Semantic segmentation of microbial alterations based on SegFormer.

Introduction: Precise semantic segmentation of microbial alterations is paramount for their evaluation and treatment. This study focuses on harnessing the SegFormer segmentation model for precise semantic segmentation of strawberry diseases, aiming to improve disease detection accuracy under natural acquisition conditions. Methods: Three distinct Mix Transformer encoders - MiT-B0, MiT-B3, and MiT-B5 - were thoroughly analyzed to enhance disease detection, targeting diseases such as Angular leaf spot, Anthracnose rot, Blossom blight, Gray mold, Leaf spot, Powdery mildew on fruit, and Powdery mildew on leaves. The dataset consisted of 2,450 raw images, expanded to 4,574 augmented images. The Segment Anything Model integrated into the Roboflow annotation tool facilitated efficient annotation and dataset preparation. Results: The results reveal that MiT-B0 demonstrates balanced but slightly overfitting behavior, MiT-B3 adapts rapidly with consistent training and validation performance, and MiT-B5 offers efficient learning with occasional fluctuations, providing robust performance. MiT-B3 and MiT-B5 consistently outperformed MiT-B0 across disease types, with MiT-B5 achieving the most precise segmentation in general. Discussion: The findings provide key insights for researchers to select the most suitable encoder for disease detection applications, propelling the field forward for further investigation. The success in strawberry disease analysis suggests potential for extending this approach to other crops and diseases, paving the way for future research and interdisciplinary collaboration.

Biosynthesis and Characterization of Silver Nanoparticles Produced by Phormidium ambiguum and Desertifilum tharense Cyanobacteria.

The world faces a challenge with the pervasion of multidrug-resistant bacteria that encourages scientists to develop and discover alternative, ecofriendly, and easy-to-produce new antibacterial agents. Our work is part of the greater effort of scientists around the world to achieve this goal by the biological synthesis of silver nanoparticles using cyanobacterial extracellular and intracellular components as nonchemical reducing agents. Two Egyptian cyanobacteria were isolated and identified according to 16S rRNA gene sequencing as Phormidium ambiguum and a novel species Desertifilum tharense. The sequences were deposited with accession numbers MW762709 and MW762710 for Desertifilum tharense and Phormidium ambiguum, respectively, in the GenBank. The results of UV-Vis analysis showed promising extracellular Ag-NPs synthesis by Desertifilum tharense and Phormidium ambiguum under light conditions. Therefore, these Ag-NPs were characterized and evaluated for antibacterial and antioxidant activity. TEM and SEM analyses revealed the spherical crystals with face-centered cubic structures and size range of 6.24-11.4 nm and 6.46-12.2 nm for Ag-NPs of Desertifilum tharense and Phormidium ambiguum, respectively. XRD and EDX results confirmed the successful synthesis of Ag-NPs in their oxide form or chloride form. The FTIR spectrum data confirmed the presence of hydroxyl and amide groups. Desertifilum tharense Ag-NPs displayed the largest inhibition zone that ranged from 9 mm against Micrococcus luteus ATCC 10240 to 25 mm against methicillin-resistant Staphylococcus aureus (MRSA) ATCC 43300. For Phormidium ambiguum Ag-NPs, the inhibition zone diameter was in the range of 9 mm to 18 mm. The biosynthesized Ag-NPs significantly inhibited the growth of medically important resistance-pathogenic Gram-positive and Gram-negative bacteria. The Ag-NPs of Phormidium ambiguum exhibited the highest scavenging activity of 48.7% when compared with that of Desertifilum tharense, which displayed 43.753%.

Integration of Radiometric Ground-Based Data and High-Resolution QuickBird Imagery with Multivariate Modeling to Estimate Maize Traits in the Nile Delta of Egypt.

In site-specific management, rapid and accurate identification of crop stress at a large scale is critical. Radiometric ground-based data and satellite imaging with advanced spatial and spectral resolution allow for a deeper understanding of crop stress and the level of stress in a given area. This research aimed to assess the potential of radiometric ground-based data and high-resolution QuickBird satellite imagery to determine the leaf area index (LAI), biomass fresh weight (BFW) and chlorophyll meter (Chlm) of maize across well-irrigated, water stress and salinity stress areas in the Nile Delta of Egypt. Partial least squares regression (PLSR) and multiple linear regression (MLR) were evaluated to estimate the three measured traits based on vegetation spectral indices (vegetation-SRIs) derived from these methods and their combination. Maize field visits were conducted during the summer seasons from 28 to 30 July 2007 to collect ground reference data concurrent with the acquisition of radiometric ground-based measurements and QuickBird satellite imagery. The results showed that the majority of vegetation-SRIs extracted from radiometric ground-based data and high-resolution satellite images were more effective in estimating LAI, BFW, and Chlm. In general, the vegetation-SRIs of radiometric ground-based data showed higher R2 with measured traits compared to the vegetation-SRIs extracted from high-resolution satellite imagery. The coefficient of determination (R2) of the significant relationships between vegetation-SRIs of both methods and three measured traits varied from 0.64 to 0.89. For example, with QuickBird high-resolution satellite images, the relationships of the green normalized difference vegetation index (GNDVI) with LAI and BFW showed the highest R2 of 0.80 and 0.84, respectively. Overall, the ground-based vegetation-SRIs and the satellite-based indices were found to be in good agreement to assess the measured traits of maize. Both the calibration (Cal.) and validation (Val.) models of PLSR and MLR showed the highest performance in predicting the three measured traits based on the combination of vegetation-SRIs from radiometric ground-based data and high-resolution QuickBird satellite imagery. For example, validation (Val.) models of PLSR and MLR showed the highest performance in predicting the measured traits based on the combination of vegetation-SRIs from radiometric ground-based data and high-resolution QuickBird satellite imagery with R2 (0.91) of both methods for LAI, R2 (0.91-0.93) for BFW respectively, and R2 (0.82) of both methods for Chlm. The models of PLSR and MLR showed approximately the same performance in predicting the three measured traits and no clear difference was found between them and their combinations. In conclusion, the results obtained from this study showed that radiometric ground-based measurements and high spectral resolution remote-sensing imagery have the potential to offer necessary crop monitoring information across well-irrigated, water stress and salinity stress in regions suffering lack of freshwater resources.

Polymer-Peptide Modified Gold Nanorods to Improve Cell Conjugation and Cell labelling for Stem Cells Photoacoustic Imaging.

The use of gold nanorods (GNRs) as a contrast agent in bioimaging and cell tracking has numerous advantages, primarily due to the unique optical properties of gold nanorods which allow for the use of infrared regions when imaging. Owing to their unique geometry, Au NRs exhibit surface plasmon modes in the near-infrared wavelength range, which is ideal for carrying out optical measurements in biological fluids and tissue. Gold nanorod functionalization is essential, since the Cetyltrimethyl ammonium bromide CTAB gold nanorods are toxic, and for further in vitro and in vivo experiments the nanorods should be functionalized to become optically stable and biocompatible. In the present study, gold nanorods with an longitudinal surface plasmon resonance (LSPR) position around 800 nm were synthesized in order to be used for photoacoustic imaging applications for stem cell tracking. The gold nanorods were functionalized using both thiolated poly (ethylene glycol) (PEG) to stabilize the gold nanorods surface and a CALNN-TAT peptide sequence. Both ligands were attached to the gold nanorods through an Au-sulfur bond. CALNN-TAT is known as a cell penetrating peptide which ensures endocytosis of the gold nanorods inside the mesenchymal stem cells of mice (MSCD1). Surface modifications of gold nanorods were achieved using optical spectroscopy (UV-VIS), electron microscopy (TEM), zeta-potential, and FTIR. Gold nanorods were incubated in MSCD1 in order to achieve a cellular uptake that was characterized by a transmission electron microscope (TEM). For photoacoustic imaging, Multi-Spectral Optoacoustic Tomography (MSOT) was used. The results demonstrated good cellular uptake for PEG-CALNN-TAT GNRs and the successful use of modified gold nanorods as both a contrast agent in photoacoustic imaging and as a novel tracking bioimaging technique.

Release of toxic elements in fishpond sediments under dynamic redox conditions: Assessing the potential environmental risk for a safe management of fisheries systems and degraded waterlogged sediments.

Waterlogged soils and sediments contaminated with potentially toxic elements (PTEs) constitute a complicated case of degraded areas; their management requires understanding of the dynamic redox-driven PTE mobilization. Such studies about PTE redox-induced dynamics in fishpond sediments are still scarce, but of great importance concerning environmental and human health risk. We studied the redox potential (EH)-induced impacts on the solubility of As, Co, Cu, Mo, Ni, Se, V, and Zn in the sediments of a fish farm in the Nile Delta, Egypt, using an automated apparatus of biogeochemical microcosm. We assessed the fate of elements as affected by the EH-induced changes in pH, Fe, Mn, SO42-, Cl-, and the dissolved aliphatic (DOC) and aromatic (DAC) organic carbon. Sediment redox ranged from -480 mV to +264 mV. Flooding the sediments caused a significant decrease in pH from 8.2 to 5.7. Dissolved concentrations of As, Co, Ni, Se, and Zn, as well as DOC, Fe, and Mn increased under the reducing acidic conditions. The release of As, Co, Ni, Se, and Zn could be attributed to the decrease of EH and the subsequent decrease of pH, as well as to the increase of DOC, and/or the dissolution of Fe-Mn oxides caused by redox reactions. Dissolved concentrations of Cu, Mo, and V increased under oxic conditions and were significantly positive correlated with EH, pH, DAC, and SO42-. This enhancement might be caused by the EH-dependent increase of pH under oxic conditions (particularly for Mo and V), which also led to DAC increase. Sulfide oxidation and the release of the associated elements may have also had a contribution, particularly in the release of Cu. Therefore, the release dynamics of dissolved Cu, Mo, and V in the sediments were controlled, to a certain extent, by the changes of EH/pH, DAC, and sulfur chemistry. We conclude that the biogeochemical differences in the behaviour of the studied elements under variable redox regimes substantially affected the fishponds via possible enhancement of PTE mobilization. Our work shows that the potential environmental risks related to PTE mobilization and fish food security should be taken into consideration for the management of degraded aquaculture systems and waterlogged soils and sediments.

Bioaccumulation and translocation of nine heavy metals by Eichhornia crassipes in Nile Delta, Egypt: perspectives for phytoremediation.

The current research was carried out to estimate the potential of water hyacinth (WH) for removal of nine heavy metals (HMs) from three irrigation canals in Nile Delta. Sampling was achieved in monospecific and homogeneous WH stands at three irrigation canals in the study area, and WH biomass was sampled at monthly intervals from April 2014 to November 2014 using five randomly distributed quadrats (each 0.5 × 0.5 m) at each canal. All HM concentrations were significantly higher in the roots compared with the other WH organs. The WH was recognized by a bioaccumulation factor >1.0 for all HMs. The WH was recognized by translocation factor <1.0 for all HMs (except Pb). In many cases, the concentrations of the HMs in the different organs of WH were correlated with the same HMs in the water. Such correlations indicate that WH reflects the cumulative influences of environmental pollution from the water, and thereby suggesting its potential use in the bio-monitoring of most examined HMs. In conclusion, WH is a promising macrophyte for remediation of irrigation canals polluted with Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn.

Potentially toxic elements in saltmarsh sediments and common reed (Phragmites australis) of Burullus coastal lagoon at North Nile Delta, Egypt: A survey and risk assessment.

Burullus lagoon is the second largest lake in Egypt. However, there has never been a comprehensive survey which studied nineteen potentially toxic elements in sediments and plants and evaluated the associated potential risk. Thus, we aimed to study the total and potentially available content of As, Al, Cd, Co, Cr, Cu, Fe, Hg, Mn, Mo, Ni, Sb, Se, Sn, Tl, V, and Zn in the sediments and common reed (Phragmites australis) at thirty two sites along the entire lagoon and connected drains. Contamination Factor (CF), Pollution Load Index (PLI), Geo-accumulation Index (Igeo), and Enrichment Factor (EF) were calculated to assess the grade of contamination. Element accumulation factor (AF) and bio-concentration ratio (BCR) were also calculated. Aluminum showed the highest median (mg kg-1) total content (41,200), followed by Fe (30,300), Mn (704.7), V (82.0), Zn (75.5), Cr (51.2), Cu (47.8), Ni (44.3), As (31.9), Tl (24.6), Co (21.4), Se (20.3), Sb (17.6), Sn (15.6), Mo (11.3), and Hg (16.6 µg kg-1). Values of the EF, CF, and Igeo showed that the sediments were heavily contaminated with As, Sb, Se, Tl, Mo, Sn, Co, Ni, and Cu. The drained sediment had significantly higher values of total and potentially available element content than the lagoon sediments. Sediments of the middle and western area showed significantly higher contents of total and available elements than the eastern section. The BCR and AF values indicate that the studied plant is efficient in taking up high amounts of Zn, Fe, As, Sn, Tl, Ni, Mo, Mn; then Co, Cu, and V. The results exhibit a dramatic contamination at certain sites of the lagoon, and the studied PTEs have a predominant role in contamination-related ecological risk. Further investigations concerning redox-induced mobilization of PTEs in sediments, the risk of fish contamination and the potential health hazards are highly recommended.