numerical classification
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2022 ◽  
Author(s):  
Wanxin Li ◽  
Lila Kari ◽  
Yaoliang Yu ◽  
Laura A Hug

We propose MT-MAG, a novel machine learning-based taxonomic assignment tool for hierarchically-structured local classification of metagenome-assembled genomes (MAGs). MT-MAG is capable of classifying large and diverse real metagenomic datasets, having analyzed for this study a total of 240 Gbp of data in the training set, and 7 Gbp of data in the test set. MT-MAG is, to the best of our knowledge, the first machine learning method for taxonomic assignment of metagenomic data that offers a "partial classification" option. MT-MAG outputs complete or a partial classification paths, and interpretable numerical classification confidences of its classifications, at all taxonomic ranks. MT-MAG is able to completely classify 48% more sequences than DeepMicrobes to the Species level (the only comparable taxonomic rank for DeepMicrobes), and it outperforms DeepMicrobes by an average of 33% in weighted accuracy, and by 89% in constrained accuracy.


2022 ◽  
Vol 81 (1) ◽  
Author(s):  
Kiril Vassilev ◽  
Momchil Nazarov ◽  
Constantin Mardari ◽  
Borislav Grigorov ◽  
Stoyan Georgiev ◽  
...  

Class Polygono-Poetea annuae Rivas-Mart. 1975 includes therophyte-rich vegetation on trampled habitats. The study presents the first analysis of the syntaxonomy of this class and its ecology in Bulgaria. One hundred seventy-five relevés from this class were collected and stored in the Balkan Vegetation Database during 2017–2020. Numerical classification (hierarchical divisive) and ordination were performed by JUICE and CANOCO software packages. Diagnostic species were determined by calculating the Phi-coefficient. Four associations, Sclerochloo durae-Polygonetum arenastri, Polygonetum arenastri, Lolio-Polygonetum arenastri and Poëtum annuae, were recognized. Their floristic composition has been shaped mainly by climatic and soil conditions. Sclerochloo durae-Polygonetum arenastri association has been found at lower altitudes, occurring in fully lighted habitats with high radiation, whereas Poëtum annuae has been found at higher altitudes in wetter and cooler areas. On the other hand, stands of Polygonetum arenastri have been found on nutrient-rich soils, whereas communities of Lolio-Polygonetum arenastri were distributed in warmer and nutrient-poor areas. The Polygono-Poetea annuae class is still poorly studied in Bulgaria and much more information from all regions of the country needs to be collected and analyzed.


2021 ◽  
Vol 42 ◽  
pp. e68062
Author(s):  
Pauline Delbosc ◽  
Mathieu Le Dez ◽  
Jean-Bernard Bouzillé ◽  
Kevin Cianfaglione ◽  
Frédéric Bioret

Carici-Genistetea lobelii Klein 1972 corresponds to cyrno-sardinian oromediterranean cushion scrub and related grasslands. In France, this class is only present in Corsica and the syntaxonomic scheme is debated among phytosociologists. The aim of this paper is to highlight the main plant associations of Carici-Genistetea lobelii Klein 1972 and to define the diagnostic species for each phytosociological unit. We compiled 519 vegetation plots and we applied EuropeanVegetationChecklist expert system for the classes of European vegetation to retain only vegetation plots belonging to Carici-Genistetea lobelii. We obtained a dataset with 189 vegetation plots and we classified them with Modified TWINSPAN classification. Our analyses recognized 6 plant associations and 3 sub-associations already described in the literature; and to describe a new alliance corresponding to the supra-mediterranean vegetations (Genistion salzmannii), a new association (Brimeuro fastigiatae-Juniperetum nanae) and its sub-association (alnetosum suaveolentis). For each of them, we identified diagnostic, constant and dominant species and produced their distribution map. Formal definitions were then written for each phytosociological unit (from subassociation to class) and grouped in an expert system to automatically classify the vegetations of Carici-Genistetea lobelii.


Hacquetia ◽  
2021 ◽  
Vol 20 (1) ◽  
pp. 197-216
Author(s):  
Henadii M. Lysenko ◽  
Ivan M. Danylyk ◽  
Svitlana M. Iemelianova ◽  
Liubov M. Borsukevych ◽  
Svitlana V. Sosnovska

Abstract The aim of our study is to establish the determinant ecological factors that have the greatest differential impact on the distribution of meadow steppe plant communities of Western Podolia (Ukraine) on the base of a synphytoindication analysis. There were 8 study sites within the study area in the L’viv and Ivano-Frankivsk regions. To determine the coenotic affinity of the studied species, 48 relevés were analyzed. Numerical classification based on the Modified TWINSPAN algorithm divided the dataset into five clusters, which have been identified as the associations Pastinaco sativae-Arrhenatheretum elatioris, Geranio sanguinei-Trifolietum alpestris, Inuletum ensifoliae, Jurineo calcareae-Stipetum capillatae and Lembotropio nigricans-Potentilletum arenariae. The results of gradient analyses indicate that the distribution of meadow steppe communities in the Podolia Upland closely correlates with a number of climatic (thermoregime and continentality of climate) and especially edaphic (soil humidity, soil acidity and carbonate content) ecological factors.


2021 ◽  
Vol 157 ◽  
pp. 16161-16171
Author(s):  
AGANI Zénabou ◽  
BOKO K. Cyrille ◽  
AKOUEDEGNI C. Guénole ◽  
SIDI IMOROU Habirou ◽  
BELLO Orou Daouda ◽  
...  

Objectif : Au Bénin, la production de lait des vaches locales ne permet pas de couvrir les besoins nutritionnels de la population. Pour l’améliorer, les agroéleveurs font recours à des recettes galactogènes. Cette étude évalue leur efficacité sur la production laitière des vaches de race Borgou. Méthodologie et Résultats : Au Bénin, une enquête réalisée auprès de 534 éleveurs a permis de recenser 286 recettes galactogènes utilisées par les agroéleveurs. Sur la base d’une classification numérique des recettes citées par au moins 20 % des enquêtés, dix (10) recettes ont été retenues pour des enquêtes approfondies. Bobgunnia madagascariensis, Euphorbia balsamifera, Curcubita maxima sont fréquemment impliquées dans les préparations galactogènes. Les racines et les graines sont les organes les plus utilisés. Les graines de Vigna unguiculata ou d’Arachis Hypogea sont toujours associées aux préparations. La production laitière est plus élevée après administration aux vaches et peut atteindre 2,5 litres par jour. Conclusion et application des résultats : L’étude confirme l’efficacité des préparations galactogènes utilisées par les agroéleveurs pour améliorer la production laitière des vaches locales. Il est intéressant de constater que les espèces végétales (Bobgunnia madagascariensis, Curcubita maxima, Euphorbia basalmifera) fréquemment utilisées sont présentes dans la flore béninoise. Les graines de Vigna unguiculata ou d’Arachis Hypogea sont toujours associées aux préparations galactogènes. Les racines et les graines sont les organes les plus utilisés. Quelle que soit la recette utilisée, la production du lait est plus élevée après administration des préparations aux vaches (P < 0,05) et peut toutefois atteindre 2,5 litres contre 1,5 par jour relevée en élevage semi-intensif pour les races locales. Le gain laitier suite à l’administration des recettes s’étale entre 0,6 et 1,1 litre par jour. Il ne reste maintenant qu’à identifier pour les recettes la forme galénique la mieux adaptée aux conditions socio-économiques de ces éleveurs traditionnels. Mots-clés : Bobgunnia madagascariensis, Euphorbia balsamifera, Curcubita maxima, recette galactogènes, vaches Borgou, Bénin. Agani et al., J. Appl. Biosci. 2021 Préparations galactogènes utilisées par les agroéleveurs au Bénin : espèces végétales, proportions d’organes impliqués et production laitière chez les vaches Borgou 16162 Galactogenic formulations used by agro-pastoralists in Benin: plant species, proportions of organs involved, and milk production in Borgou cows. ABSTRACT Objective: In Benin, the milk production of local cows does not cover the nutritional needs of the population. To improve it, agro-pastoralists use galactogenic formulations. This study evaluates their effectiveness on the milk production of Borgou cows. Methodology and Results: In Benin, a survey of 534 breeders identified 286 galactogenic formulations used by agro-breeders. Based on a numerical classification of the formulations cited by at least 20% of respondents, ten (10) formulations were retained for in-depth investigations. Bobgunnia madagascariensis, Euphorbia balsamifera, Curcubita maxima were frequently involved in these galactogenic preparations. The roots and seeds are the most used organs. The seeds of Vigna unguiculata or Arachis Hypogea were also always associated with preparations. Milk production was higher after administration to cows and could reach 2.5 litres per day. Conclusion and application of the results: The study confirms the effectiveness of galactogenic feed formulations used by agro-breeders to improve milk production in local cows. It is interesting to note that the plant species (Bobgunnia madagascariensis, Curcubita maxima, Euphorbia basalmifera) frequently used are present in the Beninese flora. The seeds of Vigna unguiculata or Arachis Hypogea are always associated with galactogenic preparations. The roots and seeds are the most used organs. Whatever the recipe used, the milk production is higher after administration of the formulas to the cows (P <0.05) and can however reach 2.5 litres against 1.5 per day observed in semi-intensive breeding for local breeds.. The milk gain from the administration of the recipes ranges from 0.6 to 1.1 litres per day. All that remains now is to identify the dosage form best suited to the socio-economic conditions of these traditional breeders for the recipes. Keywords: Bobgunnia madagascariensis, Euphorbia balsamifera, Curcubita maxima, galactogenic recipe, Borgou cows, Benin.


Author(s):  
Jacek Grzybowski ◽  
Tomasz BLACHOWICZ

Numerical classification of textile materials, aramid, viscose, and PAN/WV, is proposed using lacunarity analysis of monochromatic digital representation of optical microscopic images. The method is sensitive to the spatial distribution of fibers, and equivalently, to the empty spaces between them. This means that lacunarity is able to quantitatively express a given level of spatial in-plane symmetries of single-face fabrics.


Hacquetia ◽  
2020 ◽  
Vol 19 (1) ◽  
pp. 81-97
Author(s):  
Kiril Vassilev ◽  
Momchil Nazarov ◽  
Nikolay Velev

AbstractMantle vegetation includes plant communities dominated mostly by shrubs and occurs in habitats where the typical tree layers meet difficulties to evolve. This study was conducted in three areas of Bulgaria – Western Balkan Range, Western Sredna Gora Mt. and the Fore-Balkan. Numerical classification and ordination were performed by PC-ORD and JUICE software packages. Diagnostic species were determined by calculating the Phi-coefficient. Two associations and one plant community of the Berberidion alliance were recognized – Corno-Ligustretum Horvat ex Trinajstić ---amp--- Z. Pavletić 1991, Pruno spinosae-Ligustretum vulgaris Tüxen 1952 and Elytrigia repens-Crataegus monogyna community. The latter considered as a successional stage of shrub encroachment into the grasslands. Its species composition is very close to that of the ass. Corno-Ligustretum. The species composition of ass. Pruno-Ligustretum represents a mixture of species characteristic for dry and mesic grasslands, fringe and forest vegetation. The Crataego-Prunetea class is still poorly studied in Bulgaria and much more data from all regions in the country have to be collected.


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