MethodsX最新文献

This paper describes a method that can perform robust detection and classification in out-of-distribution rotated images in the medical domain. In real-world medical imaging tools, noise due to the rotation of the body part is frequently observed. This noise reduces the accuracy of AI-based classification and prediction models. Hence, it is important to develop models which are rotation invariant. To that end, the proposed method - RISC (rotation invariant self-supervised vision framework) addresses this issue of rotational corruption. We present state-of-the-art rotation-invariant classification results and provide explainability for the performance in the domain. The evaluation of the proposed method is carried out on real-world adversarial examples in Medical Imagery-OrganAMNIST, RetinaMNIST and PneumoniaMNIST. It is observed that RISC outperforms the rotation-affected benchmark methods by obtaining 22%, 17% and 2% accuracy boost on OrganAMNIST, PneumoniaMNIST and RetinaMNIST rotated baselines respectively. Further, explainability results are demonstrated.

This methods paper describes:

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  a representation learning approach that can perform robust detection and classification in out-of-distribution rotated images in the medical domain.

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  It presents a method that incorporates self-supervised rotation invariance for correcting rotational corruptions.

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  GradCAM-based explainability for the rotational SSL pretext task and the downstream classification outcomes for the three benchmark datasets are presented

Single-cell sequencing has revolutionized our understanding of cellular heterogeneity and cell state, enabling investigations across diverse fields such as developmental biology, immunology, and cancer biology. However, obtaining a high-quality single-cell suspension is still challenging, particularly when starting with limited materials like Zebrafish embryos, a powerful animal model for studying developmental processes and human diseases. Here, we present an optimized protocol for isolating single cells from individual zebrafish embryos, offering a valuable resource for researchers interested in working with limited starting material. The protocol facilitates unique investigations utilizing individual embryos, such as inter-individual genetic differences and embryo-specific lineage tracing analysis. Using a refined single-cell isolation protocol alongside zebrafish as a model organism, researchers can access a resource for exploring the emergence of all types and states of cells, advancing our understanding of cellular processes and disease mechanisms.

Molecular hybridization represents a strategic approach in drug design, where two or more pharmacophoric elements from distinct bioactive molecules are integrated into a single hybrid compound. In this study, we synthesized hybrid compounds of chalcone, triazole, and eugenol through straightforward reactions using 4-hydroxyacetophenone as the starting material. Initially, 4-hydroxyacetophenone (1) underwent alkylation with 1,4-dibromobutane to produce compound 2 with an 84 % yield. Compound 2 was then subjected to azidation, resulting in azidobutoxyacetophenone 3 with a 71 % yield. Subsequently, compound 3 was reacted with either benzaldehyde or 4-methoxybenzaldehyde via base-catalyzed aldol condensation, yielding azidobutoxychalcones 4a (69 %) and 4b (84 %). Finally, azide-alkyne [3+2] cycloaddition between 4a/4b and propargylated eugenol afforded chalcone derivatives bearing eugenol-1,2,3-triazole hybrids 5a and 5b, each with a 90 % yield.

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  Synthesized chalcones featuring an eugenol-1,2,3-triazole scaffold using 4-hydroxyacetophenone as the starting material.

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  Synthesis was accomplished through a four-step reaction sequence.

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  Products were obtained in good yield.

The acidophilic archaeon Ferroplasma acidiphilum exhibits remarkable adaptations to life in highly acidic environments. Nevertheless, the investigation of its molecular biology is challenging because of the slow growth of the organism, low biomass yield, and limitations of standard growth measurement techniques caused by iron oxidation.

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  A novel two-step turbidimetric growth measurement (2TGM) method was developed to address the shortcomings associated with iron precipitation in culture media. The method comprises two distinct preparation steps.

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  The initial 2TGM step involves centrifuging culture samples at high speed to remove F. acidiphilum cells and iron precipitates, thus preparing a blank.

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  The second 2TGM step involves centrifuging the culture at a lower speed with the objective of selectively removing iron precipitates, thus allowing F. acidiphilum cells to remain suspended in the supernatant. This preparation enables subsequent measurement of cell density.

There is a growing demand for cost-effective and sustainable technologies for treating wastewater as water consumption increases and conventional technologies become more expensive. Nanoparticles have a great deal of potential for use in the treatment of waste water. Their unique surface area allows them to effectively remove toxic metal ions, pathogenic microorganisms, organic and inorganic solutes from water. This study investigated the potential of orange and banana peels as renewable nano adsorbents for removing dyes and dissolved organic compounds from textile wastewater. Orange and banana peels are an optimal selection due to their favourable chemical characteristics, namely the presence of cellulose, pectic, hemicellulose, and lignin. Their capacity to adsorb diverse anionic and cationic compounds on their surface-active sites is attributed to their unique functional group compositions. Silver nanoparticles are able to adsorb heavy metals due to their exceptionally low electrical and thermal resistance and surface plasmon resonance. The samples were thoroughly characterised using field emission scanning electron microscopy (FESEM), UV–Visible spectrometry, Fourier transform infrared spectroscopy (FTIR) and XRD. The nanoparticles were prepared (10 gm,50 gm,100 gm) and subsequently introduced to the wastewater sample. The optical density values were recorded at various time points. The optical density values demonstrate a decline over the course of the experiment, with a notable decrease observed over time. The results of this study provide valuable insights into the efficacy of these natural adsorbents and their potential for sustainable water purification technologies. For the purpose of this research, high performance instrumentation methods were performed as follows:

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  Field emission scanning electron microscopy for surface morphology studies.

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  Gas chromatography-mass spectrometry (GC–MS) for analytical technique that combines gas chromatography (GC) and mass spectrometry (MS) to identify unknown substances or contaminants.

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  Optical density values were measured for different timings of degradation.