搜索结果：Microbiology (Reading, England)

Microorganisms are ubiquitous in nature, and microbial activities are closely intertwined with the entire life cycle system and human life. Developing novel technologies for the detection, characterization and manipulation of microorganisms promotes their applications in clinical, environmental and industrial areas. Over the last two decades, terahertz (THz) technology has emerged as a new optical tool for microbiology. The great potential originates from the unique advantages of THz waves including the high sensitivity to water and inter-/intra-molecular motions, the non-invasive and label-free detecting scheme, and their low photon energy. THz waves have been utilized as a stimulus to alter microbial functions, or as a sensing approach for quantitative measurement and qualitative differentiation. This review specifically focuses on recent research progress of THz technology applied in the field of microbiology, including two major parts of THz biological effects and the microbial detection applications. In the end of this paper, we summarize the research progress and discuss the challenges currently faced by THz technology in microbiology, along with potential solutions. We also

Advancements in artificial intelligence (AI) have transformed many scientific fields, with microbiology and microbiome research now experiencing significant breakthroughs through machine learning applications. This review provides a comprehensive overview of AI-driven approaches tailored for microbiology and microbiome studies, emphasizing both technical advancements and biological insights. We begin with an introduction to foundational AI techniques, including primary machine learning paradigms and various deep learning architectures, and offer guidance on choosing between traditional machine learning and sophisticated deep learning methods based on specific research goals. The primary section on application scenarios spans diverse research areas, from taxonomic profiling, functional annotation \& prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, clinical microbiology, to prevention \& therapeutics. Finally, we discuss challenges in this field and highlight some recent breakthroughs. Together, this review underscores AI's transformative role in microbiology and microbiome research, paving the way for innovative methodologies an

The study of microorganisms, or microbiology, has demonstrated significant development since its inception and is currently a key field of biological sciences that has a huge impact on modern society and scientific research. Over the centuries, this discipline has undergone significant changes, shaping our understanding of infectious diseases and food safety. Starting from the simplest observations of microscopic organisms such as bacteria, viruses, fungi and protozoa, and ending with modern molecular and genomic research methods. This article describes a brief historical path of microbiology development. The heuristic, morphological, physiological, immunological, and molecular genetic stages are the main periods into which the development of this science is traditionally divided, despite the lack of full-fledged and precise boundaries between them.

The Antibiotic Resistance Microbiology Dataset (ARMD) is a de-identified resource derived from electronic health records (EHR) that facilitates research in antimicrobial resistance (AMR). ARMD encompasses big data from adult patients collected from over 15 years at two academic-affiliated hospitals, focusing on microbiological cultures, antibiotic susceptibilities, and associated clinical and demographic features. Key attributes include organism identification, susceptibility patterns for 55 antibiotics, implied susceptibility rules, and de-identified patient information. This dataset supports studies on antimicrobial stewardship, causal inference, and clinical decision-making. ARMD is designed to be reusable and interoperable, promoting collaboration and innovation in combating AMR. This paper describes the dataset's acquisition, structure, and utility while detailing its de-identification process.

This study addresses from the Optimal Experimental Design perspective the use of the isothermal experimentation procedure to precisely estimate the parameters defining models used in predictive microbiology. Starting from a case study set out in the literature, and taking the Baranyi model as the primary model, and the Ratkowsky square-root model as the secondary, D- and c-optimal designs are provided for isothermal experiments, taking the temperature both as a value fixed by the experimenter and as a variable to be designed. The designs calculated show that those commonly used in practice are not efficient enough to estimate the parameters of the secondary model, leading to greater uncertainty in the predictions made via these models. Finally, an analysis is carried out to determine the effect on the efficiency of the possible reduction in the final experimental time.

The SSPACE Astrobiology Payload (SAP) series, starting with the SAP-1 project is designed to conduct in-situ microbiology experiments in low earth orbit. This payload series aims to understand the behaviour of microbial organisms in space, particularly those critical for human health, and the corresponding effects due to microgravity and solar/galactic radiation. SAP-1 focuses on studying Bacillus clausii and Bacillus coagulans, bacteria beneficial to humans. It aims to provide a space laboratory for astrobiology experiments under microgravity conditions. The hardware developed for these experiments is indigenous and tailored to meet the unique requirements of autonomous microbiology experiments by controlling pressure, temperature, and nutrition flow to bacteria. A rotating platform, which forms the core design, is innovatively utilised to regulate the flow and mixing of nutrients with dormant bacteria. The technology demonstration models developed at SSPACE have yielded promising results, with ongoing efforts to refine, adapt for space conditions, and prepare for integration with nanosatellites or space modules. The anticipated payload will be compact, approximately 1U in size (1

Large vision-language models have achieved remarkable capabilities by training on massive internet-scale data, yet a fundamental asymmetry persists: while LLMs can leverage self-supervised pretraining on abundant text and image data, the same is not true for many behavioral modalities. Video-based behavioral data -- gestures, eye movements, social signals -- remains scarce, expensive to annotate, and privacy-sensitive. A promising alternative is simulation: replace real data collection with controlled synthetic generation to produce automatically labeled data at scale. We introduce infrastructure for this paradigm applied to eye movement, a behavioral signal with applications across vision-language modeling, virtual reality, robotics, accessibility systems, and cognitive science. We present a pipeline for generating synthetic labeled eye movement video by extracting real human iris trajectories from reference videos and replaying them on a 3D eye movement simulator via headless browser automation. Applying this to the task of script-reading detection during video interviews, we release final_dataset_v1: 144 sessions (72 reading, 72 conversation) totaling 12 hours of synthetic eye m

Microbiology culture reports contain critical information for important clinical and public health applications. However, microbiology reports often have complex, semi-structured, free-text data that present a barrier for secondary use. Here we present the development and validation of an open-source package designed to ingest free-text microbiology reports, determine whether the culture is positive, and return a list of SNOMED-CT mapped bacteria. Our rule-based natural language processing algorithm was developed using microbiology reports from two different electronic health record systems in a large healthcare organization, and then externally validated on the reports of two other institutions with manually-extracted results as a benchmark. Our algorithm achieved F-1 scores >0.95 on all classification tasks across both validation sets. Our concept extraction Python package, MicrobEx, is designed to be reused and adapted to individual institutions as an upstream process for other clinical applications, such as machine learning studies, clinical decision support, and disease surveillance systems.

Reading augmentation systems increasingly help readers process text at scale. While these tools address real constraints of time and cognitive load, they often implicitly frame reading as information transmission, or "reading to discard," delegating interpretation and effort to the machine. Yet this delegation changes the outcome of reading. For example, in scholarly reading, deciding what a research text implies and why it matters is central to the work of scholarly production. We propose creative reading as an alternative goal: reading augmentation that supports readers in creating both readings and themselves as readers. By putting literary and narrative theories into conversation with scholarly sensemaking and creativity support, we present a provocation-oriented design space for valuing the process of reading as a way of preserving a plurality of readings and transforming readers over time.

Background knowledge is typically needed for successful comprehension of topical and domain specific reading passages, such as in the STEM domain. However, there are few automated measures of student knowledge that can be readily deployed and scored in time to make predictions on whether a given student will likely be able to understand a specific content area text. In this paper, we present our effort in developing K-tool, an automated system for generating topical vocabulary tests that measure students' background knowledge related to a specific text. The system automatically detects the topic of a given text and produces topical vocabulary items based on their relationship with the topic. This information is used to automatically generate background knowledge forms that contain words that are highly related to the topic and words that share similar features but do not share high associations to the topic. Prior research indicates that performance on such tasks can help determine whether a student is likely to understand a particular text based on their knowledge state. The described system is intended for use with middle and high school student population of native speakers of E

Educational e-book platforms provide valuable information to teachers and researchers through two main sources: reading activity data and reading content data. While reading activity data is commonly used to analyze learning strategies and predict low-performing students, reading content data is often overlooked in these analyses. To address this gap, this study proposes LECTOR (Lecture slides and Topic Relationships), a model that summarizes information from reading content in a format that can be easily integrated with reading activity data. Our first experiment compared LECTOR to representative Natural Language Processing (NLP) models in extracting key information from 2,255 lecture slides, showing an average improvement of 5% in F1-score. These results were further validated through a human evaluation involving 28 students, which showed an average improvement of 21% in F1-score over a model predominantly used in current educational tools. Our second experiment compared reading preferences extracted by LECTOR with traditional reading activity data in predicting low-performing students using 600,712 logs from 218 students. The results showed a tendency to improve the predictive p

Interpretability methods for large language models (LLMs) typically derive directions from textual supervision, which can lack external grounding. We propose using human brain activity not as a training signal but as a coordinate system for reading and steering LLM states. Using the SMN4Lang MEG dataset, we construct a word-level brain atlas of phase-locking value (PLV) patterns and extract latent axes via ICA. We validate axes with independent lexica and NER-based labels (POS/log-frequency used as sanity checks), then train lightweight adapters that map LLM hidden states to these brain axes without fine-tuning the LLM. Steering along the resulting brain-derived directions yields a robust lexical (frequency-linked) axis in a mid TinyLlama layer, surviving perplexity-matched controls, and a brain-vs-text probe comparison shows larger log-frequency shifts (relative to the text probe) with lower perplexity for the brain axis. A function/content axis (axis 13) shows consistent steering in TinyLlama, Qwen2-0.5B, and GPT-2, with PPL-matched text-level corroboration. Layer-4 effects in TinyLlama are large but inconsistent, so we treat them as secondary (Appendix). Axis structure is stable

Human Immunodeficiency Virus (HIV) has posed a major global health challenge for decades, and forecasting HIV diagnoses continues to be a critical area of research. However, capturing the complex spatial and temporal dependencies of HIV transmission remains challenging. Conventional Message Passing Neural Network (MPNN) models rely on a fixed binary adjacency matrix that only encodes geographic adjacency, which is unable to represent interactions between non-contiguous counties. Our study proposes a deep learning architecture Mobility-Aware Transformer-Message Passing Neural Network (MAT-MPNN) framework to predict county-level HIV diagnosis rates across California, Florida, and the New England region. The model combines temporal features extracted by a Transformer encoder with spatial relationships captured through a Mobility Graph Generator (MGG). The MGG improves conventional adjacency matrices by combining geographic and demographic information. Compared with the best-performing hybrid baseline, the Transformer MPNN model, MAT-MPNN reduced the Mean Squared Prediction Error (MSPE) by 27.9% in Florida, 39.1% in California, and 12.5% in New England, and improved the Predictive Mode

We propose a new method of determining regional and city boundaries based on the Valeriepieris circle, the smallest circle containing a given fraction of the data. By varying the fraction in the circle we can map complex spatial data to a simple model of concentric rings which we then fit to determine natural density cutoffs. We apply this method to population, occupation, economic and transport data from England and Wales, finding that the regions determined by this method affirm well known social facts such as the disproportionate wealth of London or the relative isolation of the North East and South West of England. We then show how different data sets give us different views of the same cities, providing insight into their development and dynamics.

To enable egocentric contextual AI in always-on smart glasses, it is crucial to be able to keep a record of the user's interactions with the world, including during reading. In this paper, we introduce a new task of reading recognition to determine when the user is reading. We first introduce the first-of-its-kind large-scale multimodal Reading in the Wild dataset, containing 100 hours of reading and non-reading videos in diverse and realistic scenarios. We then identify three modalities (egocentric RGB, eye gaze, head pose) that can be used to solve the task, and present a flexible transformer model that performs the task using these modalities, either individually or combined. We show that these modalities are relevant and complementary to the task, and investigate how to efficiently and effectively encode each modality. Additionally, we show the usefulness of this dataset towards classifying types of reading, extending current reading understanding studies conducted in constrained settings to larger scale, diversity and realism.

This paper aims to map and identify topics of interest within the field of Microbiology and identify the main sources driving such attention. We combine data from Web of Science and Altmetric.com, a platform which retrieves mentions to scientific literature from social media and other non-academic communication outlets. We focus on the dissemination of microbial publications in Twitter, news media and policy briefs. A two-mode network of social accounts shows distinctive areas of activity. We identify a cluster of papers mentioned solely by regional news media. A central area of the network is formed by papers discussed by the three outlets. A large portion of the network is driven by Twitter activity. When analyzing top actors contributing to such network, we observe that more than half of the Twitter accounts are bots, mentioning 32% of the documents in our dataset. Within news media outlets, there is a predominance of popular science outlets. With regard to policy briefs, both international and national bodies are represented. Finally, our topic analysis shows that the thematic focus of papers mentioned varies by outlet. While news media cover the wider range of topics, policy b

For more than 3.5 billion years, life experienced dramatic environmental extremes on Earth. These include shifts from oxygen-less to over-oxygenated atmospheres and cycling between hothouse conditions and global glaciations. Meanwhile, an ecological revolution took place. The planet evolved from one dominated by microbial life to one containing the plants and animals that are most familiar today. The activities of many key cellular inventions evolved early in the history of life, collectively defining the nature of our biosphere and underpinning human survival. There is a critical need for a new disciplinary synthesis to reveal how microbes and their molecular systems survived ever changing global conditions over deep time. This review critically examines our current understanding of early microbial life and describes the foundations of an emerging area in microbiology and evolutionary synthetic biology to reconstruct the earliest microbial innovations.

Microbiology is the science of microbes, particularly bacteria. Many bacteria are motile: they are capable of self-propulsion. Among these, a significant class execute so-called run-and-tumble motion: they follow a fairly straight path for a certain distance, then abruptly change direction before repeating the process. This dynamics has something in common with Brownian motion (it is diffusive at large scales), and also something in contrast. Specifically, motility parameters such as the run speed and tumble rate depend on the local environment and hence can vary in space. When they do so, even if a steady state is reached, this is not generally invariant under time-reversal: the principle of detailed balance, which restores the microscopic time-reversal symmetry of systems in thermal equilibrium, is mesoscopically absent in motile bacteria. This lack of detailed balance (allowed by the flux of chemical energy that drives motility) creates pitfalls for the unwary modeller. Here I review some statistical mechanical models for bacterial motility, presenting them as a paradigm for exploring diffusion without detailed balance. I also discuss the extent to which statistical physics is u

The observation of neuron-like behaviour in bacteria, such as the occurrence of electric spiking and extended bioelectric signalling, points to the role of membrane dynamics in prokaryotes. Electrophysiology of bacteria, however, has been overlooked for long time, due to the difficulties in monitoring bacterial bioelectric phenomena with those probing techniques that are commonly used for eukaryotes. Optical technologies can allow a paradigm shift in the field of electrophysiology of bacteria, as they would permit to elicit and monitor signalling rapidly, remotely and with high spatiotemporal precision. In this perspective, we discuss about the potentiality of light interrogation methods in microbiology, encouraging the development of all-optical electrophysiology of bacteria.