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arXiv 2025年

作者： Reyes, Jorge Dunkel, Jörn Program in Computational and Systems Biology Massachusetts Institute of Technology CambridgeMA02139 United States Department of Mathematics Massachusetts Institute of Technology CambridgeMA02139 United States

Chemical reaction networks underpin biological and physical phenomena across scales, from microbial interactions to planetary atmosphere dynamics. Bacterial communities exhibit complex competitive interactions for resources, human organs and tissues demonstrate specialized biochemical functions, and planetary atmospheres are capable of displaying diverse organic and inorganic chemical processes. Despite their complexities, comparing these networks methodically remains a challenge due to the vast underlying degrees of freedom. In biological systems, comparative genomics has been pivotal in tracing evolutionary trajectories and classifying organisms via DNA sequences. However, purely genomic classifications often fail to capture functional roles within ecological systems. Metabolic changes driven by nutrient availability highlight the need for classification schemes that integrate metabolic information. Here we introduce and apply a computational framework for a classification scheme of organisms that compares matrix representations of chemical reaction networks using the Grassmann distance, corresponding to measuring distances between the fundamental subspaces of stoichiometric matrices. Applying this framework to human gut microbiome data confirms that metabolic distances are distinct from phylogenetic distances, underscoring the limitations of genetic information in metabolic classification. Importantly, our analysis of metabolic distances reveals functional groups of organisms enriched or depleted in specific metabolic processes and shows robustness to metabolically silent genetic perturbations. The generalizability of metabolic Grassmann distances is illustrated by application to chemical reaction networks in human tissue and planetary atmospheres, highlighting its potential for advancing functional comparisons across diverse chemical reaction systems. © 2025, CC BY-NC-ND.

关键词： Earth atmosphere

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Decay rates of optical modes unveiling the island structures in mixed phase space

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Physical Review A 2025年第3期111卷 033509-033509页

作者： Chang-Hwan Yi Barbara Dietz Jae-Ho Han Jung-Wan Ryu Center for Theoretical Physics of Complex Systems IBS Daejeon 34126 Korea Basic Science Program Korea University of Science and Technology (UST) Daejeon 34113 Korea Department of Physics Korea Advanced Institute of Science and Technology (KAIST) Daejeon 34141 Korea

We explore the decay rates of optical modes in asymmetric microcavities with mixed phase space across a wide range of wavelengths that extend deep into the semiclassical, i.e., short-wavelength, limit. Implementing an efficient numerical method, we computed 106 eigenmodes and discovered that certain decay rates form sequential separate branches with increasing wave number that eventually merge into smooth curves. The analysis of the localization properties and Husimi distributions reveals that each branch corresponds to a periodic orbit in the closed classical system. Our findings show that these decay rates gradually resolve the structure of the islands in mixed phase space as we approach the short-wavelength limit. We present an effective semiclassical model incorporating wave-number-dependent localization, Fresnel reflection, and the Goos-Hänchen shift and demonstrate that these effects are crucial in accounting for the observed branches of decay rate curves.

关键词： Microcavities

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Hybrid IT Project Management Methodology Based on Best Practices of Project Management and Critical Success Factors Influencing IT Project Management 8th

Hybrid IT Project Management Methodology Based on Best Pract...

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8th International Conference on Intelligent Technologies, ICIT 2023

作者： Hayashida-Marchinares, Augusto Herrera, Jose Rivera, Luis Rodriguez, Ciro Rodriguez Krupa, Miroslav Ph. D. Program of the Faculty of Systems Engineering and Informatics Universidad Nacional Mayor de San Marcos Lima Peru Laboratory of Mathematical Sciences Center of Sciences and Technologies Universidade Estadual Do Norte Fluminense-UENF Rio de Janeiro Brazil Department of Management Faculty of Business Administration Prague University of Economics and Business Prague Czech Republic

ISBN: (纸本)9789819738588

Information Technology (IT) project management is important for the growth of organizations. It involves planning and executing projects to achieve strategic objectives. This paper reviews IT project management methodologies and critical success factors to identify best practices for project success. This paper uses a literature review and analysis of the current state of the art of IT project management methodologies. A total of 39 articles were selected and reviewed. The results of the review include a comparison of the main IT project management methodologies and the critical success factors for project success. The conclusion of the paper is that Hybrid Project Management Models are a promising approach for IT project management. This approach combines the foundations and best practices of traditional and agile project management methodologies, making it well-suited for the complex and dynamic nature of IT projects. Additionally, the paper identifies the following critical success factors for IT project success: Clear and well-defined project objectives, Effective communication and collaboration between stakeholders, Appropriate risk management and contingency planning, Strong leadership and project management skills and Adequate resources and support. By understanding and addressing these critical success factors, organizations can increase their chances of success in IT projects. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2025.

关键词： Project management

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Emerging Techniques in Spatial Multiomics: Fundamental Principles and Applications to Dermatology

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Journal of Investigative Dermatology 2025年第5期145卷 1017-1032页

作者： Jia, Bojing B. Sun, Bryan K. Lee, Ernest Y. Ren, Bing Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA United States Medical Scientist Training Program University of California San Diego La Jolla CA United States Department of Dermatology University of California Irvine Irvine CA United States Department of Dermatology University of California San Francisco San Francisco CA United States Center for Epigenomics Department of Cellular & Molecular Medicine University of California San Diego La Jolla CA United States Institute of Genomic Medicine Moores Cancer Center School of Medicine University of California San Diego La Jolla CA United States

Molecular pathology, such as high-throughput genomic and proteomic profiling, identifies precise disease targets from biopsies but require tissue dissociation, losing valuable histologic and spatial context. Emerging spatial multi-omic technologies now enable multiplexed visualization of genomic, proteomic, and epigenomic targets within a single tissue slice, eliminating the need for labeling multiple adjacent slices. Although early work focused on RNA (spatial transcriptomics), spatial technologies can now concurrently capture DNA, genome accessibility, histone modifications, and proteins with spatially-resolved single-cell resolution. This review outlines the principles, advantages, limitations, and potential for spatial technologies to advance dermatologic research. By jointly profiling multiple molecular channels, spatial multiomics enables novel studies of copy number variations, clonal heterogeneity, and enhancer dysregulation, replete with spatial context, illuminating the skin's complex heterogeneity. © 2024 The Authors

关键词： Dermatopathology Digital pathology Multiomics Multiplexed imaging Spatial sequencing

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Improving LED-Based Photoacoustic Image Quality Using an Optimized Deconvolution Technique

Improving LED-Based Photoacoustic Image Quality Using an Opt...

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Photons Plus Ultrasound: Imaging and Sensing 2025

作者： Ogawa, Ryuhei Sato, Naoto Saito, Atsushi Singh, Mithun Kuniyil Ajith Kawamoto, Hiroaki Sankai, Yoshiyuki Master’s Program in Intelligent and Mechanical Interaction Systems University of Tsukuba Tsukuba Japan Research & Development Division Cyberdyne Inc. Tsukuba Japan Research & Business Development Division Cyberdyne Inc. Rotterdam Netherlands Institute of Systems and Information Engineering University of Tsukuba Tsukuba Japan

ISBN: (纸本)9781510683860

LED-based photoacoustic imaging (PAI) with linear array ultrasound probes has gained attention due to its cost-effectiveness, safety, and potential for portable applications. However, its low signal-to-noise ratio (SNR) and limited visibility of blood vessel lumens remain challenges. To address these issues, we propose an innovative deconvolution approach that leverages the differential of the LED light pulse to enhance photoacoustic image quality. Our optimized reconstruction algorithm improves blood vessel visualization by applying deconvolution of the PA signals with the differential of the LED pulse, leading to improved lumen visibility and enhanced imaging of peripheral blood vessels in both 2D and potentially 3D. Our method precisely measures the LED pulse profile using the LED arrays integrated into our AcousticX system. The second differential of this pulse is then utilized as the point spread function (PSF) in the deconvolution process. This technique effectively enhances PA signals by emphasizing the leading and trailing edges of the pulse, thereby improving blood vessel visibility and overall image quality. To validate our approach, we conducted experiments using tissue-mimicking phantoms and human volunteers with the AcousticX system. The algorithm was tested offline in MATLAB and in real-time on the AcousticX platform. Results demonstrate substantial artifact suppression, improved SNR, and enhanced image contrast, ultimately enabling clearer visualization of the blood vessels. This advancement improves the competitiveness of LED-based PAI systems compared to laser-based alternatives and broadens their potential for clinical applications, accelerating their translation into medical practice. © 2025 SPIE.

关键词： Ultrasonic imaging

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Thévenin Network Approach for Modeling Mutual Coupling in Narrowband Uniform Linear Arrays

Thévenin Network Approach for Modeling Mutual Coupling in N...

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IEEE Latin American Symposium on Circuits and systems (LASCAS)

作者： José A. Apolinário Cláudio A. B. Saunders Filho Antonio L. L. Ramos Program of Electrical Engineering Military Institute of Engineering (IME) Rio de Janeiro Brazil Department of Science and Industry Systems (IRI) TNM University of South-Eastern Norway (USN) Kongsberg Norway

ISBN: (数字)9798331522124

ISBN: (纸本)9798331522131

This paper investigates mutual coupling in narrow-band uniform linear antenna arrays through Thévenin network modeling. After an in-depth analysis, we derive a Thévenin network representing a given mutual coupling matrix and develop a method to achieve an equivalent decoupled model that significantly reduces computational and memory requirements in practical applications.

关键词： Mutual coupling Analytical models Circuits and systems Array signal processing Computational modeling Memory management Linear antenna arrays Integrated circuit modeling Narrowband

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Mental Status Identification for Infertile Patients Using Artificial Intelligence Models 14th

Mental Status Identification for Infertile Patients Using Ar...

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14th International Conference on Frontier Computing, FC 2024

作者： Hsu, Hao-Siang Wang, Jong-Yi Chiou, Hai-Chi Wu, Fu-Hsing Lin, Chuen-Horng Chan, Yung‑Kuan Department of Computer Science and Information Engineering National Taichung University of Science and Technology Taichung404336 Taiwan Department of Health Services Administration China Medical University Taichung406040 Taiwan Bachelor Degree Program of Artificial Intelligence National Taichung University of Science and Technology Taichung404336 Taiwan Department of Management Information Systems National Chung-Hsing University Taichung402202 Taiwan

ISBN: (纸本)9789819623945

Infertile patients may be a high-risk group of mental disorder. The precise identification of the mental status of infertile patients can provide decision support to healthcare professionals and may be helpful in providing preventive measures accordingly. Rare studies focused on the mental status identification using artificial intelligence (AI) models for infertile people. This study aimed to precisely identify the mental status (anxiety and depression) of infertile patients using three AI models, the XGBoost, decision tree, and stacking models. The dataset, retrieved from a structured questionnaire survey in 2011, which included 400 infertility outpatients seeking reproductive treatments at three teaching hospitals in Taiwan was adopted for training and testing AI models. Aforementioned AI models were designed and reached identification performances of accuracy, precision, recall and area under ROC curve (AUC) equaling 0.75–0.82, 0.70–0.80, 0.64–0.72, and 0.64–0.72, respectively. The XGBoost model (accuracy = 0.82, precision = 0.80, recall = 0.72, and AUC = 0.72) outperformed or equaled the decision tree and stacking models in terms of accuracy, precision, recall, and AUC values. Designed AI models for mental status identification can be integrated into the clinical decision support system (CDSS) to provide the anxiety and depression group automatically. Accordingly, the worsening of infertility-related anxiety and depression can be prevented. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2025.

关键词： artificial intelligence infertile patients Mental status identification stacking model XGBoost

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Comparison of Histomorphometric Aspects between Oral Lichen Planus Lesions and Oral Lichenoid Lesions

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Head and neck pathology 2025年第1期19卷 61页

作者： Ana Carla Barletta Sanches Juliana Santos de Jesus Azevedo Liliana Aparecida Pimenta-Barros Valéria Souza Freitas Danielle Resende Camisasca Gabriela Botelho Martins Postgraduate Program in Interactive Processes of Organs and Systems of the Institute of Health Sciences of the Federal University of Bahia Bahia Brazil. anacarlabarletta@***. Postgraduate Program in Interactive Processes of Organs and Systems of the Institute of Health Sciences of the Federal University of Bahia Bahia Brazil. PhD in Oral Pathology from the University of São Paulo Full Professor at the Federal University of Espírito Santo Professor of the Postgraduate Program in Dental Sciences at the Federal University of Espírito Santo Vitória Espírito Santo Brazil. PhD in Oral Pathology from the Federal University of Rio Grande do Norte Adjunct Professor at the State University of Feira de Santana Professor of the Postgraduate Program in Public Health at the State University of Feira de Santana Bahia Brazil. PhD in Pathology from the Fluminense Federal University Associate Professor at the Federal University of Espírito Santo Espírito Santo Brazil. Professor of the Postgraduate Program in Dental Sciences at the Federal University of Espírito Santo Vitória Espírito Santo Brazil. PhD in Clinical Stomatology from the Pontifical Catholic University of Rio Grande do Sul Associate Professor at the Multidisciplinary Institute of Rehabilitation and Health of the Federal University of Bahia Bahia Brazil. Professor of the Postgraduate Program in Interactive Processes of Organs and Systems of the Institute of Health Sciences of the Federal University of Bahia Bahia Brazil.

INTRODUCTION:Oral lichen planus (OLP) and oral lichenoid lesions (OLL) are considered potentially malignant oral disorders, presenting with similar clinical and histopathological manifestations that make differential diagnosis difficult and reinforce the need for new techniques for their evaluation. OBJECTIVE:This study aimed to compare the histomorphometric characteristics of OLP and OLL. METHODOLOGY:This retrospective cross-sectional study was based on 30 histological sections of incisional biopsies of OLP and OLL stained with hematoxylin-eosin for the analysis of morphological parameters, such as keratosis, acanthosis, inflammatory infiltrate band, eosinophilic band, degeneration of the basal layer, involvement of the epithelium-chorion interface, and degree of subepithelial inflammatory infiltrate; and morphometric parameters, such as keratin thickness, distance from the basal layer to the epithelial surface, and thickness of the inflammatory infiltrate band. Chi-square and Fisher's exact tests were used to compare categorical variables and injury types. The t-test was used to compare morphometric variables between the two types of injury. RESULTS:There was no significant association between the type of lesion and the clinical characteristics of the patients (p > 0.05). The degree of dysplasia, used as an inclusion criterion, was associated with lesion type (p = 0.0003). There were no significant differences between the morphometric variables evaluated for the two types of lesions (p > 0.05). CONCLUSION:Based on the methodology used and the sample established for this study, there were clinical and histomorphometric similarities between OLP and OLL. This justifies further discussion on whether these lesions are a spectrum of presentations of the same condition or truly distinct conditions.

关键词： Epithelium Inflammation Morphological and microscopic findings Oral lichen planus

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Lessons from national biobank projects utilizing whole-genome sequencing for population-scale genomics

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Genomics and Informatics 2025年第1期23卷 1-16页

作者： Lee, Hyeji Kim, Wooheon Kwon, Nahyeon Kim, Chanhee Kim, Sungmin An, Joon-Yong Department of Integrated Biomedical and Life Science Korea University Seoul 02841 South Korea L-HOPE Program for Community-Based Total Learning Health Systems Korea University Seoul 02841 South Korea School of Biosystem and Biomedical Science College of Health Science Korea University Seoul 02841 South Korea Division of Genome Science Department of Precision Medicine National Institute of Health Cheongju 28159 South Korea

Large-scale national biobank projects utilizing whole-genome sequencing have emerged as transformative resources for understanding human genetic variation and its relationship to health and disease. These initiatives, which include the UK Biobank, All of Us Research program, Singapore’s PRECISE, Biobank Japan, and the National Project of Bio-Big Data of Korea, are generating unprecedented volumes of high-resolution genomic data integrated with comprehensive phenotypic, environmental, and clinical information. This review examines the methodologies, contributions, and challenges of major WGS-based national genome projects worldwide. We first discuss the landscape of national biobank initiatives, highlighting their distinct approaches to data collection, participant recruitment, and phenotype characterization. We then introduce recent technological advances that enable efficient processing and analysis of large-scale WGS data, including improvements in variant calling algorithms, innovative methods for creating multi-sample VCFs, optimized data storage formats, and cloud-based computing solutions. The review synthesizes key discoveries from these projects, particularly in identifying expression quantitative trait loci and rare variants associated with complex diseases. Our review introduces the latest findings from the National Project of Bio-Big Data of Korea, which has advanced our understanding of population-specific genetic variation and rare diseases in Korean and East Asian populations. Finally, we discuss future directions and challenges in maximizing the impact of these resources on precision medicine and global health equity. This comprehensive examination demonstrates how large-scale national genome projects are revolutionizing genetic research and healthcare delivery while highlighting the importance of continued investment in diverse, population-specific genomic resources. © The Author(s) 2025.

关键词： Biobank Multi-omics integration Population genetics Precision medicine Whole-genome sequencing

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Deep Learning-Based Residual Useful Lifetime Prediction for Assets With Uncertain Failure Modes

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Journal of Computing and Information Science in Engineering 2025年第4期25卷 041002页

作者： Su, Yuqi Fang, Xiaolei Operations Research Graduate Program North Carolina State University 915 Partners Way Raleigh NC 27607 Edward P. Fitts Department of Industrial and Systems Engineering North Carolina State University 915 Partners Way Raleigh NC 27607

Industrial prognostics focuses on utilizing degradation signals to forecast and continually update the residual useful life of complex engineering systems. However, existing prognostic models for systems with multiple failure modes face several challenges in real-world applications, including overlapping degradation signals from multiple components, the presence of unlabeled historical data, and the similarity of signals across different failure modes. To tackle these issues, this research introduces two prognostic models that integrate the mixture (log)-location-scale distribution with deep learning. This integration facilitates the modeling of overlapping degradation signals, eliminates the need for explicit failure mode identification, and utilizes deep learning to capture complex nonlinear relationships between degradation signals and residual useful lifetimes. Numerical studies validate the superior performance of these proposed models compared to existing methods.

关键词： Failure mechanisms mixture (log)-location-scale distribution Failure Weibull distribution multiple failure modes Signals Service life (Equipment) prognostics data analytics Deep learning machine learning for engineering applications Engineering systems and industry applications industrial Internet of things big data and analytics

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