ArXiv Pub Date : 2024-11-22

Anwar Said, Roza G Bayrak, Tyler Derr, Mudassir Shabbir, Daniel Moyer, Catie Chang, Xenofon Koutsoukos

{"title":"NeuroGraph: Benchmarks for Graph Machine Learning in Brain Connectomics.","authors":"Anwar Said, Roza G Bayrak, Tyler Derr, Mudassir Shabbir, Daniel Moyer, Catie Chang, Xenofon Koutsoukos","doi":"","DOIUrl":"","url":null,"abstract":"Machine learning provides a valuable tool for analyzing high-dimensional functional neuroimaging data, and is proving effective in predicting various neurological conditions, psychiatric disorders, and cognitive patterns. In functional magnetic resonance imaging (MRI) research, interactions between brain regions are commonly modeled using graph-based representations. The potency of graph machine learning methods has been established across myriad domains, marking a transformative step in data interpretation and predictive modeling. Yet, despite their promise, the transposition of these techniques to the neuroimaging domain has been challenging due to the expansive number of potential preprocessing pipelines and the large parameter search space for graph-based dataset construction. In this paper, we introduce NeuroGraph, a collection of graph-based neuroimaging datasets, and demonstrated its utility for predicting multiple categories of behavioral and cognitive traits. We delve deeply into the dataset generation search space by crafting 35 datasets that encompass static and dynamic brain connectivity, running in excess of 15 baseline methods for benchmarking. Additionally, we provide generic frameworks for learning on both static and dynamic graphs. Our extensive experiments lead to several key observations. Notably, using correlation vectors as node features, incorporating larger number of regions of interest, and employing sparser graphs lead to improved performance. To foster further advancements in graph-based data driven neuroimaging analysis, we offer a comprehensive open-source Python package that includes the benchmark datasets, baseline implementations, model training, and standard evaluation.","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10690301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138479810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Foundations of a Compositional Systems Biology. 合成系统生物学的前奏。

ArXiv Pub Date : 2024-11-22

Eran Agmon

{"title":"Foundations of a Compositional Systems Biology.","authors":"Eran Agmon","doi":"","DOIUrl":"","url":null,"abstract":"Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure or dynamics of specific subsystems in controlled conditions, compositional systems biology aims to connect these models, asking critical questions about the space between models: What variables should a submodel expose through its interface? How do coupled models connect and translate across scales? How do domain-specific models connect across biological and physical disciplines to drive the synthesis of new knowledge? This approach requires robust software to integrate diverse datasets and submodels, providing researchers with tools to flexibly recombine, iteratively refine, and collaboratively expand their models. This article offers a comprehensive framework to support this vision, including: a conceptual and graphical framework to define interfaces and composition patterns; standardized schemas that facilitate modular data and model assembly; biological templates that integrate detailed submodels that connect molecular processes to the emergence of the cellular interface; and user-friendly software interfaces that empower research communities to construct and improve multiscale models of cellular systems. By addressing these needs, compositional systems biology will foster a unified and scalable approach to understanding complex cellular systems.","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11312625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DYNAMICS OF AN LPAA MODEL FOR TRIBOLIUM GROWTH: INSIGHTS INTO POPULATION CHAOS. 蒺藜生长的 LPAA 模型动力学：洞察种群混沌

ArXiv Pub Date : 2024-11-21

Samantha J Brozak, Sophia Peralta, Tin Phan, John D Nagy, Yang Kuang

{"title":"DYNAMICS OF AN LPAA MODEL FOR TRIBOLIUM GROWTH: INSIGHTS INTO POPULATION CHAOS.","authors":"Samantha J Brozak, Sophia Peralta, Tin Phan, John D Nagy, Yang Kuang","doi":"","DOIUrl":"","url":null,"abstract":"Flour beetles (genus Tribolium) have long been used as a model organism to understand population dynamics in ecological research. A rich and rigorous body of work has cemented flour beetles' place in the field of mathematical biology. One of the most interesting results using flour beetles is the induction of chaos in a laboratory beetle population, in which the well-established LPA (larvae-pupae-adult) model was used to inform the experimental factors which would lead to chaos. However, whether chaos is an intrinsic property of flour beetles remains an open question. Inspired by new experimental data, we extend the LPA model by stratifying the adult population into newly emerged and mature adults and considering cannibalism as a function of mature adults. We fit the model to longitudinal data of larvae, pupae, and adult beetle populations to demonstrate the model's ability to recapitulate the transient dynamics of flour beetles. We present local and global stability results for the trivial and positive steady states and explore bifurcations and limit cycles numerically. Our results suggest that while chaos is a possibility, it is a rare phenomenon within realistic ranges of the parameters obtained from our experiment, and is likely induced by environmental changes connected to media changes and population censusing.","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11601799/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

ACE-Net: AutofoCus-Enhanced Convolutional Network for Field Imperfection Estimation with application to high b-value spiral Diffusion MRI. ACE-Net：应用于高 b 值螺旋扩散磁共振成像的场不完善估计自动增强卷积网络。

ArXiv Pub Date : 2024-11-21

Mengze Gao, Zachary Shah, Xiaozhi Cao, Nan Wang, Daniel Abraham, Kawin Setsompop

引用次数: 0

Optically-Trapped Nanodiamond-Relaxometry Detection of Nanomolar Paramagnetic Spins in Aqueous Environments. 水环境中纳摩尔顺磁自旋的光俘获纳米钻石再axometry 检测。

ArXiv Pub Date : 2024-11-20

Shiva Iyer, Changyu Yao, Olivia Lazorik, Md Shakil Bin Kashem, Pengyun Wang, Gianna Glenn, Michael Mohs, Yinyao Shi, Michael Mansour, Erik Henriksen, Kater Murch, Shankar Mukherji, Chong Zu

{"title":"Optically-Trapped Nanodiamond-Relaxometry Detection of Nanomolar Paramagnetic Spins in Aqueous Environments.","authors":"Shiva Iyer, Changyu Yao, Olivia Lazorik, Md Shakil Bin Kashem, Pengyun Wang, Gianna Glenn, Michael Mohs, Yinyao Shi, Michael Mansour, Erik Henriksen, Kater Murch, Shankar Mukherji, Chong Zu","doi":"","DOIUrl":"","url":null,"abstract":"Probing electrical and magnetic properties in aqueous environments remains a frontier challenge in nanoscale sensing. Our inability to do so with quantitative accuracy imposes severe limitations, for example, on our understanding of the ionic environments in a diverse array of systems, ranging from novel materials to the living cell. The Nitrogen-Vacancy (NV) center in fluorescent nanodiamonds (FNDs) has emerged as a good candidate to sense temperature, pH, and the concentration of paramagnetic species at the nanoscale, but comes with several hurdles such as particle-to-particle variation which render calibrated measurements difficult, and the challenge to tightly confine and precisely position sensors in aqueous environment. To address this, we demonstrate relaxometry with NV centers within optically-trapped FNDs. In a proof of principle experiment, we show that optically-trapped FNDs enable highly reproducible nanomolar sensitivity to the paramagnetic ion, (mathrm{Gd}^{3+}). We capture the three distinct phases of our experimental data by devising a model analogous to nanoscale Langmuir adsorption combined with spin coherence dynamics. Our work provides a basis for routes to sense free paramagnetic ions and molecules in biologically relevant conditions.","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10862932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139731193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Time-resolved diamond magnetic microscopy of superparamagnetic iron-oxide nanoparticles. 超顺磁性氧化铁纳米粒子的时间分辨金刚石磁性显微镜。

ArXiv Pub Date : 2024-11-20

B A Richards, N Ristoff, J Smits, A Jeronimo Perez, I Fescenko, M D Aiello, F Hubert, Y Silani, N Mosavian, M Saleh Ziabari, A Berzins, J T Damron, P Kehayias, D L Huber, A M Mounce, M P Lilly, T Karaulanov, A Jarmola, A Laraoui, V M Acosta

{"title":"Time-resolved diamond magnetic microscopy of superparamagnetic iron-oxide nanoparticles.","authors":"B A Richards, N Ristoff, J Smits, A Jeronimo Perez, I Fescenko, M D Aiello, F Hubert, Y Silani, N Mosavian, M Saleh Ziabari, A Berzins, J T Damron, P Kehayias, D L Huber, A M Mounce, M P Lilly, T Karaulanov, A Jarmola, A Laraoui, V M Acosta","doi":"","DOIUrl":"","url":null,"abstract":"Superparamagnetic iron-oxide nanoparticles (SPIONs) are promising probes for biomedical imaging, but the heterogeneity of their magnetic properties is difficult to characterize with existing methods. Here, we perform widefield imaging of the stray magnetic fields produced by hundreds of isolated ~30-nm SPIONs using a magnetic microscope based on nitrogen-vacancy centers in diamond. By analyzing the SPION magnetic field patterns as a function of applied magnetic field, we observe substantial field-dependent transverse magnetization components that are typically obscured with ensemble characterization methods. We find negligible hysteresis in each of the three magnetization components for nearly all SPIONs in our sample. Most SPIONs exhibit a sharp Langevin saturation curve, enumerated by a characteristic polarizing applied field, B_c. The B_c distribution is highly asymmetric, with a standard deviation (1.4 mT) that is larger than the median (0.6 mT). Using time-resolved magnetic microscopy, we directly record SPION N'eel relaxation, after switching off a 31 mT applied field, with a temporal resolution of ~60 ms that is limited by the ring-down time of the electromagnet coils. For small bias fields B_{hold}=1.5-3.5 mT, we observe a broad range of SPION N'eel relaxation times--from milliseconds to seconds--that are consistent with an exponential dependence on B_{hold}. Our time-resolved diamond magnetic microscopy study reveals rich SPION sample heterogeneity and may be extended to other fundamental studies of nanomagnetism.","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11601802/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Virtual Staining of Label-Free Tissue in Imaging Mass Spectrometry. 成像质谱中的无标记组织虚拟染色。

ArXiv Pub Date : 2024-11-20

Yijie Zhang, Luzhe Huang, Nir Pillar, Yuzhu Li, Lukasz G Migas, Raf Van de Plas, Jeffrey M Spraggins, Aydogan Ozcan

{"title":"Virtual Staining of Label-Free Tissue in Imaging Mass Spectrometry.","authors":"Yijie Zhang, Luzhe Huang, Nir Pillar, Yuzhu Li, Lukasz G Migas, Raf Van de Plas, Jeffrey M Spraggins, Aydogan Ozcan","doi":"","DOIUrl":"","url":null,"abstract":"Imaging mass spectrometry (IMS) is a powerful tool for untargeted, highly multiplexed molecular mapping of tissue in biomedical research. IMS offers a means of mapping the spatial distributions of molecular species in biological tissue with unparalleled chemical specificity and sensitivity. However, most IMS platforms are not able to achieve microscopy-level spatial resolution and lack cellular morphological contrast, necessitating subsequent histochemical staining, microscopic imaging and advanced image registration steps to enable molecular distributions to be linked to specific tissue features and cell types. Here, we present a virtual histological staining approach that enhances spatial resolution and digitally introduces cellular morphological contrast into mass spectrometry images of label-free human tissue using a diffusion model. Blind testing on human kidney tissue demonstrated that the virtually stained images of label-free samples closely match their histochemically stained counterparts (with Periodic Acid-Schiff staining), showing high concordance in identifying key renal pathology structures despite utilizing IMS data with 10-fold larger pixel size. Additionally, our approach employs an optimized noise sampling technique during the diffusion model's inference process to reduce variance in the generated images, yielding reliable and repeatable virtual staining. We believe this virtual staining method will significantly expand the applicability of IMS in life sciences and open new avenues for mass spectrometry-based biomedical research.","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11601796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Omnidirectional Wireless Power Transfer for Millimetric Magnetoelectric Biomedical Implants. 毫米磁电生物医学植入物的全向无线功率传输。

ArXiv Pub Date : 2024-11-19

Wei Wang, Zhanghao Yu, Yiwei Zou, Joshua E Woods, Prahalad Chari, Yumin Su, Jacob T Robinson, Kaiyuan Yang

{"title":"Omnidirectional Wireless Power Transfer for Millimetric Magnetoelectric Biomedical Implants.","authors":"Wei Wang, Zhanghao Yu, Yiwei Zou, Joshua E Woods, Prahalad Chari, Yumin Su, Jacob T Robinson, Kaiyuan Yang","doi":"","DOIUrl":"","url":null,"abstract":"Miniature bioelectronic implants promise revolutionary therapies for cardiovascular and neurological disorders. Wireless power transfer (WPT) is a significant method for miniaturization, eliminating the need for bulky batteries in devices. Despite successful demonstrations of millimetric battery free implants in animal models, the robustness and efficiency of WPT are known to degrade significantly under misalignment incurred by body movements, respiration, heart beating, and limited control of implant orientation during surgery. This article presents an omnidirectional WPT platform for millimetric bioelectronic implants, employing the emerging magnetoelectric (ME) WPT modality, and magnetic field steering technique based on multiple transmitter (TX) coils. To accurately sense the weak coupling in a miniature implant and adaptively control the multicoil TX array in a closed loop, we develop an active echo (AE) scheme using a tiny coil on the implant. Our prototype comprises a fully integrated 14.2 mm3 implantable stimulator embedding a custom low power system on chip (SoC) powered by an ME film, a TX with a custom three channel AE RX chip, and a multicoil TX array with mutual inductance cancellation. The AE RX achieves negative 161 dBm per Hz input referred noise with 64 dB gain tuning range to reliably sense the AE signal, and offers fast polarity detection for driver control. AE simultaneously enhances the robustness, efficiency, and charging range of ME WPT. Under 90 degree rotation from the ideal position, our omnidirectional WPT system achieves 6.8x higher power transfer efficiency (PTE) than a single coil baseline. The tracking error of AE negligibly degrades the PTE by less than 2 percent from using ideal control.","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11601786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning. 利用 AlphaFold 3 辅助拓扑深度学习快速应对病毒的快速进化。

ArXiv Pub Date : 2024-11-19

JunJie Wee, Guo-Wei Wei

{"title":"Rapid response to fast viral evolution using AlphaFold 3-assisted topological deep learning.","authors":"JunJie Wee, Guo-Wei Wei","doi":"","DOIUrl":"","url":null,"abstract":"The fast evolution of SARS-CoV-2 and other infectious viruses poses a grand challenge to the rapid response in terms of viral tracking, diagnostics, and design and manufacture of monoclonal antibodies (mAbs) and vaccines, which are both time-consuming and costly. This underscores the need for efficient computational approaches. Recent advancements, like topological deep learning (TDL), have introduced powerful tools for forecasting emerging dominant variants, yet they require deep mutational scanning (DMS) of viral surface proteins and associated three-dimensional (3D) protein-protein interaction (PPI) complex structures. We propose an AlphaFold 3 (AF3)-assisted multi-task topological Laplacian (MT-TopLap) strategy to address this need. MT-TopLap combines deep learning with topological data analysis (TDA) models, such as persistent Laplacians (PL) to extract detailed topological and geometric characteristics of PPIs, thereby enhancing the prediction of DMS and binding free energy (BFE) changes upon virus mutations. Validation with four experimental DMS datasets of SARS-CoV-2 spike receptor-binding domain (RBD) and the human angiotensin-converting enzyme-2 (ACE2) complexes indicates that our AF3 assisted MT-TopLap strategy maintains robust performance, with only an average 1.1% decrease in Pearson correlation coefficients (PCC) and an average 9.3% increase in root mean square errors (RMSE), compared with the use of experimental structures. Additionally, AF3-assisted MT-TopLap achieved a PCC of 0.81 when tested with a SARS-CoV-2 HK.3 variant DMS dataset, confirming its capability to accurately predict BFE changes and adapt to new experimental data, thereby showcasing its potential for rapid and effective response to fast viral evolution.","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11601794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hierarchical Trait-State Model for Decoding Dyadic Social Interactions. 解码二元社会互动的分层特质-状态模型

ArXiv Pub Date : 2024-11-19

Qianying Wu, Shigeki Nakauchi, Mohammad Shehata, Shinsuke Shimojo

{"title":"Hierarchical Trait-State Model for Decoding Dyadic Social Interactions.","authors":"Qianying Wu, Shigeki Nakauchi, Mohammad Shehata, Shinsuke Shimojo","doi":"","DOIUrl":"","url":null,"abstract":"Traits are patterns of brain signals and behaviors that are stable over time but differ across individuals, whereas states are phasic patterns that vary over time, are influenced by the environment, yet oscillate around the traits. The quality of a social interaction depends on the traits and states of the interacting agents. However, it remains unclear how to decipher both traits and states from the same set of brain signals. To explore the hidden neural traits and states in relation to the behavioral ones during social interactions, we developed a pipeline to extract latent dimensions of the brain from electroencephalogram (EEG) data collected during a team flow task. Our pipeline involved two stages of dimensionality reduction: first, non-negative matrix factorization (NMF), followed by linear discriminant analysis (LDA). This pipeline resulted in an interpretable, seven-dimensional EEG latent space that revealed a trait-state hierarchical structure, with macro-segregation capturing neural traits and micro-segregation capturing neural states. Out of the seven latent dimensions, we found that three that significantly contributed to variations across individuals and task states. Using representational similarity analysis, we mapped the EEG latent space to a skill-cognition space, establishing a connection between hidden neural signatures and social interaction behaviors. Our method demonstrates the feasibility of representing both traits and states within a single model that correlates with changes in social behavior.","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11601788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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