Predicting Microhabitat Suitability for an Endangered Small Mammal Using Sentinel-2 Data

Accurate mapping is a main challenge for endangered small-sized terrestrial species. Freely available spatio-temporal data at high resolution from multispectral satellite offer excellent opportunities for improving predictive distribution models of such species based on fine-scale habitat features, thus making it easier to achieve comprehensive biodiversity conservation goals. However, there are still few examples showing the utility of remote-sensing-based products in mapping microhabitat suitability for small species of conservation concern. Here, we address this issue using Sentinel-2 sensor-derived habitat variables, used in combination with more commonly used explanatory variables (e.g., topography), to predict the distribution of the endangered Cabrera vole (Microtus cabrerae) in agrosilvopastorial systems. Based on vole surveys conducted in two different seasons over a ~176,000 ha landscape in Southern Portugal, we assessed the significance of each predictor in explaining Cabrera vole occurrence using the Boruta algorithm, a novel Random forest variant for dealing with high dimensionality of explanatory variables. Overall, results showed a strong contribution of Sentinel-2-derived variables for predicting microhabitat suitability of Cabrera voles. In particular, we found that photosynthetic activity (NDI45), specific spectral signal (SWIR1), and landscape heterogeneity (Rao’s Q) were good proxies of Cabrera voles’ microhabitat, mostly during temporally greener and wetter conditions. In addition to remote-sensing-based variables, the presence of road verges was also an important driver of voles’ distribution, highlighting their potential role as refuges and/or corridors. Overall, our study supports the use of remote-sensing data to predict microhabitat suitability for endangered small-sized species in marginal areas that potentially hold most of the biodiversity found in human-dominated landscapes. We believe our approach can be widely applied to other species, for which detailed habitat mapping over large spatial extents is difficult to obtain using traditional descriptors. This would certainly contribute to improving conservation planning, thereby contributing to global conservation efforts in landscapes that are managed for multiple purposes

Flexible and structural coloured composite films from cellulose nanocrystals/hydroxypropyl cellulose lyotropic suspensions

FEDER funds through the COMPETE 2020 Program, National Funds through FCT -Portuguese Foundation for Science and Technology and POR Lisboa2020, PTDC/CTM-BIO/6178/2014, M-ERA-NET2/0007/2016 (CellColor) and PTDC/CTM-REF/30529/2017 (NanoCell2SEC).Lyotropic colloidal aqueous suspensions of cellulose nanocrystals (CNCs) can, after solvent evaporation, retain their chiral nematic arrangement. As water is removed the pitch value of the suspension decreases and structural colour-generating films, which are mechanically brittle in nature, can be obtained. Increasing their flexibility while keeping the chiral nematic structure and biocompatible nature is a challenging task. However, if achievable, this will promote their use in new and interesting applications. In this study, we report on the addition of different amounts of hydroxypropyl cellulose (HPC) to CNCs suspension within the coexistence of the isotropic-anisotropic phases and infer the influence of this cellulosic derivative on the properties of the obtained solid films. It was possible to add 50 wt.% of HPC to a CNCs aqueous suspension (to obtain a 50/50 solids ratio) without disrupting the LC phase of CNCs and maintaining a left-handed helical structure in the obtained films. When 30 wt.% of HPC was added to the suspension of CNCs, a strong colouration in the film was still observed. This colour shifts to the near-infrared region as the HPC content in the colloidal suspension increases to 40 wt.% or 50 wt.% The all-cellulosic composite films present an increase in the maximum strain as the concentration of HPC increases, as shown by the bending experiments and an improvement in their thermal properties.publishersversionpublishe

Comparing extraction method efficiency for high-throughput palaeoproteomic bone species identification

High-throughput proteomic analysis of archaeological skeletal remains provides information about past fauna community compositions and species dispersals in time and space. Archaeological skeletal remains are a finite resource, however, and therefore it becomes relevant to optimize methods of skeletal proteome extraction. Ancient proteins in bone specimens can be highly degraded and consequently, extraction methods for well-preserved or modern bone might be unsuitable for the processing of highly degraded skeletal proteomes. In this study, we compared six proteomic extraction methods on Late Pleistocene remains with variable levels of proteome preservation. We tested the accuracy of species identification, protein sequence coverage, deamidation, and the number of post-translational modifications per method. We find striking differences in obtained proteome complexity and sequence coverage, highlighting that simple acid-insoluble proteome extraction methods perform better in highly degraded contexts. For well-preserved specimens, the approach using EDTA demineralization and protease-mix proteolysis yielded a higher number of identified peptides. The protocols presented here allowed protein extraction from ancient bone with a minimum number of working steps and equipment and yielded protein extracts within three working days. We expect further development along this route to benefit large-scale screening applications of relevance to archaeological and human evolution research

A teoria dos conceitos nucleares e as suas aplicações em Ciências Sociais, Educação, Matemática e Engenharia

El presente artículo tiene como principal objetivo dar a conocer la Teoría de los Conceptos Nucleares y la técnica de Redes Asociativas Pathfinder. El enfoque metodológico se enmarca en los métodos mixtos, con sistemas de apoyo digitales (webQDA y GOLUCA) susceptibles de realizar análisis tanto cualitativos como cuantitativos. El artículo empieza por presentar la Teoría de los Conceptos Nucleares y su técnica asociada para posteriormente mostrar ejemplos de su aplicación dentro de distintos campos de estudio, nombradamente en las Ciencias Sociales a través del estudio sobre las trayectorias educativas en relación al abandono y retorno al sistema educativo, en las Matemáticas a través del estudio de unidades didácticas y recursos educativos digitales aplicados al tema de las operaciones aritméticas, trigonometría y probabilidad, en las Ingeniería Telemática e Ingeniería Informática a través del análisis del proceso de enseñanza de los alumnos de la asignatura de Base de Datos del Grado de Ingeniería Informática en Tecnologías de la Información (GIITI) del Centro Universitario de Mérida – Universidad de Extremadura.The main objective of this article is to disseminate the Theory of Nuclear Concepts and the Pathfinder Associative Networks technique. The methodological approach is based on mixed methods, with digital support systems (webQDA and GOLUCA) that allow qualitative and quantitative analysis. The article presenting the Theory of Nuclear Concepts and the associated technique to later and show examples of its application in different areas of study, namely in the Social Sciences through the study of educational trajectories in relation to abandonment and return to the educational system , in Mathematics through the study of didactic units and digital educational resources applied to the topic of arithmetic operations, trigonometry and probabilities, in Telematics Engineering and Computer Engineering, through the analysis of the teaching process of the students of the Database discipline of Degree in Engineering in Information Technology (GIITI) of the University Center of Mérida - University of Extremadura.O principal objetivo deste artigo é divulgar a Teoria dos Conceitos Nucleares e técnica e a técnica Pathfinder Associative Networks. A abordagem metodológica enquadra-se nos métodos mistos, com sistemas digitais deapoio (webQDA e GOLUCA) que permitem a realização de análises qualitativas e quantitativas. O artigo começa por apresentar a Teoria dos Conceitos Nucleares e a técnica associada para, posteriormente, mostrar exemplos da sua aplicação em diferentes áreas de estudo, nomeadamente nas Ciências Sociais através do estudo sobre as trajetórias educativas em relação ao abandono e ao retorno ao sistema educativo, em Matemática através do estudo de unidades didáticas e de recursos educativos digitais aplicados ao tema das operações aritméticas, da trigonometria e da probabilidades, em Engenharia Telemática e Engenharia Informática, através da análise do processo de ensino dos estudantes da disciplina de Bases de Dados da Licenciatura em Engenharia em Tecnologias da Informação (GIITI) do Centro Universitário de Mérida - Universidade de Extremadura.peerReviewe

Erratum to: A systematic review of the characteristics and validity of monitoring technologies to assess Parkinson’s disease

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated."Background: There is growing interest in having objective assessment of health-related outcomes using technology-based devices that provide unbiased measurements which can be used in clinical practice and scientific research. Many studies have investigated the clinical manifestations of Parkinson’s disease using such devices. However, clinimetric properties and clinical validation vary among the different devices. Methods: Given such heterogeneity, we sought to perform a systematic review in order to (i) list, (ii) compare and (iii) classify technological-based devices used to measure motor function in individuals with Parkinson's disease into three groups, namely wearable, non-wearable and hybrid devices. A systematic literature search of the PubMed database resulted in the inclusion of 168 studies. These studies were grouped based on the type of device used. For each device we reviewed availability, use, reliability, validity, and sensitivity to change. The devices were then classified as (i) ‘recommended’, (ii) ‘suggested’ or (iii) ‘listed’ based on the following criteria: (1) used in the assessment of Parkinson’s disease (yes/no), (2) used in published studies by people other than the developers (yes/no), and (3) successful clinimetric testing (yes/no). Results: Seventy-three devices were identified, 22 were wearable, 38 were non-wearable, and 13 were hybrid devices. In accordance with our classification method, 9 devices were ‘recommended’, 34 devices were ‘suggested’, and 30 devices were classified as ‘listed’. Within the wearable devices group, the Mobility Lab sensors from Ambulatory Parkinson’s Disease Monitoring (APDM), Physilog®, StepWatch 3, TriTrac RT3 Triaxial accelerometer, McRoberts DynaPort, and Axivity (AX3) were classified as ‘recommended’. Within the non-wearable devices group, the Nintendo Wii Balance Board and GAITRite® gait analysis system were classified as ‘recommended’. Within the hybrid devices group only the Kinesia® system was classified as ‘recommended’."The present research is part of the EU project SENSE-PARK, funded under the Seventh Framework Programme, Cooperation – ICT, Grant Agreement no. 288557

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

Global age-sex-specific fertility, mortality, healthy life expectancy (HALE), and population estimates in 204 countries and territories, 1950-2019 : a comprehensive demographic analysis for the Global Burden of Disease Study 2019

Background: Accurate and up-to-date assessment of demographic metrics is crucial for understanding a wide range of social, economic, and public health issues that affect populations worldwide. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 produced updated and comprehensive demographic assessments of the key indicators of fertility, mortality, migration, and population for 204 countries and territories and selected subnational locations from 1950 to 2019. Methods: 8078 country-years of vital registration and sample registration data, 938 surveys, 349 censuses, and 238 other sources were identified and used to estimate age-specific fertility. Spatiotemporal Gaussian process regression (ST-GPR) was used to generate age-specific fertility rates for 5-year age groups between ages 15 and 49 years. With extensions to age groups 10–14 and 50–54 years, the total fertility rate (TFR) was then aggregated using the estimated age-specific fertility between ages 10 and 54 years. 7417 sources were used for under-5 mortality estimation and 7355 for adult mortality. ST-GPR was used to synthesise data sources after correction for known biases. Adult mortality was measured as the probability of death between ages 15 and 60 years based on vital registration, sample registration, and sibling histories, and was also estimated using ST-GPR. HIV-free life tables were then estimated using estimates of under-5 and adult mortality rates using a relational model life table system created for GBD, which closely tracks observed age-specific mortality rates from complete vital registration when available. Independent estimates of HIV-specific mortality generated by an epidemiological analysis of HIV prevalence surveys and antenatal clinic serosurveillance and other sources were incorporated into the estimates in countries with large epidemics. Annual and single-year age estimates of net migration and population for each country and territory were generated using a Bayesian hierarchical cohort component model that analysed estimated age-specific fertility and mortality rates along with 1250 censuses and 747 population registry years. We classified location-years into seven categories on the basis of the natural rate of increase in population (calculated by subtracting the crude death rate from the crude birth rate) and the net migration rate. We computed healthy life expectancy (HALE) using years lived with disability (YLDs) per capita, life tables, and standard demographic methods. Uncertainty was propagated throughout the demographic estimation process, including fertility, mortality, and population, with 1000 draw-level estimates produced for each metric. Findings: The global TFR decreased from 2·72 (95% uncertainty interval [UI] 2·66–2·79) in 2000 to 2·31 (2·17–2·46) in 2019. Global annual livebirths increased from 134·5 million (131·5–137·8) in 2000 to a peak of 139·6 million (133·0–146·9) in 2016. Global livebirths then declined to 135·3 million (127·2–144·1) in 2019. Of the 204 countries and territories included in this study, in 2019, 102 had a TFR lower than 2·1, which is considered a good approximation of replacement-level fertility. All countries in sub-Saharan Africa had TFRs above replacement level in 2019 and accounted for 27·1% (95% UI 26·4–27·8) of global livebirths. Global life expectancy at birth increased from 67·2 years (95% UI 66·8–67·6) in 2000 to 73·5 years (72·8–74·3) in 2019. The total number of deaths increased from 50·7 million (49·5–51·9) in 2000 to 56·5 million (53·7–59·2) in 2019. Under-5 deaths declined from 9·6 million (9·1–10·3) in 2000 to 5·0 million (4·3–6·0) in 2019. Global population increased by 25·7%, from 6·2 billion (6·0–6·3) in 2000 to 7·7 billion (7·5–8·0) in 2019. In 2019, 34 countries had negative natural rates of increase; in 17 of these, the population declined because immigration was not sufficient to counteract the negative rate of decline. Globally, HALE increased from 58·6 years (56·1–60·8) in 2000 to 63·5 years (60·8–66·1) in 2019. HALE increased in 202 of 204 countries and territories between 2000 and 2019