RootPainter: deep learning segmentation of biological images with corrective annotation.

Convolutional neural networks (CNNs) are a powerful tool for plant image analysis, but challenges remain in making them more accessible to researchers without a machine-learning background. We present RootPainter, an open-source graphical user interface based software tool for the rapid training of deep neural networks for use in biological image analysis. We evaluate RootPainter by training models for root length extraction from chicory (Cichorium intybus L.) roots in soil, biopore counting, and root nodule counting. We also compare dense annotations with corrective ones that are added during the training process based on the weaknesses of the current model. Five out of six times the models trained using RootPainter with corrective annotations created within 2 h produced measurements strongly correlating with manual measurements. Model accuracy had a significant correlation with annotation duration, indicating further improvements could be obtained with extended annotation. Our results show that a deep-learning model can be trained to a high accuracy for the three respective datasets of varying target objects, background, and image quality with < 2 h of annotation time. They indicate that, when using RootPainter, for many datasets it is possible to annotate, train, and complete data processing within 1 d.

The interaction between wheat roots and soil pores in structured field soil.

Wheat (Triticum aestivum L.) root growth in the subsoil is usually constrained by soil strength, although roots can use macropores to elongate to deeper layers. The quantitative relationship between the elongation of wheat roots and the soil pore system, however, is still to be determined. We studied the depth distribution of roots of six wheat varieties and explored their relationship with soil macroporosity from samples with the field structure preserved. Undisturbed soil cores (to a depth of 100 cm) were collected from the field and then non-destructively imaged using X-ray computed tomography (at a spatial resolution of 90 µm) to quantify soil macropore structure and root number density (the number of roots cm-2 within a horizontal cross-section of a soil core). Soil macroporosity changed significantly with depth but not between the different wheat lines. There was no significant difference in root number density between wheat varieties. In the subsoil, wheat roots used macropores, especially biopores (i.e. former root or earthworm channels) to grow into deeper layers. Soil macroporosity explained 59% of the variance in root number density. Our data suggested that the development of the wheat root system in the field was more affected by the soil macropore system than by genotype. On this basis, management practices which enhance the porosity of the subsoil may therefore be an effective strategy to improve deep rooting of wheat.

Impression cytology: a novel sampling technique for conjunctival cytology of the feline eye.

OBJECTIVE: Impression cytology is a noninvasive investigation of the ocular surface. It uses the adhesive features of different filter papers to collect a monolayer of epithelial cells from the cornea and/or conjunctiva. Samples obtained by impression cytology exhibit all characteristics of an ideal cytology specimen. The aim of this study was to test the feasibility of impression cytology and determine the most appropriate filter paper to achieve maximum diagnostic value of the feline eye. ANIMALS STUDIED: Ten healthy cats. PROCEDURES: The study was conducted in two phases. In the first phase, eight different filter papers (FPs) with various pore sizes were tested: 3.0-, 1.2-, 0.8-, 0.45-, 0.22-, 0.05- and 0.025-µm cellulose acetate papers and a 0.4-µm Biopore membrane (BM). Samples were obtained from the superior bulbar and from the inferior palpebral conjunctiva. In the second phase, three different sampling methods - with and without topical anesthesia, and with topical anesthesia and drying of the conjunctiva - were compared employing the BM encased in the intended BM device (BMD). Samples were evaluated for cellularity and quality of cells. RESULTS: In the first phase, samples obtained from the superior bulbar conjunctiva with the BM had the most sufficient cellularity and quality. In the second phase, BMD with topical anesthesia and additional drying of the conjunctiva was the most ideal method. CONCLUSION: The BMD may prove to be a suitable diagnostic tool for clinicians. Sampling is quick, processing is simple, and a large area of intact cells can be harvested.

Soil microplastics inhibit the movement of springtail species.

Previous studies have indicated the means by which micro-sized plastic particles may affect the soil environment, and this could be linked to the behavior of plastics in the soil system and how these particles are influenced by biological responses. Soil-dwelling organisms play a key role in modifying the soil system by constructing bio-pores, and these structural changes are potentially related to the behavior of plastic particles. In this study, we found that micro-sized plastic particles moved into bio-pores within seconds, and that this influx disrupted the movement of springtails (Lobella sokamensis). The springtails moved to avoid becoming trapped, and this behavior created bio-pores in the soil system. The influx of plastic particles into these cavities subsequently immobilized the springtails within. This phenomenon was observed at low a concentration of plastic particles (8 mg/kg), and it likely occurs in actual soil environments. The findings of this study indicate that the behavior of plastic particles in the soil not only disrupts the movement of springtails but also has wider implications for effective management of soils.

Changes in bacteria composition and efficiency of constructed wetlands under sustained overloads: A modeling experiment.

The average organic and hydraulic loads that Constructed Wetlands (CWs) receive are key parameters for their adequate long-term functioning. However, over their lifespan they will inevitably be subject to either episodic or sustained overloadings. Despite that the consequences of sustained overloading are well known (e.g., clogging), the threshold of overloads that these systems can tolerate is difficult to determine. Moreover, the mechanisms that might sustain the buffering capacity (i.e., the reduction of peaks in nutrient load) during overloads are not well understood. The aim of this work is to evaluate the effect of sudden but sustained organic and hydraulic overloads on the general functioning of CWs. To that end, the mathematical model BIO_PORE was used to simulate five different scenarios, based on the features and operation conditions of a pilot CW system: a control simulation representing the average loads; 2 simulations representing +10% and +30% sustained organic overloads; one simulation representing a sustained +30% hydraulic overload; and one simulation with sustained organic and hydraulic overloads of +15% each. Different model outputs (e.g., total bacterial biomass and its spatial distribution, effluent concentrations) were compared among different simulations to evaluate the effects of such operation changes. Results reveal that overloads determine a temporary decrease in removal efficiency before microbial biomass adapts to the new conditions and COD removal efficiency is recovered. Increasing organic overloads cause stronger temporary decreases in COD removal efficiency compared to increasing hydraulic loads. The pace at which clogging develops increases by 10% for each 10% increase on the organic load.

Disentangling interactions between microbial communities and roots in deep subsoil.

Soils, paleosols and terrestrial sediments serve as archives for studying climate change, and represent important terrestrial carbon pools. Archive functioning relies on the chronological integrity of the respective units. Incorporation of younger organic matter (OM) e.g. by plant roots and associated microorganisms into deep subsoil and underlying soil parent material may reduce reliability of paleoenvironmental records and stability of buried OM. Long-term effects of sedimentary characteristics and deep rooting on deep subsoil microbial communities remain largely unknown. We characterized fossil and living microbial communities based on molecular markers in a Central European Late Pleistocene loess-paleosol sequence containing recent and ancient roots with ages of several millenia. The molecular approach, comprising free and phospholipid fatty acids (FAs), core and intact polar glycerol dialkyl glycerol tetraethers (GDGTs), as well as 16S rRNA genes from bacterial DNA, revealed the presence of living microorganisms along the sequence, with bacterial community composition comparable to that of modern topsoils. Up to 88% redundancy between bacterial genetic fingerprint and molecular signature of fossil microorganisms suggested a time-integrated signal of the molecular markers accumulated over a time span potentially lasting from sedimentation over one or more rooting phases until today. Free FAs, core GDGTs and DNA, considered as remains of fossil microorganisms, corresponded with ancient and recent root quantities, whereas phospholipid FAs and intact polar GDGTs, presumably derived from living microorganisms, correlated only with living roots. The biogeochemical and ecological disequilibrium induced by postsedimentary rooting may entail long-term microbial processes like OM mineralization, which may continue even millenia after the lifetime of the root. Deep roots and their fossil remains have been observed in various terrestrial settings, and roots as well as associated microorganisms cause both, OM incorporation and mineralization. Therefore, these findings are crucial for improved understanding of OM dynamics and carbon sequestration potential in deep subsoils.

Effect of key design parameters on bacteria community and effluent pollutant concentrations in constructed wetlands using mathematical models.

Constructed wetlands are currently recognized as an effective environmental biotechnology for wastewater treatment, but the influence of their design parameters on internal functioning and contaminant removal efficiency is still under discussion. In this work, the effect of aspect ratio and water depth on bacteria communities as well as treatment efficiency of horizontal subsurface flow constructed wetlands (HSSF) under the Mediterranean climate was evaluated, using a mathematical model. For this purpose, experimental results from four pilot-scale wetlands of equal surface area but different aspect ratios and water depth were used. The HSSF system was fed with municipal wastewater. The experimental data were simulated using the BIO_PORE model, developed in the COMSOL Multiphysics™ platform. Simulations with the BIO_PORE model fitted well to the experimental results, showing a higher removal efficiency for the shallower HSSF for COD (93.7% removal efficiency) and ammonia nitrogen (73.8%). The aspect ratio had a weak relationship with the bacteria distribution and the removal efficiency. In contrast, the water depth was a factor. The results of the present study confirm a previous hypothesis in which depth has an important impact on the biochemical reactions causing contaminants transformation and degradation.

Frontal sinus mucocele with orbital complications: Management by varied surgical approaches.

A mucocele of a para-nasal sinus is an accumulation of mucoid secretion and desqua-mated epithelium within the sinus with distension of its walls and is regarded as a cyst like expansile and destructive lesion. If the cyst invades the adjacent orbit and continues to expand within the orbital cavity, the mass may mimic the behavior of many benign growths primary in the orbit. The frontal sinus is most commonly involved, whereas sphenoid, ethmoid, and maxillary mucoceles are rare. Floor of frontal sinus is shared with the superior orbital wall which explains the early displacement of orbit in enlarging frontal mucoceles. Frontal sinus mucoceles are prone to recurrences if not managed adequately. Here, we are evaluating different approaches used to manage various stages of frontal mucoceles which presented to us with orbital complications. Three cases of frontal sinus mucocele are discussed which presented to our OPD with different clinical symptoms and all cases were managed by different surgical approaches according to their severity. We also concluded that it is prudent to collaborate with the neurosurgeons for adequate management of such complex mucoceles by a craniotomy approach.

Descripción de la metaplasia escamosa por citología de impresión en pacientes con ojo seco / Description of squamous metaplasia by cytology of impression in patients with dry eye

El ojo seco se caracteriza por una deficiencia en la cantidad o calidad de la película lagrimal, que conlleva a cambios histológicos en la superficie ocular como la metaplasia escamosa. Objetivo: Determinar el grado de metaplasia escamosa de la superficie conjuntival en pacientes con ojo seco con diferentes grados de severidad clínica. Metopdología: A 63 ojos de pacientes con diagnóstico clínico de ojo seco, clasificados como leve, moderado y severo, se les tomó citología de impresión en la conjuntiva bulbar temporal y nasal, con membranas de biopore (Millipore PICM012550 poro 0.4m). Las membranas se fijaron con etanol al 96 por ciento y colorearon con ácido periódico de Shiff- hematoxilina, y se montaron entre lámina y laminilla con Entellan. El grado de metaplasia escamosa se determinó de acuerdo al número de las células caliciformes (contadas con rejilla calibrada a 40X) y a los cambios morfológicos de las células epiteliales, utilizando la graduación de Murube y Rivas (2002). Resultados: Aproximadamente la mitad de los pacientes con ojo seco leve (49 por ciento ) presento grado 1 de metaplasia escamosa, el 53,8 por ciento de los pacientes con ojo seco moderado presentó grado 2 y el 57.1 por ciento de los pacientes con ojo seco severo presentó grado 3. Conclusiones: El grado de metaplasia escamosa por citología de impresión es fácilmente evidenciado en pacientes con ojo seco moderado y severo contribuyendo a la confirmación del diagnóstico clínico y seguimiento de la enfermedad.

Dry eye is characterized by a deficiency in thequantity or quality of the lachrymal film, whichimplies histological changes in the surface of the eyesuch as squamous metaplasia. The purpose was todetermine the degree of the squamous metaplasiain the conjunctiva surface in patients with dry eyewith different degrees of clinical severity. Methods:63 eyes diagnosed with light, moderate and severedry eye and 20 eyes like controls subject were madeimpression cytology in the temporal and nasal bulbarconjunctiva with membranes of biopore (MilliporePICM012550). Membranes were fixed with ethanolat 96 percent and colored with periodic acid of Shiffhematoxylin,and they were mounted betweenslide and small slide with Entellan. The degree ofsquamous metaplasia was determined regarding thenumber of goblet cells and the morphologic changes ofepithelial cells, using the Murube and Rivas grading.Results: approximately half of the patients with lightdry eye (49 percent) presented a degree 1 of squamousmetaplasia, 53.8 percent of the patients with moderatedry eye presented a degree 2 and the 57.1 percent of thepatients with severe dry eye presented a degree 3.Conclusions: the degree of squamous metaplasia bycytology of impression is easily evidenced in patientswith moderate and severe dry eye, which contributesto the configuration of the clinical diagnosis and thefollow up of the disease.