Deep learning based soft-sensor for continuous chlorophyll estimation on decentralized data.

Monitoring the concentration of pigments like chlorophyll (Chl) in water-bodies is a key task to contribute to their conservation. However, with the existing sensor technology, measurement in real-time and with enough frequency to ensure proper risk management is not completely feasible. In this work, with the concept of data-driven soft-sensing, three hydrophysical features are used together with three meteorological ones to estimate the concentration of Chl in two tributaries of the River Thames. Data driven models, specifically neural networks, are used with three learning approaches: individual, centralized and federated. Data reduction scenarios are proposed in order to analyze the performance of each approach when less data is available. The best results in the training are usually obtained with the individual approach. However, the federated learning provides better generalization ability. It was also observed that in most of the cases the results of the federated learning approach improve those of the centralized one.

Trichoderma koningiopsis (Hypocreaceae) has the smallest mitogenome of the genus Trichoderma.

Introduction: Fungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns. Methods: The complete mitochondrial genome sequence of the mycoparasitic fungus Trichoderma koningiopsis was determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project of T. koningiopsis genome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes. Results: T. koningiopsis strain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such as atp6, atp8, atp9, cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in the T. koningiopsis POS7 mitogenome, one of them in cox3 gene and the other in rnl gene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes of T. koningiopsis strain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina. T. koningiopsis strain POS7 was clustered together with other representatives of Trichoderma lineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers. Discussion: The mitochondrial genome of T. koningiopsis POS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.

Forecasting COVID-19 spreading through an ensemble of classical and machine learning models: Spain's case study.

In this work the applicability of an ensemble of population and machine learning models to predict the evolution of the COVID-19 pandemic in Spain is evaluated, relying solely on public datasets. Firstly, using only incidence data, we trained machine learning models and adjusted classical ODE-based population models, especially suited to capture long term trends. As a novel approach, we then made an ensemble of these two families of models in order to obtain a more robust and accurate prediction. We then proceed to improve machine learning models by adding more input features: vaccination, human mobility and weather conditions. However, these improvements did not translate to the overall ensemble, as the different model families had also different prediction patterns. Additionally, machine learning models degraded when new COVID variants appeared after training. We finally used Shapley Additive Explanation values to discern the relative importance of the different input features for the machine learning models' predictions. The conclusion of this work is that the ensemble of machine learning models and population models can be a promising alternative to SEIR-like compartmental models, especially given that the former do not need data from recovered patients, which are hard to collect and generally unavailable.

EFECTO DEL FILTRADO DE SECUENCIAS EN EL ENSAMBLADO DEL GENOMA DE Bacillus altitudinis 19RS3 AISLADO DE Ilex paraguariensis / Effect of sequence filtering on the assembly of the Bacillus altitudinis 19RS3 genome isolated from Ilex paraguariensis

RESUMEN El filtrado de secuencias es un paso esencial sin importar el tipo de tecnología aplicada para la secuenciación de un genoma, en el cual las lecturas de baja calidad o una parte son eliminadas. En un ensamblado la construcción de un genoma se realiza a partir de la unión de lecturas cortas en cóntigos. Algunos ensambladores miden la relación que existe entre secuencias de una longitud fija (k-mer) que puede verse afectada por la presencia de secuencias de baja calidad. Un enfoque común para evaluar los ensamblados se basa en el análisis del número de cóntigos, la longitud del cóntigo más largo y el valor del N50, definido como la longitud del cóntigo que representa el 50 % de la longitud del conjunto. En este contexto, el presente estudio tuvo como objetivo evaluar el efecto del uso de lecturas crudas y filtradas en los valores de los parámetros de calidad obtenidos en el ensamblado del genoma de Bacillus altitudinis 19RS3 aislada de Ilex paraguariensis. Se realizó el análisis de calidad de ambos archivos de partida con el software FastqC y se filtraron las lecturas con el softwareTrimmomatic. Para el ensamblado se utilizó el software SPAdes y para su evaluación la herramienta QUAST. El mejor ensamblado para B. altitudinis 19RS3 se obtuvo a partir de las lecturas filtradas con el valor de k-mer 79, que generó 16 cóntigos mayores a 500 pb con un N50 de 931 914 pb y el cóntigo más largo de 966 271 pb.

ABSTRACT Sequence filtering is an essential step regardless of the type of technology applied for sequencing a genome, in which low-quality readings or a portion are eliminated. In an assembly, the construction of a genome is carried out from the union of short reads in contigs. Some assemblers measure the relationship between sequences of a fixed length (k-mer) that can be affected by the presence of low-quality sequences. A common approach to evaluating assemblies is based on the analysis of the number of contigs, the length of the longest contig, and the value of N50 defined as the length of the contig representing 50 % of the length of the assembly. In this context, the objective of this study was to evaluate the effect of the use of crude and filtered reads on the values of the quality parameters obtained from the genome assembly of Bacillus altituidinis 19RS3 isolated from Ilex paraguariensis. The quality analysis of both starting files was performed with the FastqC software and the readings were filtered with the Trimmomatic software. The SPAdes software was used for the assembly and the QUAST tool for its evaluation. The best assembly for B. altitudinis 19RS3 was obtained from the filtered readings with the value of k-mer 79, which generated 16 contigs greater than 500 bp with a N50 of 931 914 bp and the longest contig of 966 271 bp.

De novo genome assembly of Bacillus altitudinis 19RS3 and Bacillus altitudinis T5S-T4, two plant growth-promoting bacteria isolated from Ilex paraguariensis St. Hil. (yerba mate).

Plant growth-promoting bacteria (PGPB) are a heterogeneous group of bacteria that can exert beneficial effects on plant growth directly or indirectly by different mechanisms. PGPB-based inoculant formulation has been used to replace chemical fertilizers and pesticides. In our previous studies, two endophytic endospore-forming bacteria identified as Bacillus altitudinis were isolated from roots of Ilex paraguariensis St. Hil. seedlings and selected for their plant growth-promoting (PGP) properties shown in vitro and in vivo. The purposes of this work were to assemble the genomes of B. altitudinis 19RS3 and T5S-T4, using different assemblers available for Windows and Linux and to select the best assembly for each strain. Both genomes were also automatically annotated to detect PGP genes and compare sequences with other genomes reported. Library construction and draft genome sequencing were performed by Macrogen services. Raw reads were filtered using the Trimmomatic tool. Genomes were assembled using SPAdes, ABySS, Velvet, and SOAPdenovo2 assemblers for Linux, and Geneious and CLC Genomics Workbench assemblers for Windows. Assembly evaluation was done by the QUAST tool. The parameters evaluated were the number of contigs ≥ 500 bp and ≥ 1000 bp, the length of the longest contig, and the N50 value. For genome annotation PROKKA, RAST, and KAAS tools were used. The best assembly for both genomes was obtained using Velvet. The B. altitudinis 19RS3 genome was assembled into 15 contigs with an N50 value of 1,943,801 bp. The B. altitudinis T5S-T4 genome was assembled into 24 contigs with an N50 of 344,151 bp. Both genomes comprise several genes related to PGP mechanisms, such as those for nitrogen fixation, iron metabolism, phosphate metabolism, and auxin biosynthesis. The results obtained offer the basis for a better understanding of B. altitudinis 19RS3 and T5S-T4 and make them promissory for bioinoculant development.

Isolation and selection of endophytic spore-forming bacteria with plant growth promoting properties isolated from Ilex paraguariensis St. Hil. (yerba mate).

Yerba mate (Ilex paraguariensis St. Hil.) is a species native to the subtropical regions of South America. Despite being an important crop for the region, there are few studies on the use of microorganisms to improve the growth of seedlings in the nursery stage. The objective of this study was to isolate spore-forming endophytic bacteria with plant growth promoting properties associated with yerba mate seedlings and determine their phytobeneficial effect under controlled laboratory conditions. Isolates were selected based on their sporulation capacity and evaluated for in vitro plant growth promoting properties (nitrogen fixation, phosphate solubilization, production of siderophores and synthesis of indolic compounds). Yerba mate seedlings were inoculated with the most promising isolates, which were identified via analyses of the sequence of their 16S rDNA gene as Bacillus circulans (12RS3) and Bacillus altitudinis (19RS3, T5S-T4). After 120 days plants showed higher root dry weight when inoculated with isolate 19RS3 and higher shoot dry weight with 19RS3 and T5S-T4. In conclusion, further studies to determine the ability of these isolates to adapt to the climatic conditions and to survive amidst the native soil microflora in yerba mate cultivated native soils, will be crucial for developing such strains as biofertilizer.

Enzymatic hydrolysis of barley straw for biofuel industry using a novel strain of Trametes villosa from Paranaense rainforest.

Agricultural practices generate lignocellulosic waste that can be bioconverted by fungi to generate value-added products such as biofuels. In this context, fungal enzymes are presented as an alternative for their use in the hydrolysis of cellulose to sugars that can be fermented to ethanol. The aim of this work was to characterize LBM 033 strain and to analyze its efficiency in the hydrolysis of cellulosic substrates, including barley straw. LBM 033 strain was identified as Trametes villosa by molecular techniques, through the use of the ITS and rbp2 markers and the construction of phylogenetic trees. The cell-free supernatant of T. villosa LBM 033 showed high titers of hydrolytic enzymatic activities, necessary for the hydrolysis of the holocellulosic substrates, hydrolyzing pure cellulose to cellobiose and glucose and also degraded the polysaccharides contained in barley straw to short soluble oligosaccharides. These results indicate that macro fungi from tropical soil environments, such as T. villosa LBM 033 can be a valuable resource for in-house, cost effective production of enzymes that can be applied in the hydrolysis stage, which could reduce the total cost of bioethanol production.

Estimation of high frequency nutrient concentrations from water quality surrogates using machine learning methods.

Continuous high frequency water quality monitoring is becoming a critical task to support water management. Despite the advancements in sensor technologies, certain variables cannot be easily and/or economically monitored in-situ and in real time. In these cases, surrogate measures can be used to make estimations by means of data-driven models. In this work, variables that are commonly measured in-situ are used as surrogates to estimate the concentrations of nutrients in a rural catchment and in an urban one, making use of machine learning models, specifically Random Forests. The results are compared with those of linear modelling using the same number of surrogates, obtaining a reduction in the Root Mean Squared Error (RMSE) of up to 60.1%. The profit from including up to seven surrogate sensors was computed, concluding that adding more than 4 and 5 sensors in each of the catchments respectively was not worthy in terms of error improvement.

Model-based evaluation of a trickling filter facility upgrade to biological nutrient removal.

This article presents the feasibility evaluation and preliminary design of a wastewater treatment plant upgrade supported by simulation. The existing facility was based on trickling filters, and the objective of the upgrade was to achieve nutrients removal. The proposed solution modifies the existing primary clarifier to host an anaerobic-anoxic suspended growth reactor, which is an alternative that, to our knowledge, has not been proposed or explored so far. The trickling filters would remain as aerobic reactors. In this study, the novel treatment scheme has been assessed for the first time, through model simulations. The modified treatment train was simulated, showing that the anoxic zone is able to denitrify satisfactorily achieving the required effluent nitrogen concentration. However, to promote biological phosphorus removal, an additional aerobic zone combined with a bypass of activated sludge from the anoxic zone to the first trickling filter is needed, in order to provide aerobic conditions to the phosphate accumulating organisms. Several combinations of additional aerobic volume and sludge bypass flowrate were found to successfully achieve both nitrogen and phosphorus removal, using the existing facilities without the need for new reactors neither implementing modifications that could put the trickling filters' physical integrity at risk. The novel treatment scheme could be applied in other cases with similar flowsheet in the same context.

First Whole-Genome Shotgun Sequence of a Promising Cellulase Secretor, Trichoderma koningiopsis Strain POS7.

Trichoderma koningiopsis strain POS7 produces significantly large amounts of cellulase enzymes in solid-state fermentation. The Illumina-based sequence analysis reveals an approximate genome size of 36.6 Mbp, with a G+C content of 48.82% for T. koningiopsis POS7. Based on ab initio prediction, 12,661 coding genes were annotated.

[Isolation of Aspergillus section Nigri strains in yerba mate in Posadas (Misiones, Argentina) and evaluation of their ochratoxigenic potential]. / Aislamiento de cepas de Aspergillus sección Nigri en la yerba mate comercializada en Posadas (Misiones, Argentina) y evaluación de su potencial ocratoxigénico.

The objectives of the present work were to investigate the isolation frequency of genus Aspergillus in canchada yerba mate (YMCH) and elaborated yerba mate (YME) (Ilex paraguariensis) and the proportion of section Nigri isolates, as well as to determine ochratoxin A production by Aspergillus species section Nigri. Three hundred twenty eight Aspergillus strains from 20 samples of YMCH and 1306 Aspergillus strains from 36 samples of YME were isolated; of the total, 279 from the first group of strains and 1215 from the latter group, belonged to section Nigri. For the detection of ochratoxin A production, the strains were cultivated on Czapeck yeast extract agar and the toxin was detected by thin layer chromatography under UV light. Uniserate species predominance was observed in the 1494 strains of Aspergillus section Nigri obtained (Aspergillus japonicus var. japonicus and Aspergillus japonicus var. aculeatus), whereas none of the strains analysed showed ochratoxin A production in vitro at the detection level of the methodology employed.

Aislamiento de cepas de Aspergillus sección Nigri en la yerba mate comercializada en Posadas (Misiones, Argentina) y evaluación de su potencial ocratoxigénico / [Isolation of Aspergillus section Nigri strains in yerba mate in Posadas (Misiones, Argentina) and evaluation of their ochratoxigenic potential].

The objectives of the present work were to investigate the isolation frequency of genus Aspergillus in canchada yerba mate (YMCH) and elaborated yerba mate (YME) (Ilex paraguariensis) and the proportion of section Nigri isolates, as well as to determine ochratoxin A production by Aspergillus species section Nigri. Three hundred twenty eight Aspergillus strains from 20 samples of YMCH and 1306 Aspergillus strains from 36 samples of YME were isolated; of the total, 279 from the first group of strains and 1215 from the latter group, belonged to section Nigri. For the detection of ochratoxin A production, the strains were cultivated on Czapeck yeast extract agar and the toxin was detected by thin layer chromatography under UV light. Uniserate species predominance was observed in the 1494 strains of Aspergillus section Nigri obtained (Aspergillus japonicus var. japonicus and Aspergillus japonicus var. aculeatus), whereas none of the strains analysed showed ochratoxin A production in vitro at the detection level of the methodology employed.

Aislamiento de cepas de Aspergillus sección Nigri en la yerba mate comercializada en Posadas (Misiones, Argentina) y evaluación de su potencial ocratoxigénico. / [Isolation of Aspergillus section Nigri strains in yerba mate in Posadas (Misiones, Argentina) and evaluation of their ochratoxigenic potential].

The objectives of the present work were to investigate the isolation frequency of genus Aspergillus in canchada yerba mate (YMCH) and elaborated yerba mate (YME) (Ilex paraguariensis) and the proportion of section Nigri isolates, as well as to determine ochratoxin A production by Aspergillus species section Nigri. Three hundred twenty eight Aspergillus strains from 20 samples of YMCH and 1306 Aspergillus strains from 36 samples of YME were isolated; of the total, 279 from the first group of strains and 1215 from the latter group, belonged to section Nigri. For the detection of ochratoxin A production, the strains were cultivated on Czapeck yeast extract agar and the toxin was detected by thin layer chromatography under UV light. Uniserate species predominance was observed in the 1494 strains of Aspergillus section Nigri obtained (Aspergillus japonicus var. japonicus and Aspergillus japonicus var. aculeatus), whereas none of the strains analysed showed ochratoxin A production in vitro at the detection level of the methodology employed.

Sonographic findings for the common extensor tendon of the elbow in the general population.

OBJECTIVE: To describe structural characteristics and sonographic alterations of the common extensor tendon (CET). METHODS: In 240 patients, we determined the body mass index; sonographic CET thickness, morphologic characteristics, and alterations; and color Doppler measurements of the epicondylar artery width and peak systolic velocity. Age, sex, epicondylalgia history, activities (work, sports, and hobbies), and dominant and nondominant elbows were noted. RESULTS: The CET was thicker in the dominant elbow (4.77 versus 4.61 mm [P = .023]), male patients (dominant, 5.09 versus 4.46 mm [P < .001]; nondominant, 5.00 versus 4.21 mm [P < .001]), patients involved in risk activities (dominant, 5.21 versus 4.70 mm [P < .001]; nondominant, 5.12 versus 4.53 mm [P < .001]), and those with a history of epicondylalgia (right, 5.27 versus 4.70 mm [P < .001]; left, 4.86 versus 4.60 mm [P = .316]). Thickness correlated weakly with age (dominant, r = 0.284; nondominant, r = 0.215) and moderately with weight (dominant, r = 0.492; nondominant, r = 0.502). The mean epicondylar artery diameter was 1.35 mm (SD, 0.96 mm); mean peak velocity, 13.01 cm/s (SD, 4.90 cm/s). Morphologic abnormalities were found in 79.5% of patients with a history of epicondylalgia; 7.7% with no history had abnormalities; and 55.9% with abnormalities but no history were older than 55 years. Bone spurs (49.2% versus 16.4% [P < .001]), tendon calcifications (21.5% versus 3.9% [P < .001]), and bone cortex abnormalities (12.3% versus 1.7% [P < .001]) were found more often in non-normal elbows; 79.4% of bone spurs in normal elbows occurred in patients older than 55 years. CONCLUSIONS: Mild sonographic alterations in the CET and bone spurs should be considered with caution when assessing epicondylar pain, especially in patients older than 55 years and those with a history of epicondylalgia.

Experiencia transdisciplinaria de intercambio interinstitucional en ciencias de la salud Aragua talleres sobre investigación y conociemiento / A transdiciplinary experience of interinstitutional exchangue in the health sciences Aragua state workshops on research and knowledge

En la búsqueda de nuevas fronteras para la producción de saberes, expresión de las prácticas de vida de profesionales universitarios con distinta formación, l¡deres comunitarios y gerentes institucionales del sector salud, realizamos tres talleres, 75 horas de trabajo con evaluación, para discutir y reflexionar sobre las concepciones que, sobre la producción de conocimiento y la salud, teníamos 20 participantes de estos talleres de autorreflexión. Discutimos sobre la producción o consumo de conocimientos en las Universidades e instituciones gubernamentales y el saber popular en las comunidades. Trabajamos el método de las historias de vida y la Hermenéutica, las construcciones teóricas: episteme moderna, episteme popular, matricentralidad como cultura dominante del pueblo venezolano, los nudos de sentido en las prácticas de vida, sociedad moderna, postmodernidad, el concepto de slaud para los académicos y para el pueblo. Se producen descubrimientos sobre otros saberes, sentires y pareceres, distintos al académico institucional. Concluimos que existe la necesidad de iniciar un profundo proceso de reflexión sobre lo que vivimos haciendo, pensando, sintiendo y planificando al interior de las instituciones sociales. Se demanda la producción y construcción de pol¡ticas para el bienestar social general de la población, que dialogue y tome en cuenta la manera de ser y hacer del pueblo venezolano. Este trabajo, adquiere mayor importancia en la coyuntura actual del proceso constitucional venezolano

Conversación

Seminario dirigido por J.-A. Miller realizado en Madrid el 28 de noviembre de 1998