Bichar Dip Shrestha Gurung

Urban wastewater microbiomes are complex and temporally dynamic, offering valuable insight into community-scale microbial ecology and potential public health trends. However, existing wastewater-based studies often remain descriptive, lacking tools for predictive modeling. In this study, we introduce a digital twin framework that forecasts microbial abundance trajectories in urban wastewater using an interpretable generative model, Q-net. Trained on a 30-week longitudinal metagenomic dataset from seven wastewater treatment plants, the model captures temporal microbial dynamics with high fidelity (R ² > 0.97 for key taxa; R ² = 0.998 at the final timepoint). Beyond accurate forecasting, Q-net provides transparent model structure through conditional inference trees and enables simulation of realistic microbial trends under hypothetical scenarios. This work demonstrates the potential of digital twins to move wastewater microbiome studies from static snapshots to dynamic, predictive systems, with broad implications for environmental monitoring and microbial ecosystem modeling.

In an environment, microbes often work in communities to achieve most of their essential functions, including the production of essential nutrients. Microbial biofilms are communities of microbes that attach to a nonliving or living surface by embedding themselves into a self-secreted matrix of extracellular polymeric substances. These communities work together to enhance their colonization of surfaces, produce essential nutrients, and achieve their essential functions for growth and survival. They often consist of diverse microbes including bacteria, viruses, and fungi. Biofilms play a critical role in influencing plant phenotypes and human microbial infections. Understanding how these biofilms impact plant health, human health, and the environment is important for analyzing genotype–phenotype-driven rule-of-life functions. Such fundamental knowledge can be used to precisely control the growth of biofilms on a given surface. Metagenomics is a powerful tool for analyzing biofilm genomes through function-based gene and protein sequence identification (functional metagenomics) and sequence-based function identification (sequence metagenomics). Metagenomic sequencing enables a comprehensive sampling of all genes in all organisms present within a biofilm sample. However, the complexity of biofilm metagenomic study warrants the increasing need to follow the Findability, Accessibility, Interoperability, and Reusable (FAIR) Guiding Principles for scientific data management. This will ensure that scientific findings can be more easily validated by the research community. This study proposes a dockerized, self-learning bioinformatics workflow to increase the community adoption of metagenomics toolkits in a metagenomics and meta-transcriptomics investigation. Our biofilm metagenomics workflow self-learning module includes integrated learning resources with an interactive dockerized workflow. This module will allow learners to analyze resources that are beneficial for aggregating knowledge about biofilm marker genes, proteins, and metabolic pathways as they define the composition of specific microbial communities. Cloud and dockerized technology can allow novice learners—even those with minimal knowledge in computer science—to use complicated bioinformatics tools. Our cloud-based, dockerized workflow splits biofilm microbiome metagenomics analyses into four easy-to-follow submodules. A variety of tools are built into each submodule. As students navigate these submodules, they learn about each tool used to accomplish the task. The downstream analysis is conducted using processed data obtained from online resources or raw data processed via Nextflow pipelines. This analysis takes place within Vertex AI’s Jupyter notebook instance with R and Python kernels. Subsequently, results are stored and visualized in Google Cloud storage buckets, alleviating the computational burden on local resources. The result is a comprehensive tutorial that guides bioinformaticians of any skill level through the entire workflow. It enables them to comprehend and implement the necessary processes involved in this integrated workflow from start to finish. This manuscript describes the development of a resource module that is part of a learning platform named ”NIGMS Sandbox for Cloud-based Learning” https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.

Characterizing defects in 2D materials, such as cracks in chemical vapor deposited (CVD)-grown hexagonal boron nitride (hBN), is essential for evaluating material quality and reliability. Traditional characterization methods are often time-consuming and subjective and can be hindered by the limited optical contrast of hBN. To address this, we utilized a YOLOv8n deep learning model for automated crack detection in transferred CVD-grown hBN films, using MATLAB’s Image Labeler and Supervisely for meticulous annotation and training. The model demonstrates promising crack-detection capabilities, accurately identifying cracks of varying sizes and complexities, with loss curve analysis revealing progressive learning. However, a trade-off between precision and recall highlights the need for further refinement, particularly in distinguishing fine cracks from multilayer hBN regions. This study demonstrates the potential of ML-based approaches to streamline 2D material characterization and accelerate their integration into advanced devices.

In the rapidly evolving field of artificial intelligence, the ability to harness and integrate knowledge across various domains stands as a paramount challenge and opportunity. This study introduces a novel approach to cross-domain knowledge discovery through the deployment of multi-AI agents, each specialized in distinct knowledge domains. These AI agents, designed to function as domain-specific experts, collaborate in a unified framework to synthesize and provide comprehensive insights that transcend the limitations of single-domain expertise. By facilitating seamless interaction among these agents, our platform aims to leverage the unique strengths and perspectives of each, thereby enhancing the process of knowledge discovery and decision-making. We present a comparative analysis of the different multi-agent workflow scenarios evaluating their performance in terms of efficiency, accuracy, and the breadth of knowledge integration. Through a series of experiments involving complex, interdisciplinary queries, our findings demonstrate the superior capability of domain specific multi-AI agent system in identifying and bridging knowledge gaps. This research not only underscores the significance of collaborative AI in driving innovation but also sets the stage for future advancements in AI-driven, cross-disciplinary research and application. Our methods were evaluated on a small pilot data and it showed a trend we expected, if we increase the amount of data we custom train the agents, the trend is expected to be more smooth.

Keywords play a crucial role in bridging the gap between human understanding and machine processing of textual data. They are essential to data enrichment because they form the basis for detailed annotations that provide a more insightful and in-depth view of the underlying data. Keyword/domain driven term extraction is a pivotal task in natural language processing, facilitating information retrieval, document summarization, and content categorization. This review focuses on keyword extraction methods, emphasizing the use of three major Large Language Models(LLMs): Llama2-7B, GPT-3.5, and Falcon-7B. We employed a custom Python package to interface with these LLMs, simplifying keyword extraction. Our study, utilizing the Inspec and PubMed datasets, evaluates the performance of these models. The Jaccard similarity index was used for assessment, yielding scores of 0.64 (Inspec) and 0.21 (PubMed) for GPT-3.5, 0.40 and 0.17 for Llama2-7B, and 0.23 and 0.12 for Falcon-7B. This paper underlines the role of prompt engineering in LLMs for better keyword extraction and discusses the impact of hallucination in LLMs on result evaluation. It also sheds light on the challenges in using LLMs for keyword extraction, including model complexity, resource demands, and optimization techniques.

Microbial corrosion, scientifically referred to as microbial-induced corrosion (MIC), constitutes a noteworthy and frequently underestimated concern within diverse industrial domains. This phenomenon manifests when microorganisms, including bacteria, archaea, and fungi, engage with structural materials, resulting in the degradation of infrastructure and equipment. The accurate prognostication of material microbial corrosion rates is of upmost importance in the formulation of proactive strategies for maintenance and corrosion control. In this study, a novel methodology is introduced, which harnesses the capabilities of XGBoost, an advanced gradient boosting algorithm, for the precise prediction of material microbial corrosion rates. This predictive process is facilitated by employing tabular data that is intricately embedded within a comprehensive large language models (LLMs). The integration of tabular data into the language model yields a sophisticated contextual comprehension of the data, thereby augmenting the model's precision by its aptitude to discern intricate relationships and semantic nuances intrinsic to the tabular data.

The ChemoReceptor-Effector Interaction Database (CREID) is a collection of bacterial chemoreceptor and effector protein and interaction data to understand the process that chemoreceptors and effectors play in various environments. Our website includes terms associated with chemosensory pathways to educate users and those involved in collaborative research to help them understand this complex biological network. It includes 2,440 proteins involved in chemoreceptor and effector systems from 7 different bacterial families with 1,996 chemoeffector interactions. It is available at https://react-creid.bicbioeng.org. Key Highlights CREID links bacterial chemoreceptors with their associated effectors. Researchers interested in what attracts or repels bacteria can use CREID as a comprehensive source for information. Biosensor developers can leverage CREID to discover better interactions for their applications. CREID reveals knowledge gaps in chemoreceptor-effector interactions for both model and non-model organisms.