Sepsis is a life-threatening condition which requires rapid diagnosis and treatment. Traditional microbiological methods are time-consuming and expensive. In response to these challenges, deep learning algorithms were developed to identify 14 bacteria species and 3 yeast-like fungi from microscopic images of Gram-stained smears of positive blood samples from sepsis patients. A total of 16,637 Gram-stained microscopic images were used in the study. The analysis used the Cellpose 3 model for segmentation and Attention-based Deep Multiple Instance Learning for classification. Our model achieved an accuracy of 77.15% for bacteria and 71.39% for fungi, with ROC AUC of 0.97 and 0.88, respectively. The highest values, reaching up to 96.2%, were obtained for Cutibacterium acnes, Enterococcus faecium, Stenotrophomonas maltophilia and Nakaseomyces glabratus. Classification difficulties were observed in closely related species, such as Staphylococcus hominis and Staphylococcus haemolyticus, due to morphological similarity, and within Candida albicans due to high morphotic diversity. The study confirms the potential of our model for microbial classification, but it also indicates the need for further optimisation and expansion of the training data set. In the future, this technology could support microbial diagnosis, reducing diagnostic time and improving the effectiveness of sepsis treatment due to its simplicity and accessibility. Part of the results presented in this publication was covered by a patent application at the European Patent Office EP24461637.1 "A computer implemented method for identifying a microorganism in a blood and a data processing system therefor".

This study, our main topic is to devlop a new deep-learning approachs for plant leaf disease identification and detection using leaf image datasets. We also discussed the challenges facing current methods of leaf disease detection and how deep learning may be used to overcome these challenges and enhance the accuracy of disease detection. Therefore, we have proposed a novel method for the detection of various leaf diseases in crops, along with the identification and description of an efficient network architecture that encompasses hyperparameters and optimization methods. The effectiveness of different architectures was compared and evaluated to see the best architecture configuration and to create an effective model that can quickly detect leaf disease. In addition to the work done on pre-trained models, we proposed a new model based on CNN, which provides an efficient method for identifying and detecting plant leaf disease. Furthermore, we evaluated the efficacy of our model and compared the results to those of some pre-trained state-of-the-art architectures.

Infectious diseases remain a critical global health challenge, and the integration of standardized ontologies plays a vital role in managing related data. The Infectious Disease Ontology (IDO) and its extensions, such as the Coronavirus Infectious Disease Ontology (CIDO), are essential for organizing and disseminating information related to infectious diseases. The COVID-19 pandemic highlighted the need for updating IDO and its virus-specific extensions. There is an additional need to update IDO extensions specific to bacteria, fungus, and parasite infectious diseases. We adopt the "hub and spoke" methodology to generate pathogen-specific extensions of IDO: Virus Infectious Disease Ontology (VIDO), Bacteria Infectious Disease Ontology (BIDO), Mycosis Infectious Disease Ontology (MIDO), and Parasite Infectious Disease Ontology (PIDO). The creation of pathogen-specific reference ontologies advances modularization and reusability of infectious disease data within the IDO ecosystem. Future work will focus on further refining these ontologies, creating new extensions, and developing application ontologies based on them, in line with ongoing efforts to standardize biological and biomedical terminologies for improved data sharing and analysis.

Mycotoxins are a group of naturally occurring, toxic chemical compounds produced by certain species of moulds (fungi), during growth on various crops and foodstuffs, including cereals, nuts, spices and dairy products (The World Health Organization (WHO), 2023). The ingestion of certain mycotoxins has been linked to a range of harmful health impacts on both humans and animals, from short-term poisoning to long-term consequences such as liver cancer, and in some cases, death (Mavrommatis et al., 2021; Marroquín-Cardona et al., 2014; Liu and Wu, 2010). Mycotoxins are secondary metabolites (that is, compounds produced by an organism that are not essential for its primary life processes) and are often produced during the pre-harvest, harvest, and storage phases under favourable conditions of humidity and temperature (Marroquín-Cardona et al., 2014; Van der Fels-Klerx et al., 2022). The most prevalent mycotoxins include aflatoxins, tricothecenes, fumonisins, zearalenones, ochratoxins and patulin, and are produced by certain plant-pathogenic species of Aspergillus, Fusarium, and Penicillium (Tola and Kebede, 2016). Mycotoxin contamination in crop products has been found to vary significantly across different geographical locations and is influenced by annual weather conditions (Logrieco et al., 2021; Leggieri et al., 2020).

Recent studies indicate that Generative Pre-trained Transformer 4 with Vision (GPT-4V) outperforms human physicians in medical challenge tasks. However, these evaluations primarily focused on the accuracy of multi-choice questions alone. Our study extends the current scope by conducting a comprehensive analysis of GPT-4V's rationales of image comprehension, recall of medical knowledge, and step-by-step multimodal reasoning when solving New England Journal of Medicine (NEJM) Image Challenges - an imaging quiz designed to test the knowledge and diagnostic capabilities of medical professionals. Evaluation results confirmed that GPT-4V outperforms human physicians regarding multi-choice accuracy (88.0% vs. 77.0%, p=0.034). GPT-4V also performs well in cases where physicians incorrectly answer, with over 80% accuracy. However, we discovered that GPT-4V frequently presents flawed rationales in cases where it makes the correct final choices (27.3%), most prominent in image comprehension (21.6%). Regardless of GPT-4V's high accuracy in multi-choice questions, our findings emphasize the necessity for further in-depth evaluations of its rationales before integrating such models into clinical workflows.

Inferring over and extracting information from Large Language Models (LLMs) trained on a large corpus of scientific literature can potentially drive a new era in biomedical research, reducing the barriers for accessing existing medical evidence. This work examines the potential of LLMs for dialoguing with biomedical background knowledge, using the context of antibiotic discovery. The systematic analysis is applied to ten state-of-the-art models, from models specialised on biomedical scientific corpora to general models such as ChatGPT, GPT-4 and Llama 2 in two prompting-based tasks: chemical compound definition generation and chemical compound-fungus relation determination. The work provides a systematic assessment on the ability of LLMs to encode and express these relations, verifying for fluency, prompt-alignment, semantic coherence, factual knowledge and specificity of generated responses. Results show that while recent models have improved in fluency, factual accuracy is still low and models are biased towards over-represented entities. The ability of LLMs to serve as biomedical knowledge bases is questioned, and the need for additional systematic evaluation frameworks is highlighted. The best performing GPT-4 produced a factual definition for 70% of chemical compounds and 43.6% factual relations to fungi, whereas the best open source model BioGPT-large 30% of the compounds and 30% of the relations for the best-performing prompt. The results show that while LLMs are currently not fit for purpose to be used as biomedical factual knowledge bases, there is a promising emerging property in the direction of factuality as the models become domain specialised, scale-up in size and level of human feedback.

HBO's smash-hit adaptation The Last of Us is the latest in a string of horror stories featuring fungi as the source of fear. The zombie-like outbreak that takes place in the show, which is based on the dystopian video game series of the same name, stems from a mutated version of a parasitic mushroom which fictionally evolves to attack humans instead of insects. In Mexican Gothic, by Silvia Moreno-Garcia, the narrator knows something isn't right with a family and their mansion, and soon discovers an intergenerational secret intertwined with a mycelium network. In last year's What Moves the Dead, by T. Kingfisher, it's a mycologist who discovers the root of the town's sudden mysterious illnesses. Science-fiction's fungal fascination goes back much farther.

Diagnosis of fungal infections can rely on microscopic examination, however, in many cases, it does not allow unambiguous identification of the species due to their visual similarity. Therefore, it is usually necessary to use additional biochemical tests. That involves additional costs and extends the identification process up to 10 days. Such a delay in the implementation of targeted treatment is grave in consequences as the mortality rate for immunosuppressed patients is high. In this paper, we apply machine learning approach based on deep learning and bag-of-words to classify microscopic images of various fungi species. Our approach makes the last stage of biochemical identification redundant, shortening the identification process by 2-3 days and reducing the cost of the diagnostic examination.

It's no wonder it's called'destroyer of insects.' Scientists have identified a fungus that infects fruit flies and kills them from the inside out – but, not before causing them to ascend to a high point and spread their wings like a marionette on a string, to spew spores from their abdomen. The behaviour-manipulating fungus invades the fruit fly's nervous system and forces it to embark on the fatal climb, known as summit disease, before devouring the brain and muscles. According to researchers from the University of California, Berkeley, the fungus responsible for the horrifying infection is called Entomophthora muscae – with the genus translating to'destroyer of insects.' Then-doctoral student Carolyn Elya began examining the fungus' effect after noticing dead fruit flies around a rotting watermelon on her apartment's balcony. After she stopped feeding them the antifungal food used in the labs, fruit flies she brought to her home to observe became infected as well.