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Ciwars: A Web Server for Antibiotic Resistance Surveillance Using Longitudinal Metagenomic Data

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SSRN

SSRN 2024年

作者： Emon, Muhit Islam Cheung, Yat Fei Stoll, James Rumi, Monjura Afrin Brown, Connor Choi, Joung Min Moumi, Nazifa Ahmed Ahmed, Shafayat Song, Haoqiu Sein, Justin Yao, Shunyu Khan, Ahmad Gupta, Suraj Kulkarni, Rutwik Butt, Ali Vikesland, Peter Pruden, Amy Zhang, Liqing Department of Computer Science Virginia Tech BlacksburgVA24060 United States Fralin Life Science Institute Virginia Tech BlacksburgVA24060 United States Department of Civil and Environmental Engineering Virginia Tech BlacksburgVA24060 United States The Interdisciplinary PhD Program in Genetics Bioinformatics and Computational Biology Virginia Tech BlacksburgVA24060 United States

The rise of antibiotic resistance (AR) poses substantial threats to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate continuous AR monitoring through longitudinal metagenomic data are lacking. To address this, we introduce Cyberinfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive ARG and taxonomic profiling, along with detection of anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and demonstrates its potential for informing effective and timely interventions to mitigate the spread and transmission of AR. CIWARS is broadly applicable to longitudinal metagenomic data from any environment and thus could be a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use when it is needed. The web server is freely available at https://***/. © 2024, The Authors. All rights reserved.

关键词： Gene encoding

COEM: Cross-Modal Embedding for MetaCell Identification

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arXiv 2022年

作者： Mao, Haiyi Jia, Minxue Dou, Jason Xiaotian Zhang, Haotian Benos, Panayiotis V. Department of Computational and Systems Biology University of Pittsburgh PA United States Joint Carnegie Mellon University University of Pittsburgh PhD Program in Computational Biology United States Department of Electrical and Computer Engineering University of Pittsburgh PA United States

Metacells are disjoint and homogeneous groups of single-cell profiles, representing discrete and highly granular cell states. Existing metacell algorithms tend to use only one modality to infer metacells, even though single-cell multi-omics datasets profile multiple molecular modalities within the same cell. Here, we present Cross-MOdal Embedding for MetaCell Identification (COEM), which utilizes an embedded space leveraging the information of both scATAC-seq and scRNA-seq to perform aggregation, balancing the trade-off between fine resolution and sufficient sequencing coverage. COEM outperforms the state-of-the-art method SEACells by efficiently identifying accurate and well-separated metacells across datasets with continuous and discrete cell types. Furthermore, COEM significantly improves peak-to-gene association analyses, and facilitates complex gene regulatory inference tasks. © 2022, CC BY.

关键词： Embeddings

CIWARS: A Web Server for Antibiotic Resistance Surveillance Using Longitudinal Metagenomic Data

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Journal of Molecular Biology 2025年第15期437卷

作者： Emon, Muhit Islam Cheung, Yat Fei Stoll, James Rumi, Monjura Afrin Brown, Connor Choi, Joung Min Moumi, Nazifa Ahmed Ahmed, Shafayat Song, Haoqiu Sein, Justin Yao, Shunyu Khan, Ahmad Gupta, Suraj Kulkarni, Rutwik Butt, Ali Vikesland, Peter Pruden, Amy Zhang, Liqing Department of Computer Science Virginia Tech Blacksburg 24060 VA United States Fralin Life Science Institute Virginia Tech Blacksburg 24060 VA United States Department of Civil and Environmental Engineering Virginia Tech Blacksburg 24060 VA United States The Interdisciplinary PhD Program in Genetics Bioinformatics and Computational Biology Virginia Tech Blacksburg 24060 VA United States

The rise of antibiotic resistance (AR) poses a substantial threat to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate analysis of longitudinal metagenomic data are lacking. To address this, we introduce CyberInfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive profiling of ARGs and taxonomic profiling of pathogen-associated bacterial taxonomic groups, identifies potential associations of ARGs with mobile genetic elements (MGEs) and pathogen-containing taxa, and assesses resistome risk based on the co-occurrence of ARGs, MGEs, and pathogen-like sequences. Additionally, it detects anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and can serve as a tool to inform effective and timely interventions to mitigate the spread and transmission of AR. Here, CIWARS is demonstrated using longitudinal metagenomic data from a wastewater treatment plant (WWTP) influent and effluent, but it can be extended to any environment. CIWARS provides a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use. The web server is freely available at https://***/. © 2025 Elsevier Ltd

关键词： anomaly detection antibiotic resistance (AR) AR indicator profiling longitudinal metagenomics wastewater-based surveillance

Precision medicine: Beyond AI

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computer Methods and programs in Biomedicine Update 2024年 5卷

作者： Filetti, Marco Petti, Manuela Farina, Lorenzo Phase 1 Unit Fondazione Policlinico Universitario Agostino Gemelli IRCCS Rome Italy Department of Experimental Medicine Sapienza University of Rome Rome Italy Department of Computer Control Management Engineering Sapienza University of Rome Via Ariosto 25 Rome 00185 Italy PhD. Program in “network oncology and precision medicine” Sapienza University of Rome Italy

Probabilistic Genotype-Phenotype Maps Reveal Mutational Robustness of RNA Folding, Spin Glasses, and Quantum Circuits

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arXiv 2023年

作者： Sappington, Anna Mohanty, Vaibhav Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States Program for Health Sciences and Technology Harvard Medical School BostonMA02115 United States Massachusetts Institute of Technology CambridgeMA02139 United States Harvard/MIT MD-PhD Program Harvard Medical School BostonMA02115 United States Department of Chemistry and Chemical Biology Harvard University CambridgeMA02138 United States

Recent studies of genotype-phenotype (GP) maps have reported universally enhanced phenotypic robustness to genotype mutations, a feature essential to evolution. Virtually all of these studies make a simplifying assumption that each genotype—represented as a sequence—maps deterministically to a single phenotype, such as a discrete structure. Here, we introduce probabilistic genotype-phenotype (PrGP) maps, where each genotype maps to a vector of phenotype probabilities, as a more realistic and universal language for investigating robustness in a variety of physical, biological, and computational systems. We study three model systems to show that PrGP maps offer a generalized framework which can handle uncertainty emerging from various physical sources: (1) thermal fluctuation in RNA folding, (2) external field disorder in spin glass ground state finding, and (3) superposition and entanglement in quantum circuits, which are realized experimentally on IBM quantum computers. In all three cases, we observe a novel biphasic robustness scaling which is enhanced relative to random expectation for more frequent phenotypes and approaches random expectation for less frequent phenotypes. We derive an analytical theory for the behavior of PrGP robustness, and we demonstrate that the theory is highly predictive of empirical robustness. © 2023, CC BY.

关键词： Quantum computers

Multiplexed Serial Imaging of Immunotherapy Response with Serrs Nanoprobes

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Multiplexed Serial Imaging of Immunotherapy Response with Se...

IEEE International Symposium on Biomedical Imaging

作者： Naxhije Berisha Konstantinos Plakas Matthieu Gigoux Taha Merghoub Chrysafis Andreou Hunter College of the City University of New York New York NY USA PhD Program in Chemistry The Graduate Center of the City University of New York NY USA Memorial Sloan Kettering Cancer Center New York NY USA Department of Chemistry University at Buffalo The State University of New York Buffalo NY USA Weill Cornell Medicine New York NY USA Department of Electrical and Computer Engineering University of Cyprus Nicosia Cyprus

ISBN: (数字)9798350313338

ISBN: (纸本)9798350313345

With the advent of new and promising cancer therapies, and with increased interest in precision medicine, there is an urgent need to develop non-invasive technologies that evaluate heterogeneity in treatment response. We demonstrate an 8-plex imaging platform based on surface enhanced resonance Raman scattering nanoparticles (SERRS NPs) to monitor the expression of 4 immunomarkers before and after treatment with checkpoint blockade therapy with anti-CTLA4 and anti-PD-1 antibodies in immunotherapy models of colon (CT26) and breast (4T1) cancers. We found that CT26 tumors showed an early treatment response, while the typically refractory 4T1 tumors demonstrated an unexpected treatment response, suggesting that the nanoparticles may have synergistically contributed to the treatment. Serial imaging of multiple markers during therapy can help predict treatment efficacy and uncover new theranostic adjuvants.

关键词： Nanoparticles Multiplexing Precision medicine Raman scattering Immunotherapy Resonance Surface treatment

A Framework for Interpretability in Machine Learning for Medical Imaging

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arXiv 2023年

作者： Wang, Alan Q. Karaman, Batuhan K. Kim, Heejong Rosenthal, Jacob Saluja, Rachit Young, Sean I. Sabuncu, Mert R. School of Electrical and Computer Engineering Cornell University Cornell Tech New YorkNY10044 United States Department of Radiology Weill Cornell Medical School New YorkNY10065 United States Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program New YorkNY10065 United States Martinos Center for Biomedical Imaging Harvard Medical School BostonMA02129 United States Computer Science and Artificial Intelligence Laboratory MIT CambridgeMA02139 United States

Interpretability for machine learning models in medical imaging (MLMI) is an important direction of research. However, there is a general sense of murkiness in what interpretability means. Why does the need for interpretability in MLMI arise? What goals does one actually seek to address when interpretability is needed? To answer these questions, we identify a need to formalize the goals and elements of interpretability in MLMI. By reasoning about real-world tasks and goals common in both medical image analysis and its intersection with machine learning, we identify five core elements of interpretability: localization, visual recognizability, physical attribution, model transparency, and actionability. From this, we arrive at a framework for interpretability in MLMI, which serves as a step-by-step guide to approaching interpretability in this context. Overall, this paper formalizes interpretability needs in the context of medical imaging, and our applied perspective clarifies concrete MLMI-specific goals and considerations in order to guide method design and improve real-world usage. Our goal is to provide practical and didactic information for model designers and practitioners, inspire developers of models in the medical imaging field to reason more deeply about what interpretability is achieving, and suggest future directions of interpretability research. © 2023, CC0.

关键词： Machine learning

From Synthetic Data to Real Palm Vein Identification: a Fine-Tuning Approach

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From Synthetic Data to Real Palm Vein Identification: a Fine...

Pattern Recognition Systems (ICPRS), International Conference on

作者： Ruber Hernández-García Edwin H. Salazar-Jurado Ricardo J. Barrientos Francisco Manuel Castro Julián Ramos-Cózar Nicolás Guil CIEAM Research Center LITRP Laboratory Universidad Católica del Maule Talca Chile DMMA PhD Program LITRP Laboratory Facultad de Ciencias Báicas Universidad Católica del Maule Talca Chile Dept. DCI Faculty of Engineering Sciences LITRP Laboratory Universidad Católica del Maule Talca Chile Dept. of Computer Architecture Universidad of Mólaga Málaga Spain

Palm vein recognition has relevant advantages in comparison with most traditional biometrics, such as high security and recognition performance. In recent years, CNN-based models for vascular biometrics have improved the state-of-the-art, but they have the disadvantage of requiring a larger number of samples for training. In this context, the generation of synthetic databases is very effective for evaluating the performance of biometric systems. The present study proposes a new perspective of a transfer learning approach for palm vein recognition, evaluating the use of Synthetic-sPVDB and NS-PVDB synthetic databases for pre-training deep learning models and validating their performance on real databases. The proposed methodology comprises two different branches as inputs. Firstly, a synthetic database is used to train a CNN model, and in the second branch, a real database is used to finetune and evaluate the performance of the resulting pre-trained model. For the feature learning process, we implemented two end-to-end CNN architectures based on AlexNet and Resnet32. The experimental results on the most representative public datasets have shown the usefulness of using palm vein synthetic images for transfer learning, outperforming the state-of-the-art results.

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Hamiltonicity via cohomology of right-angled Artin groups

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arXiv 2021年

作者： Flores, Ramón Kahrobaei, Delaram Koberda, Thomas Department of Geometry and Topology University of Seville Spain Department of Computer Science University of York United Kingdom New York University Tandon School of Engineering PhD Program in Computer Science CUNY Graduate Center Department of Mathematics University of Virginia CharlottesvilleVA22904 United States

Let Γ be a finite graph and let A(Γ) be the corresponding right-angled Artin group. We characterize the Hamiltonicity of Γ via the structure of the cohomology algebra of A(Γ). In doing so, we define and develop a new canonical graph associated to a matrix, which as a consequence provides a novel perspective on the matrix determinant. Copyright © 2021, The Authors. All rights reserved.

关键词： Topology