Saving trees for saving bats: tree-like features as key foraging habitats for insectivorous bats in intensively farmed agricultural lands

The loss of natural vegetation remnants and homogenization of agricultural landscapes have detrimental effects on bat occurrence. As bats are efficient pest controllers, it is important to understand the mechanisms underlying their persistence in agricultural landscapes. By comparing structural features of increasing complexity (open fields, single trees, tree lines and woodlands), we investigated the patterns of bat species richness, flight and feeding activities; and the potential effect of prey availability on these patterns. Open fields were significantly less bat rich and had lower levels of flight and feeding activities than treed features, which were differently used by distinct bat guilds. These differences were not driven by prey availability, which was similar across structural feature complexity. We conclude that the occurrence of different structural elements within agricultural landscapes provide a variety of commuting and feeding habitats for bat species with different requirements, reinforcing the importance of landscape heterogeneity to bat occurrence and species richness in agricultural landscapes; PRESERVAR ÁRVORES PARA CONSERVAR MORCEGOS: ESTRUTURAS COM ÁRVORES COMO HABITATS DE ALIMENTAÇÃO CHAVE PARA MORCEGOS INSECTÍVOROS EM ÁREAS DE AGRICULTURA INTENSIVA. RESUMO: A perda de vegetação natural e a homogeneização das paisagens agrícolas tem efeitos negativos na ocorrência de morcegos. Devido ao importante serviço de controlo de pragas providenciado pelos morcegos, importa perceber os mecanismos subjacentes à sua persistência nestas paisagens. Neste estudo investigámos os padrões de riqueza específica e de actividade de voo e alimentação de morcegos em estruturas de complexidade crescente (campos abertos, árvores isoladas, linhas de árvores e bosques); assim como o potencial efeito da disponibilidade de alimento sobre esses mesmos padrões. Os campos abertos apresentaram menor riqueza específica e actividades de voo e alimentação em comparação com as restantes estruturas, que foram distintamente usadas por diferentes grupos funcionais. A ocorrência de morcegos não foi influenciada por diferenças de disponibilidade de alimento entre estruturas. Os resultados da nossa investigação sugerem que estruturas com distintos graus de complexidade providenciam uma variedade de habitats que facilitam a deslocação e oferecem oportunidades de alimentação para espécies com diferentes requisitos, corroborando a importância da heterogeneidade da paisagem para a ocorrência e riqueza de espécies de morcegos em paisagens agrícolas

Identificação automatizada de morcegos através de modelos estatísticos

Desenvolvimentos recentes nas metodologias de monitorização de morcegos utilizadas em Portugal, especialmente a introdção de estações de gravação automáticas, conduziram a um problema de análise devido à quantidade de dados obtida. Face a este problema propomos desenvolver um método automatizado de análise e classificação de pulsos de ecolocalização de morcegos, através do desenvolvimento de um programa de computador baseado em modelos estatísticos e utilizando uma base de dados de pulsos de morcegos gravados em Portugal. Neste artigo apresentamos os resultados obtidos para a análise e classificação das espécies P. pipistrellus, P. pygmaeus e M. schreibersii. Para a análise estatística usámos modelos de regressão logística multinomial e conjuntos de redes neuronais artificiais, tendo sido obtidas taxas globais de classificações corretas superiores a 94%

The Technology and Innovation Unit of the National Institute of Health: A sequencing and bioinformatics core facility specializing in public health genomics

The National Institute of Health (INSA) has a long tradition in investigating the molecular etiology of genetic and complex diseases. These activities greatly benefit from centralized sequencing services provided by the Technology and Innovation Unit (UTI). Its mission is to perform sequencing and genotyping assays in the framework of research, diagnosis and epidemiological surveillance, as well as to implement data analysis pipelines for the study of human gene variants. The equipment portfolio includes a NextSeq 550, a MiSeq, two 3500 AB Genetic Analyzers, a Fragment Analyzer and a 7500 Real-time PCR system. UTI provides results for average of 36.000 sequencing/fragment samples per year. The team has already performed >300 small genome, amplicon, gene panel (including clinical exome), 16S rRNA gene and RNA/microRNA next-generation sequencing assays for INSA and for several Universities in the scope of scientific collaborations. Technical procedures are conducted under a quality control system that includes external quality assessment for next-generation sequencing/Sanger sequencing and ISO 15189 accreditation for Sanger sequencing. UTI plays a key role in public health genomics, providing state-of-the-art equipment, centralized resources, technical expertise and short response times.This work was supported by Centre for Toxicogenomics and Human Health - UID/BIM/00009/2019 - and GenomePT project – POCI-01-0145-FEDER-022184info:eu-repo/semantics/publishedVersio

A gripe em Portugal: análise preliminar da atividade gripal 2014/2015

Agradecimentos: À Rede Portuguesa de Laboratórios para o Diagnóstico da Gripe, aos Médicos-Sentinela, aos Serviços de Urgência e de Obstetrícia e aos participantes no estudo EuroEVA. À Inês Batista pelo apoio logístico prestado à Rede Médicos-Sentinela. À Doutora Cristina Furtado pela revisão científica do artigo.Objetivo: Pretende-se com a presente publicação, divulgar a análise preliminar da atividade gripal em Portugal na época de 2014/2015 (entre 15 de setembro de 2014 e 20 de março de 2015)

Influenza in Portugal, 2014/2015 season

During 2014/2015 season the influenza activity was high, the epidemic period was observed between week 1/2015 and 8/2015 with a maximum of 148 ILI cases per 105 inhabitants in week 4/2015. The influenza B virus, A(H3) and A(H1)pdm09 co-circulated during the season, although influenza B were dominant throughout the winter, except for weeks 4, 6 and 7/2015 where it was detected in co-dominance with influenza A virus, situation that contrasts with European influenza picture. The antigenic and genetic analysis of circulating influenza A(H3) and B virus showed differences regarding 2014/2015 influenza vaccine strains. 70% of A(H3) viruses belonged to subgroup 3C.2a, antigenically different from vaccine strain. A (H3) positive were recorded in higher percentage in children (0 to 4 years: 40.0% and 5 to 14 years: 39.7%) and in adults over 65 years (36, 8%). A(H1)pdm09 virus were sporadically detected and were similar to the vaccine A/California/7/2009 strain. In general, the detected influenza viruses were similar to those recommended strains for next winter`s vaccine 2015/2016

Accreditation under the International Standard ISO 15189: Experience of a Genetics Laboratory in DNA Sequencing

Introduction: Health care is to some extent influenced by the results of laboratory tests. In order to provide the best care for the patient, laboratories must seek to achieve high levels of quality and competence. International Standard ISO 15189 specifies these requirements and may be used by laboratories to perform accredited genetic tests of materials derived from the human body. Here we describe the procedures to establish Accreditation of DNA sequencing in our laboratory and the first Accreditation of its kind in Portugal. Methods: Our laboratory started to prepare to comply with ISO 15189 Accreditation requirements for DNA sequencing in 2010. Documents describing administrative and technical procedures of the sequencing workflow including sample registries, laboratory protocols, operation and maintenance of equipments, as well as preparation and use of reagents were produced. Regular examination of laboratory equipments by an external entity was implemented to confirm compliance with working requirements. Requisites for personnel training and demonstration of competence were also implemented. The laboratory participated regularly in the DNA sequencing scheme organized by the European Molecular Genetics Quality Network (EMQN). Results: The laboratory obtained formal recognition by Instituto Português de Acreditação (IPAC) in May 2014. A maximum genotyping score for DNA sequencing has been obtained in the external quality assessment scheme since 2010. Sequencing quality measured in terms of the quality read overlap metrics is currently of approximately 96% according to the EMQN scheme. The laboratory processes and analyzes an average of 28.750 samples per year. Discussion: Accreditation of a genetic test under ISO 15189 is a highly demanding and laborious task for a genetic laboratory. However, it is an important step in order to guarantee the highest quality and reproducibility of genetic test results

Caraterização virológica dos vírus da gripe que circularam em Portugal na época 2014/2015

Introdução e objetivo: A monitorização contínua das propriedades antigénicas e genéticas dos vírus da gripe é essencial, quer para a seleção anual das estirpes virais a incluir na vacina, quer para identificar novas linhas de orientação da terapêutica antiviral. O presente estudo descreve as caraterísticas antigénicas e genéticas dos vírus da gripe identificados em Portugal no inverno de 2014/2015

soundClass: An automatic sound classification tool for biodiversity monitoring using machine learning

Passive acoustic monitoring, a non-invasive technique, is increasingly used to study animal populations and habitats at much larger spatial and temporal scales than standard methods. However, easy to apply tools for reliable detection and classification of signals of interest among hundreds or even thousands of hours of recording are still lacking. We introduce the r package soundClass, a tool to train convolutional neural networks, and employ them to classify sound events in recordings. soundClass provides a sound event classification pipeline, from annotating recordings to automating trained networks usage in real-life situations. We illustrate the package functionality on bat echolocation calls, bird songs and whale echolocation clicks, showing that the package can be used to train networks for several types of sound events, taxonomic groups and environments; and exemplify its application. This tool facilitates the creation and usage of trained networks and was developed with a strong focus on graphical user interfaces to be used by non-specialist scientists in statistics and programming

How values and perceptions shape farmers' biodiversity management: insights from ten European countries

Farmers play a pivotal role in addressing biodiversity loss whilst maintaining food production. To rethink conservation in agricultural landscapes, it is crucial to understand their decisions regarding biodiversity and its management on the farms. In this study, we conducted 48 semi-structured interviews across ten European countries in 2021/22 to explore how farmers’ perceptions and valuations relate to their biodiversity management. Employing reflexive thematic analysis, we identified recurring patterns of shared meanings. Our findings underscore the profound influence of farmers’ biodiversity perceptions on their biodiversity management practices: 1) Narrow and targeted interventions were closely tied to instrumental values of biodiversity, whereas holistic management strategies were linked with recognising an inherent value of nature. 2) Targeted approaches were related to farmers’ interpretations of biodiversity as specific taxa and functions, relying on easily assessable and emotionally connoted indicators. 3) Holistic approaches aligned with a broader biodiversity concept and an emphasis on intricate functional relationships within ecosystems. 4) Actual decisions to implement measures were significantly constrained by perceived dependencies, namely production pathways, social dependencies, and landscape conditions. These findings raise a critical question about the prioritisation of ecocentric intrinsic versus anthropocentric instrumental values in conservation strategies. We propose an approach of ethical pluralism, acknowledging that instrumental values may provide practical solutions for certain challenges, while intrinsic values hold ethical significance, particularly in the context of complex or large-scale biodiversity conservation initiatives. Engaging in dialogue that accounts for diverse values will be essential for shaping effective and socially meaningful biodiversity conservation

Using a perception matrix to elicit farmers‘ perceptions towards stakeholders in the context of biodiversity-friendly farming

Farmers' pro-environmental action is substantially influenced by various stakeholders from their business and social environment. Recent studies recommend actively involving influential stakeholders in agri-environmental initiatives, information or media campaigns. While it has been argued that farmers' perceptions towards these stakeholders can help inform effective involvement, comprehensive assessments of these perceptions remain scarce, particularly in the context of biodiversity-friendly farming. To understand and compare farmers’ perceptions of these stakeholder quantitatively, we developed and applied a perception matrix. In an exploratory survey with 49 farmers across ten European countries, farmers rated twelve groups of stakeholders (e.g. government bodies, farm advisors and input suppliers) against eight perception constructs (e.g. trustworthiness, interest in protecting biodiversity). We found that perceptions differed significantly both between groups of stakeholders and between constructs. Whereas several stakeholders were, on average, perceived positively regarding their general characteristics, such as trustworthiness, reliability, understanding and support for farming, perceptions regarding their biodiversity-related behavior were significantly more negative. Our findings indicate potential to improve policy development and implementation of agri-environmental initiatives through the involvement of multiple, non-governmental, agricultural and non-agricultural stakeholders in biodiversity-friendly farming initiatives across the entire agri-food value chain. Such multi-stakeholder initiatives could help to not only reinforce biodiversity conservation action among the farming community, but across society as a whole as emphasized by the Convention on Biological Diversity. Further research is needed to confirm the observed trends on a larger, representative sample, for which the presented perception matrix is well suited