised, open-label trial with a blinded outcome assessment designed to compare SAPT versus DAPT in 3,400 ACS patients undergoing PCI with the latest-generation drug-eluting stents (DES). After successful PCI and up to 4 days following hospital admission, patients are randomised to receive SAPT with a potent P2Y12 inhibitor (ticagrelor or prasugrel) or DAPT (aspirin plus a potent P2Y12 inhibitor) for 12 months. Aspirin is discontinued immediately after randomisation in the SAPT group. The choice between ticagrelor and prasugrel is at the investigator's discretion. The primary hypothesis is that SAPT will be non-inferior to DAPT with respect to the composite endpoint of all-cause mortality, stroke, myocardial infarction or urgent target vessel revascularisation, but superior to DAPT on rates of bleeding defined by Bleeding Academic Research Consortium 2, 3 or 5 criteria. NEOMINDSET is the first study that is specifically designed to test SAPT versus DAPT immediately following PCI with DES in ACS patients. This trial will provide important insights on the efficacy and safety of withdrawing aspirin in the early phase of ACS. (ClinicalTrials.gov: NCT04360720).

Computer Aided Design Modelling and Finite Element Analysis of Premolar Proximal Cavities Restored with Resin Composites.

This study evaluated the stress distribution in five different class II cavities of premolar models restored with conventional or bulk-fill flowable composite by means of finite element analysis (FEA) under shrinkage and occlusal loading. An upper validated premolar model was imported in the software, and five class II cavities with different occlusal extensions and dimensions were prepared: horizontal cavity on the mesial surface (horizontal slot), mesio-occlusal cavity, mesial cavity (vertical slot), tunnel type cavity and direct access cavity. The models were restored with conventional or bulk-fill flowable resin composite. The tested materials were considered as homogeneous, linear, and isotropic. The Maximum Principal Stress criteria was chosen to evaluate the tensile stress results. The lowest shrinkage stress value was observed in the direct access cavity restored with bulk-fill flowable resin composite (36.12 MPa). The same cavity, restored with conventional composite showed a score of 36.14 MPa. The horizontal slot cavity with bulk-fill flowable showed a score of 46.71 MPa. The mesio-occlusal cavity with bulk-fill flowable had a score of 53.10 MPa, while with conventional composite this was 55.35 MPa. Higher shrinkage stress was found in the vertical slot cavity with conventional resin 56.14 MPa, followed by the same cavity with bulk-fill flowable 56.08 MPa. Results indicated that the use of bulk-fill flowable composite resin more significantly decreased the polymerization shrinkage stress magnitude. The larger the cavity and the volume of material necessary to restore the tooth, the greater the residual stress on enamel and dentin tissue.

The Program for Biodiversity Research in Brazil: The role of regional networks for biodiversity knowledge, dissemination, and conservation.

The Program for Biodiversity Research (PPBio) is an innovative program designed to integrate all biodiversity research stakeholders. Operating since 2004, it has installed long-term ecological research sites throughout Brazil and its logic has been applied in some other southern-hemisphere countries. The program supports all aspects of research necessary to understand biodiversity and the processes that affect it. There are presently 161 sampling sites (see some of them at Supplementary Appendix), most of which use a standardized methodology that allows comparisons across biomes and through time. To date, there are about 1200 publications associated with PPBio that cover topics ranging from natural history to genetics and species distributions. Most of the field data and metadata are available through PPBio web sites or DataONE. Metadata is available for researchers that intend to explore the different faces of Brazilian biodiversity spatio-temporal variation, as well as for managers intending to improve conservation strategies. The Program also fostered, directly and indirectly, local technical capacity building, and supported the training of hundreds of undergraduate and graduate students. The main challenge is maintaining the long-term funding necessary to understand biodiversity patterns and processes under pressure from global environmental changes.

Non-structural carbohydrates mediate seasonal water stress across Amazon forests.

Non-structural carbohydrates (NSC) are major substrates for plant metabolism and have been implicated in mediating drought-induced tree mortality. Despite their significance, NSC dynamics in tropical forests remain little studied. We present leaf and branch NSC data for 82 Amazon canopy tree species in six sites spanning a broad precipitation gradient. During the wet season, total NSC (NSCT) concentrations in both organs were remarkably similar across communities. However, NSCT and its soluble sugar (SS) and starch components varied much more across sites during the dry season. Notably, the proportion of leaf NSCT in the form of SS (SS:NSCT) increased greatly in the dry season in almost all species in the driest sites, implying an important role of SS in mediating water stress in these sites. This adjustment of leaf NSC balance was not observed in tree species less-adapted to water deficit, even under exceptionally dry conditions. Thus, leaf carbon metabolism may help to explain floristic sorting across water availability gradients in Amazonia and enable better prediction of forest responses to future climate change.

Influence of the dental implant number and load direction on stress distribution in a 3-unit implant-supported fixed dental prosthesis.

BACKGROUND: The choice between 2 or 3 implants to support a 3-unit implant-supported fixed dental prosthesis (FDP) still generates doubt in clinical practice. OBJECTIVES: The aim of this study was to evaluate stress distribution in 3-unit implant-supported FDPs according to the implant number and load direction. MATERIAL AND METHODS: A numerical simulation was performed to analyze stress and strain according to the implant number (2 or 3) and load direction (axial or oblique). A model of a jaw was created by means of the modeling software Rhinoceros, v. 5.0 SR8. External hexagon implants, micro-conical abutments and screws were also modeled. The final geometries were exported to the computer-aided engineering (CAE) software Ansys, v. 17.2, and all materials were considered homogeneous, isotropic and elastic. Different load directions were applied for each model (300 N) at the center of the prosthesis. RESULTS: The von Mises stress and strain values were obtained for the titanium structures and the bone, respectively. The implant number influenced the prosthesis biomechanics, with higher stress and strain concentrations when 2 implants were simulated. The oblique load also affected the mechanical response, showing higher stress and strain in comparison with the axial load, regardless of the implant number. CONCLUSIONS: It was concluded that for a 3-unit implant-supported FDP, a greater number of implants associated with axial loads can result in a better mechanical response during chewing.

Influence of Polymeric Restorative Materials on the Stress Distribution in Posterior Fixed Partial Dentures: 3D Finite Element Analysis.

BACKGROUND: This study evaluated the effect of interim restorative materials (acrylic resin (AR), resin composite (RC) or polyetheretherketone (PEEK) for dental computer-aided design/computer-aided manufacturing (CAD/CAM)) on the stress distribution of a posterior three-unit fixed partial denture. METHODS: The abutment teeth (first molar and first premolar) were modeled using the BioCAD protocol containing 1.5 mm of axial reduction and converging axial walls. A static structural analysis was performed in the computer-aided engineering software, and the Maximum Principal Stress criterion was used to analyze the prosthesis and the cement layers of both abutment teeth. The materials were considered isotropic, linearly elastic, homogeneous and with bonded contacts. An axial load (600 N) was applied to the occlusal surface of the second premolar. RESULTS: Regardless of the restorative material, the region of the prosthetic connectors showed the highest tensile stress magnitude. The highest stress peak was observed with the use of RC (129 MPa) compared to PEEK and AR. For the cement layers, RC showed the lowest values in the occlusal region (7 MPa) and the highest values for the cervical margin (14 MPa) compared to PEEK (21 and 12 MPa) and AR (21 and 13 MPa). CONCLUSIONS: Different interim restorative materials for posterior fixed partial dentures present different biomechanical behavior. The use of resin composite can attenuate the stress magnitude on the cement layer, and the use of acrylic resin can attenuate the stress magnitude on the connector region.

Tree mode of death and mortality risk factors across Amazon forests.

The carbon sink capacity of tropical forests is substantially affected by tree mortality. However, the main drivers of tropical tree death remain largely unknown. Here we present a pan-Amazonian assessment of how and why trees die, analysing over 120,000 trees representing > 3800 species from 189 long-term RAINFOR forest plots. While tree mortality rates vary greatly Amazon-wide, on average trees are as likely to die standing as they are broken or uprooted-modes of death with different ecological consequences. Species-level growth rate is the single most important predictor of tree death in Amazonia, with faster-growing species being at higher risk. Within species, however, the slowest-growing trees are at greatest risk while the effect of tree size varies across the basin. In the driest Amazonian region species-level bioclimatic distributional patterns also predict the risk of death, suggesting that these forests are experiencing climatic conditions beyond their adaptative limits. These results provide not only a holistic pan-Amazonian picture of tree death but large-scale evidence for the overarching importance of the growth-survival trade-off in driving tropical tree mortality.

Reference values of office central blood pressure, pulse wave velocity, and augmentation index recorded by means of the Mobil-O-Graph PWA monitor.

Assessment of central blood pressure (BP), pulse wave velocity (PWV), and augmentation index (AIx) measurements may improve cardiovascular risk stratification. This study aimed to establish reference office values for central BP, PWV, and AIx by means of a Mobil-O-Graph PWA monitor and to evaluate the impact of cardiovascular risk factors (CVRFs) on these measurements. We cross-sectionally evaluated clinical characteristics, central BP, PWV, AIx, and peripheral BP measurements among 867 apparently healthy individuals (age = 46.0 ± 15.5 years, 39% males) who were free of obesity, hypertension, active smoking, dyslipidemia, and diabetes (CVRF-No) and 5632 individuals (age = 57.0 ± 14.7 years, 44% males) with at least one of these major CVRFs (CVRF-Yes). Reference values for central BP, PWV, and AIx were provided for the CVRF-No and CVRF-Yes groups, stratified by age and sex. PWV and AIx exhibited curvilinear increases with age, and there was an interaction between age and sex for central systolic BP and PWV in both the CVRF-No and CVRF-Yes groups. The results of a multivariable analysis including the whole sample (n = 6499) showed that obesity had a direct association with central BP, while diabetes was directly related to PWV. In addition, alcohol intake was directly associated with central BP, while performance of physical activity was inversely related to AIx. In conclusion, values of office-measured central BP, PWV, and AIx obtained in an apparently healthy population and in a population with CVRFs are now available according to age and sex and may be useful to build thresholds for use in clinical practice.

Competition influences tree growth, but not mortality, across environmental gradients in Amazonia and tropical Africa.

Competition among trees is an important driver of community structure and dynamics in tropical forests. Neighboring trees may impact an individual tree's growth rate and probability of mortality, but large-scale geographic and environmental variation in these competitive effects has yet to be evaluated across the tropical forest biome. We quantified effects of competition on tree-level basal area growth and mortality for trees ≥10-cm diameter across 151 ~1-ha plots in mature tropical forests in Amazonia and tropical Africa by developing nonlinear models that accounted for wood density, tree size, and neighborhood crowding. Using these models, we assessed how water availability (i.e., climatic water deficit) and soil fertility influenced the predicted plot-level strength of competition (i.e., the extent to which growth is reduced, or mortality is increased, by competition across all individual trees). On both continents, tree basal area growth decreased with wood density and increased with tree size. Growth decreased with neighborhood crowding, which suggests that competition is important. Tree mortality decreased with wood density and generally increased with tree size, but was apparently unaffected by neighborhood crowding. Across plots, variation in the plot-level strength of competition was most strongly related to plot basal area (i.e., the sum of the basal area of all trees in a plot), with greater reductions in growth occurring in forests with high basal area, but in Amazonia, the strength of competition also varied with plot-level wood density. In Amazonia, the strength of competition increased with water availability because of the greater basal area of wetter forests, but was only weakly related to soil fertility. In Africa, competition was weakly related to soil fertility and invariant across the shorter water availability gradient. Overall, our results suggest that competition influences the structure and dynamics of tropical forests primarily through effects on individual tree growth rather than mortality and that the strength of competition largely depends on environment-mediated variation in basal area.

Study of the pterygoid canal (vidian canal) through images of cone beam computer tomography / Estudo do canal Pterigóideo (canal Vidiano) por meio de imagens de tomografia computadorizada de feixe cônico

Objective: The aim of this study was to evaluate the pterygoid canal (PC) by Cone Beam Computed Tomography (CBCT), establishing its configuration and proximity with anatomical structures. Material and Methods: We evaluated 398 CBCT exams, all from a public University radiology clinic archive. Four parameters were evaluated: single or double PC, distance between PC and the inferior part of the sphenoid sinus (SS), ratio of PC and SS and the distance between the PC and the foramen rotundum. Results: It was observed that most of the PC of the sample presented simple morphology, the most frequent type of relationship between the PC and the SS on both sides was the close contact with the wall. Among the cases that there were some distances between the PC and the inferior wall of the SS, the mean of this distance did not exceed 3.20 mm, being the left side (3.03 mm) slightly closer than the right (3.20 mm). Finally, the distances between the PC and the corresponding Foramen Rotundum are presented with mean values of 5.87 mm for the right side and 6.31 mm for the left side. Conclusion: CBCT examination is of paramount importance for PC identification; once in the studied sample, the mean values found evidence the close relation between the PC and the SS (AU)

Objetivo: O objetivo deste estudo foi avaliar o CP pela TCFC, estabelecendo sua configuração e proximidade com estruturas anatômicas. Material e Métodos: Foram avaliados 398 exames de TCFC, todos de um arquivo público da clínica de radiologia da Universidade. Foram avaliados quatro parâmetros: CP único ou duplo, distância entre PC e parte inferior do seio esfenoidal (SS), razão entre PC e SS e a distância entre o PC e o forame redondo. Resultados: Observou-se que a maioria dos CP da amostra apresentava morfologia simples, o tipo de relação mais frequente entre o CP e o SS de ambos os lados foi o contato próximo com a parede. Entre os casos em que houve algumas distâncias entre o CP e a parede inferior da ES, a média dessa distância não excedeu 3,20 mm, sendo o lado esquerdo (3,03 mm) um pouco mais próximo do que o direito (3,20 mm). Finalmente, as distâncias entre o PC e o forame redondo correspondente são apresentadas com valores médios de 5,87 mm para o lado direito e 6,31 mm para o lado esquerdo. Conclusão: O exame TCFC é de suma importância para a identificação do CP; uma vez na amostra estudada, os valores médios encontrados evidenciam a estreita relação entre o CP e o SS. (AU)

Compositional response of Amazon forests to climate change.

Most of the planet's diversity is concentrated in the tropics, which includes many regions undergoing rapid climate change. Yet, while climate-induced biodiversity changes are widely documented elsewhere, few studies have addressed this issue for lowland tropical ecosystems. Here we investigate whether the floristic and functional composition of intact lowland Amazonian forests have been changing by evaluating records from 106 long-term inventory plots spanning 30 years. We analyse three traits that have been hypothesized to respond to different environmental drivers (increase in moisture stress and atmospheric CO2 concentrations): maximum tree size, biogeographic water-deficit affiliation and wood density. Tree communities have become increasingly dominated by large-statured taxa, but to date there has been no detectable change in mean wood density or water deficit affiliation at the community level, despite most forest plots having experienced an intensification of the dry season. However, among newly recruited trees, dry-affiliated genera have become more abundant, while the mortality of wet-affiliated genera has increased in those plots where the dry season has intensified most. Thus, a slow shift to a more dry-affiliated Amazonia is underway, with changes in compositional dynamics (recruits and mortality) consistent with climate-change drivers, but yet to significantly impact whole-community composition. The Amazon observational record suggests that the increase in atmospheric CO2 is driving a shift within tree communities to large-statured species and that climate changes to date will impact forest composition, but long generation times of tropical trees mean that biodiversity change is lagging behind climate change.

Inhibitory killer cell immunoglobulin-like receptors strengthen CD8+ T cell-mediated control of HIV-1, HCV, and HTLV-1.

Killer cell immunoglobulin-like receptors (KIRs) are expressed predominantly on natural killer cells, where they play a key role in the regulation of innate immune responses. Recent studies show that inhibitory KIRs can also affect adaptive T cell-mediated immunity. In mice and in human T cells in vitro, inhibitory KIR ligation enhanced CD8+ T cell survival. To investigate the clinical relevance of these observations, we conducted an extensive immunogenetic analysis of multiple independent cohorts of HIV-1-, hepatitis C virus (HCV)-, and human T cell leukemia virus type 1 (HTLV-1)-infected individuals in conjunction with in vitro assays of T cell survival, analysis of ex vivo KIR expression, and mathematical modeling of host-virus dynamics. Our data suggest that functional engagement of inhibitory KIRs enhances the CD8+ T cell response against HIV-1, HCV, and HTLV-1 and is a significant determinant of clinical outcome in all three viral infections.

Supporting biomedical ontology evolution by identifying outdated concepts and the required type of change.

The consistent evolution of ontologies is a major challenge for systems using semantically enriched data, for example, for annotating, indexing, or reasoning. The biomedical domain is a typical example where ontologies, expressed with different formalisms, have been used for a long time and whose dynamic nature requires the regular revision of underlying systems. However, the automatic identification of outdated concepts and proposition of revision actions to update them are still open research questions. Solutions to these problems are of great interest to organizations that manage huge and dynamic ontologies. In this paper, we present an approach for (i) identifying the concepts of an ontology that require revision and (ii) suggesting the type of revision. Our analysis is based on three aspects: structural information encoded in the ontology, relational information gained from external source of knowledge (i.e., PubMed and UMLS) and temporal information derived from the history of the ontology. Our approach aims to evaluate different methods and parameters used by supervised learning classifiers to identify both the set of concepts that need revision, and the type of revision. We applied our approach to four well-known biomedical ontologies/terminologies (ICD-9-CM, MeSH, NCIt and SNOMED CT) and compared our results to similar approaches. Our model shows accuracy ranging from 68% (for SNOMED CT) to 91% (for MeSH), and an average of 71% when considering all datasets together.

Determining the Mode, Frequency, and Azimuthal Wave Number of ULF Waves During a HSS and Moderate Geomagnetic Storm.

Ultralow frequency (ULF) waves play a fundamental role in the dynamics of the inner magnetosphere and outer radiation belt during geomagnetic storms. Broadband ULF wave power can transport energetic electrons via radial diffusion, and discrete ULF wave power can energize electrons through a resonant interaction. Using observations from the Magnetospheric Multiscale mission, we characterize the evolution of ULF waves during a high-speed solar wind stream (HSS) and moderate geomagnetic storm while there is an enhancement of the outer radiation belt. The Automated Flare Inference of Oscillations code is used to distinguish discrete ULF wave power from broadband wave power during the HSS. During periods of discrete wave power and utilizing the close separation of the Magnetospheric Multiscale spacecraft, we estimate the toroidal mode ULF azimuthal wave number throughout the geomagnetic storm. We concentrate on the toroidal mode as the HSS compresses the dayside magnetosphere resulting in an asymmetric magnetic field topology where toroidal mode waves can interact with energetic electrons. Analysis of the mode structure and wave numbers demonstrates that the generation of the observed ULF waves is a combination of externally driven waves, via the Kelvin-Helmholtz instability, and internally driven waves, via unstable ion distributions. Further analysis of the periods and toroidal azimuthal wave numbers suggests that these waves can couple with the core electron radiation belt population via the drift resonance during the storm. The azimuthal wave number and structure of ULF wave power (broadband or discrete) have important implications for the inner magnetospheric and radiation belt dynamics.

Analyzing interactions on combining multiple clinical guidelines.

Accounting for patients with multiple health conditions is a complex task that requires analysing potential interactions among recommendations meant to address each condition. Although some approaches have been proposed to address this issue, important features still require more investigation, such as (re)usability and scalability. To this end, this paper presents an approach that relies on reusable rules for detecting interactions among recommendations coming from various guidelines. It extends a previously proposed knowledge representation model (TMR) to enhance the detection of interactions and it provides a systematic analysis of relevant interactions in the context of multimorbidity. The approach is evaluated in a case study on rehabilitation of breast cancer patients, developed in collaboration with experts. The results are considered promising to support the experts in this task.

Combining rules, background knowledge and change patterns to maintain semantic annotations.

Knowledge Organization Systems (KOS) play a key role in enriching biomedical information in order to make it machine-understandable and shareable. This is done by annotating medical documents, or more specifically, associating concept labels from KOS with pieces of digital information, e.g., images or texts. However, the dynamic nature of KOS may impact the annotations, thus creating a mismatch between the evolved concept and the associated information. To solve this problem, methods to maintain the quality of the annotations are required. In this paper, we define a framework based on rules, background knowledge and change patterns to drive the annotation adaption process. We evaluate experimentally the proposed approach in realistic cases-studies and demonstrate the overall performance of our approach in different KOS considering the precision, recall, F1-score and AUC value of the system.