Stacked Denoising Autoencoders and Transfer Learning for Immunogold Particles Detection and Recognition

In this paper we present a system for the detection of immunogold particles and a Transfer Learning (TL) framework for the recognition of these immunogold particles. Immunogold particles are part of a high-magnification method for the selective localization of biological molecules at the subcellular level only visible through Electron Microscopy. The number of immunogold particles in the cell walls allows the assessment of the differences in their compositions providing a tool to analise the quality of different plants. For its quantization one requires a laborious manual labeling (or annotation) of images containing hundreds of particles. The system that is proposed in this paper can leverage significantly the burden of this manual task. For particle detection we use a LoG filter coupled with a SDA. In order to improve the recognition, we also study the applicability of TL settings for immunogold recognition. TL reuses the learning model of a source problem on other datasets (target problems) containing particles of different sizes. The proposed system was developed to solve a particular problem on maize cells, namely to determine the composition of cell wall ingrowths in endosperm transfer cells. This novel dataset as well as the code for reproducing our experiments is made publicly available. We determined that the LoG detector alone attained more than 84\% of accuracy with the F-measure. Developing immunogold recognition with TL also provided superior performance when compared with the baseline models augmenting the accuracy rates by 10\%

Gains and losses in ecosystem services and disservices after converting native forest to agricultural land on an oceanic island

Habitat conversion to agricultural land is one of the main threats to terrestrial biodiversity and can affect ecosystem processes and cause changes in ecosystem services (ESs) and disservices (EDs). Yet, studies often rely only on the abundance and diversity of the service providers; the effects on ecological processes of habitat conversion are rarely directly monitored. In this study, we used the sentinel approach to evaluate how habitat conversion from native forest to agricultural land affected ESs and EDs on an oceanic island. We quantified herbivory on lettuce plants, invertebrate and vertebrate predation rates on artificial caterpillars, pollination on strawberry plants, seed predation on wheat and mustard seeds, and leaf decomposition rates in native forests, maize fields and pastures on Terceira Island, Azores (Portugal). Herbivory, invertebrate predation rates, and pollination service were not significantly different between habitats. Vertebrate predation rates in native forests (mean 6.1% d⁻¹) were significantly higher than that in pastures (0.3% d⁻¹), or high-elevation maize fields (0.5% d⁻¹), and marginally higher than in low-elevation maize fields (2.2% d⁻¹). Overall seed predation after 48 h was significantly higher on wheat (mean 16.8%) than mustard seeds (5.6%). High-elevation maize fields also had higher seed predation (27.8%) than low-elevation ones (0.6%) or pastures (3.6%), but did not differ from the native forest (12.9%). Decomposition after 90 days was highest in pastures (78.4% and 45.9%, for tea and rooibos, respectively); although no significant differences between habitats were detected, except for low-elevation maize fields (64.4% and 33.6%). Conversion from native forest to cultivated land did not cause a clear decrease in the intensity of the studied ESs/EDs except for vertebrate predation. Using direct monitoring tools to simultaneously and consistently quantify multiple ecological processes is not only possible but needed, as ecological processes can respond differently to landscape changes.This work was financed by FEDER (European Regional Development Fund) in 85% and by Azorean public funds by 15% through Operational Program Azores 2020, under the project AGRO-ECOSERVICES (ACORES01-0145-FEDER-000073).info:eu-repo/semantics/publishedVersio

Flowering Coriander (Coriandrum sativum) Strips Do Not Enhance Ecosystem Services in Azorean Orchards

ABSTRACT: Ecosystem services (ESs) and disservices (EDs) are routinely estimated from changes in service provider densities without measuring their actual levels. By using the sentinel approach (i.e., exposing a plant, seeds, and prey models in a standardized way), we tested how coriander (Coriandrum sativum) strips planted in mixed orchards on Terceira Island (Azores, Portugal) affected ESs/EDs via herbivory on lettuce plants, seed predation on wheat and weed seeds, and predation on artificial caterpillars. Vertebrates had more influence than invertebrates on ESs and EDs. Herbivory (ED) after 2 weeks was similar in the coriander and the control plots, while seed predation was higher in the control than in the coriander plots on both wheat grain (an ED: 30.8% vs. 15.3%) and weed seeds (an ES: 2.5% vs. 0.4%). Vertebrate predation (ES) rates after 48 h were significantly higher in the control (9%) than in the coriander plots (3%), while no difference was observed for invertebrate predation. Coriander strips did not support increased ES/reduced ED levels in this habitat. The sentinel approach is effective to quantitatively compare multiple ESs/EDs under different farming management strategies.info:eu-repo/semantics/publishedVersio

A simultaneous assessment of multiple ecosystem services and disservices in vineyards and orchards on Terceira Island, Azores

Monitoring ecosystem processes resulting in ecosystem services (ESs) and disservices (EDs) is crucial in agricultural ecosystems. Traditionally, ESs/EDs provided by arthropods have been estimated indirectly by measuring arthropod abundance and diversity, overlooking the recognised limitations of such approach. Using a consistent methodology based on the sentinel approach, we quantified the intensity of five ecological processes leading to four ESs and two EDs in vineyards and citrus orchards on Terceira Island, Azores. We assessed herbivory rates on lettuce plants (ED), predation rates on green plasticine caterpillars by vertebrates and invertebrates (ES), the intensity of insect pollination on strawberry plants (ES), the rates of predation on wheat and dandelion seeds (ED and ES, respectively) by rodents and invertebrates, and decomposition rates using tea and rooibos leaves (ES). Herbivory rates after 2 weeks were significantly lower in vineyards (mean ± SD; 0.5 ± 0.6%) than in citrus orchards (3.6 ± 2.9%). Vertebrate predation rates in vineyards (4.0 ± 13.6% d⁻¹) were significantly higher than in citrus orchards (2.4 ± 10.7% d⁻¹), while no differences were observed for overall and invertebrate predation rates. Pollination efficiency in vineyards (214.5 ± 23.9 seeds/fruit) was significantly higher than in citrus orchards (162.0 ± 14.7 seeds/fruit). Seed predation rates were higher, although not significantly so, in citrus orchards (2.0 ± 5.8% d⁻¹) than in vineyards (0.3 ± 0.8% d⁻¹). Decomposition was significantly higher on tea than on rooibos leaves, both in vineyards (1.15 ± 0.11 g vs. 0.72 ± 0.16 g) and citrus orchards (1.34 ± 0.06 g vs. 0.78 ± 0.13 g); no differences between mass loss in the two habitats were observed. Our results demonstrated the suitability of simple, direct monitoring tools for a quantitative comparison of agricultural habitats, confirm that landscape complexity does not always support ESs, and that the same agro-ecosystem characteristics that support ESs could occasionally also favour EDs.This work was financed by FEDER (European Regional Development Fund) in 85% and by Azorean Public Funds by 15% through Operational Program Azores 2020, under the project AGRO-ECOSERVICES (ACORES-01-0145-FEDER-000073).info:eu-repo/semantics/publishedVersio

Monitoring Arthropods in Azorean Agroecosystems : the project AGRO-ECOSERVICES

We provided an inventory of all arthropods recorded in four Azorean agroecosystems (citrus orchards, low and high elevation maize fields and vineyards) from Terceira Island. A total of 50412 specimens were collected, belonging to four classes, 20 orders, 81 families and 200 identified species of arthropods. A total of 127 species are considered introduced (n = 22646) and 69 native non-endemic (n = 24117). Four endemic species were recorded with very few specimens (n = 14) and 3635 specimens belong to unidentified taxa recorded only at genus or family level. Five species are new records for Terceira Island, with Lagria hirta (Linnaeus, 1758) (Coleoptera, Tenebrionidae) being also a new record for the Azores. This publication contributes to a better knowledge of the arthropods communities present in agro-ecosystems of Terceira Island and will serve as a baseline for future monitoring schemes targeting the long-term change in arthropod diversity and abundance.This work was financed by FEDER (European Regional Development Fund) in 85% and by Azorean Public funds by 15% through the Operational Program Azores 2020, under the project AGRO-ECOSERVICES (ACORES-01-0145-FEDER-000073). The Darwin-Core database was prepared within the scope of the project AZORESBIOPORTAL -PORBIOTA (ACORES-01-0145-FEDER-000072).info:eu-repo/semantics/publishedVersio

Guia Prático da Fauna de Artrópodes Predadores dos Ecossistemas Agrícolas dos Açores

A agricultura intensiva é uma das actividades que mais influencia a estrutura da paisagem, levando frequentemente à destruição e à perda de biodiversidade local. Por exemplo, a intensidade e gestão das actividades agrícolas pode influenciar dramaticamente a composição e abundância das comunidades de artrópodes que habitam nos agroecosistemas. Alguns artrópodes fitófagos podem causar danos aos pomares ao consumirem parte da planta ou fruto. No entanto, muitos outros podem fornecer serviços benéficos, como a polinização, o controlo de pragas e a decomposição. Os carochos, formigas e aranhas são predadores generalistas importantes para ajudar a controlar pragas de insectos, e, inclusive, reduzir a quantidade de ervas daninhas ao consumir as suas sementes. Quer os ecólogos quer os agrónomos acreditam que a simplicidade dos modernos campos agrícolas, especialmente os extensos campos em monoculturas que recebem frequentes aplicações de pesticidas, contribuem para os surtos de pragas, bastante típicos desses tipos de sistema. Os agroecossistemas mais simples podem ser ambientes relativamente hostis para os inimigos naturais, conduzindo à depauperação das comunidades de predadores e parasitóides. Os ecossistemas agrícolas mais diversificados, por outro lado, tendem a recrutar espécies ruderais, as quais, em geral, são mais resistentes à perturbação destes ambientes agrícolas. O declínio da biodiversidade dos inimigos naturais geralmente enfraquece o controlo biológico. Uma das razões por trás disso é que as comunidades mais ricas podem reunir espécies de inimigos naturais que atacam pragas usando diferentes estratégias ou nichos espaciais e temporais, de modo que a mortalidade total infligida sobre as pragas é maximizada apenas quando várias espécies inimigas ocorrem simultaneamente. O desafio que se coloca aos ecólogos e agrónomos é entender de que forma a biodiversidade dos inimigos naturais pode fortalecer o controlo biológico. Este livro contribui para a identificação e proteção dos artrópodes predadores, que são muito úteis para a agricultura e por isso benéficos para toda a sociedade. [da Nota Introdutória]FINANCIAMENTO: Este livro é um produto do projecto AGRO-ECOSERVICES (ACORES-01-0145-FEDER-000073), financiado pelo FEDER em 85% e por fundos regionais em 15%, através do Programa Operacional Açores 2020.info:eu-repo/semantics/publishedVersio

A UTILIZAÇAO DE CHORUME DE SUINOS EM MILHO PARA FORRAGEM

Apresentam-se resultados relativos a um ensaio efectuado com milho para forragem, com o objectivo de estudar o impacto no desenvolvimento da cultura de chorume de suinicultura em que as doses aplicadas foram equivalentes a quantidade de N veiculada a forragem através da adubacáo de cobertura. Verificou-se sempre um decréscimo da produgao em relagáo a modalidade em que nao se aplicou chorume, quer sob o ponto de vista quantitativo quer qualitativo da forragem, decréscimo este que se fiz sentir mais intensamente quanto menor foi o numero de vezes que se aplicou o referido efluente

Breeding for stress tolerance in fodder crops and amenity grasses. Proceedings of the 23rd Meeting of the Fodder Crops and Amenity Grasses Section of EUCARPIA, Azores, Portugal, October 1-4, 2000

Proceedings of 256 page

Terra Nostra Garden 2023 dataset of Camellia species, hybrids and their cultivars (Azores, Portugal)

Camellias cultivars collections, comprising an exquisite array of meticulously bred and curated camellia varieties, emerged as indispensable elements within the resplendent 19th century gardens that adorned landscapes across the globe. The heart of Terra Nostra Garden, nestled within the captivating surroundings of the Furnas volcano on S. Miguel Island (Azores, Portugal), started in the year 1782 as an enchanting fishpond garden, strategically positioned in front of the summer house belonging to the esteemed Thomas Hickling, the American vice-consul. Soon this garden was enlarged and embellished with species from several continents. This tradition continued during all the 19th century with the Viscount Duarte Borges da Câmara Medeiros (1848-1872) and his son the Marquis António Borges Medeiros Dias da Câmara e Sousa (1872-1913). In 1933, the 12 hectares property was acquired by the Terra Nostra Society, led by Vasco Bensaude and increased to 12.5 hectares. In 1935, the current Terra Nostra Garden Hotel was inaugurated and, two years later, the Terra Nostra Society reopened the botanical garden attached to the hotel, now called Terra Nostra Garden. Beginning in 1982, the Head Gardener embarked on a transformative journey, dedicating his expertise to the meticulous renovation and expansion of numerous botanical collections nestled within the garden's enchanting landscapes. Amongst the remarkable transformations, the revered camellias collection received special attention, as it underwent a comprehensive rejuvenation process under his skilful guidance. The recent publication of a global digital dataset of Camellia names provides the opportunity to publish the dataset of Camellia species, hybrids and its cultivars currently cultivated at Terra Nostra Garden with their validated names.In June 2023, a total of 669 Camellia phenotypes were identified across the 12.5 hectares of Terra Nostra Garden. These phenotypes include 38 species, 178 hybrids and 637 cultivars. Camellia japonica represents 81.7% of the 459 species cultivars, while C. x williamsii accounts for 32% of 178 hybrid cultivars. The most prevalent genotypes in Camellia hybrids with known parentage are those of C. japonica, C. saluenensis and C. reticulata present respectively in 64.1%, 45.5% and 37.9% of the hybrids. Regarding cultivar registration, 46.9% were registered in the US, followed by 13% from Japan and 10.8% from Portugal. Although the most ancient cultivar registered growing at the garden is Camellia reticulata Lindl. 'Damanao' from 1621, the majority (69.4%) of cultivars in the garden were registered in the 20th century, followed by the 19th century cultivars (20.7%). One cultivar, Camellia 'Patrícia Bensaude Fernandes', was produced and registered specifically by this garden

Relatório final do projeto AGRO-ECOSERVICES – Assessing ecosystem services and disservices provided by arthropod species in Azorean agroecosystems (ACORES-01-0145-FEDER-000073)

ABSTRACT: The Agro-Ecoservices project has allowed to expand our knowledge of the arthropod diversity and ecosystem services and disservices in agricultural habitats of oceanic islands and to develop and test standardised techniques for monitoring several ecological processes.info:eu-repo/semantics/publishedVersio