ArXiv最新文献

{"title":"Prediction of causal genes at GWAS loci with pleiotropic gene regulatory effects using sets of correlated instrumental variables.","authors":"Mariyam Khan, Adriaan-Alexander Ludl, Sean Bankier, Johan Lm Björkegren, Tom Michoel","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Multivariate Mendelian randomization (MVMR) is a statistical technique that uses sets of genetic instruments to estimate the direct causal effects of multiple exposures on an outcome of interest. At genomic loci with pleiotropic gene regulatory effects, that is, loci where the same genetic variants are associated to multiple nearby genes, MVMR can potentially be used to predict candidate causal genes. However, consensus in the field dictates that the genetic instruments in MVMR must be independent (not in linkage disequilibrium, which is usually not possible when considering a group of candidate genes from the same locus. Here we used causal inference theory to show that MVMR with correlated instruments satisfies the instrumental set condition. This is a classical result by Brito and Pearl (2002) for structural equation models that guarantees the identifiability of individual causal effects in situations where multiple exposures collectively, but not individually, separate a set of instrumental variables from an outcome variable. Extensive simulations confirmed the validity and usefulness of these theoretical results. Importantly, the causal effect estimates remained unbiased and their variance small even when instruments are highly correlated, while bias introduced by horizontal pleiotropy or LD matrix sampling error was comparable to standard MR. We applied MVMR with correlated instrumental variable sets at genome-wide significant loci for coronary artery disease (CAD) risk using expression Quantitative Trait Loci (eQTL) data from seven vascular and metabolic tissues in the STARNET study. Our method predicts causal genes at twelve loci, each associated with multiple colocated genes in multiple tissues. We confirm causal roles for <math><mtext>PHACTR</mtext> <mn>1</mn></math> and <math><mtext>ADAMTS</mtext> <mn>7</mn></math> in arterial tissues, among others. However, the extensive degree of regulatory pleiotropy across tissues and the limited number of causal variants in each locus still require that MVMR is run on a tissue-by-tissue basis, and testing all gene-tissue pairs with <i>cis</i>-eQTL associations at a given locus in a single model to predict causal gene-tissue combinations remains infeasible. Our results show that within tissues, MVMR with dependent, as opposed to independent, sets of instrumental variables significantly expands the scope for predicting causal genes in disease risk loci with pleiotropic regulatory effects. However, considering risk loci with regulatory pleiotropy that also spans across tissues remains an unsolved problem.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802687/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139521946","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}

{"title":"Cross-domain Fiber Cluster Shape Analysis for Language Performance Cognitive Score Prediction.","authors":"Yui Lo, Yuqian Chen, Dongnan Liu, Wan Liu, Leo Zekelman, Fan Zhang, Yogesh Rathi, Nikos Makris, Alexandra J Golby, Weidong Cai, Lauren J O'Donnell","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Shape plays an important role in computer graphics, offering informative features to convey an object's morphology and functionality. Shape analysis in brain imaging can help interpret structural and functionality correlations of the human brain. In this work, we investigate the shape of the brain's 3D white matter connections and its potential predictive relationship to human cognitive function. We reconstruct brain connections as sequences of 3D points using diffusion magnetic resonance imaging (dMRI) tractography. To describe each connection, we extract 12 shape descriptors in addition to traditional dMRI connectivity and tissue microstructure features. We introduce a novel framework, Shape--fused Fiber Cluster Transformer (SFFormer), that leverages a multi-head cross-attention feature fusion module to predict subject-specific language performance based on dMRI tractography. We assess the performance of the method on a large dataset including 1065 healthy young adults. The results demonstrate that both the transformer-based SFFormer model and its inter/intra feature fusion with shape, microstructure, and connectivity are informative, and together, they improve the prediction of subject-specific language performance scores. Overall, our results indicate that the shape of the brain's connections is predictive of human language function.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10996776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140864027","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}

{"title":"A standardised open science framework for sharing and re-analysing neural data acquired to continuous stimuli.","authors":"Giovanni M Di Liberto, Aaron Nidiffer, Michael J Crosse, Nathaniel J Zuk, Stephanie Haro, Giorgia Cantisani, Martin M Winchester, Aoife Igoe, Ross McCrann, Satwik Chandra, Edmund C Lalor, Giacomo Baruzzo","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Neurophysiology research has demonstrated that it is possible and valuable to investigate sensory processing in scenarios involving continuous sensory streams, such as speech and music. Over the past 10 years or so, novel analytic frameworks combined with the growing participation in data sharing has led to a surge of publicly available datasets involving continuous sensory experiments. However, open science efforts in this domain of research remain scattered, lacking a cohesive set of guidelines. This paper presents an end-to-end open science framework for the storage, analysis, sharing, and re-analysis of neural data recorded during continuous sensory experiments. We propose a data structure that builds on existing custom structures (Continuous-event Neural Data or CND), providing precise naming conventions and data types, as well as a workflow for storing and loading data in the general-purpose BIDS structure. The framework has been designed to interface with existing EEG/MEG analysis toolboxes, such as Eelbrain, NAPLib, MNE, and mTRF-Toolbox. We present guidelines by taking both the user view (rapidly re-analyse existing data) and the experimenter view (store, analyse, and share), making the process straightforward and accessible. Additionally, we introduce a web-based data browser that enables the effortless replication of published results and data re-analysis.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d9/72/nihpp-2309.07671v2.PMC10516115.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41179876","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}

{"title":"Mimicking large spot-scanning radiation fields for proton FLASH preclinical studies with a robotic motion platform.","authors":"Fada Guan, Dadi Jiang, Xiaochun Wang, Ming Yang, Kiminori Iga, Yuting Li, Lawrence Bronk, Julianna Bronk, Liang Wang, Youming Guo, Narayan Sahoo, David R Grosshans, Albert C Koong, Xiaorong R Zhu, Radhe Mohan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Previously, a synchrotron-based horizontal proton beamline (87.2 MeV) was successfully commissioned to deliver radiation doses in FLASH and conventional dose rate modes to small fields and volumes. In this study, we developed a strategy to increase the effective radiation field size using a custom robotic motion platform to automatically shift the positions of biological samples. The beam was first broadened with a thin tungsten scatterer and shaped by customized brass collimators for irradiating cell/organoid cultures in 96-well plates (a 7-mm-diameter circle) or for irradiating mice (1-cm² square). Motion patterns of the robotic platform were written in G-code, with 9-mm spot spacing used for the 96-well plates and 10.6-mm spacing for the mice. The accuracy of target positioning was verified with a self-leveling laser system. The dose delivered in the experimental conditions was validated with EBT-XD film attached to the 96-well plate or the back of the mouse. Our film-measured dose profiles matched Monte Carlo calculations well (1D gamma pass rate >95%). The FLASH dose rates were 113.7 Gy/s for cell/organoid irradiation and 191.3 Gy/s for mouse irradiation. These promising results indicate that this robotic platform can be used to effectively increase the field size for preclinical experiments with proton FLASH.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419177/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309268","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}

{"title":"Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics.","authors":"Xingzhi Sun, Charles Xu, João F Rocha, Chen Liu, Benjamin Hollander-Bodie, Laney Goldman, Marcello DiStasio, Michael Perlmutter, Smita Krishnaswamy","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>In many data-driven applications, higher-order relationships among multiple objects are essential in capturing complex interactions. Hypergraphs, which generalize graphs by allowing edges to connect any number of nodes, provide a flexible and powerful framework for modeling such higher-order relationships. In this work, we introduce hypergraph diffusion wavelets and describe their favorable spectral and spatial properties. We demonstrate their utility for biomedical discovery in spatially resolved transcriptomics by applying the method to represent disease-relevant cellular niches for Alzheimer's disease.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309349","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}

{"title":"A practical approach to calculating magnetic Johnson noise for precision measurements.","authors":"N S Phan, S M Clayton, Y J Kim, T M Ito","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Magnetic Johnson noise is an important consideration for many applications involving precision magnetometry, and its significance will only increase in the future with improvements in measurement sensitivity. The fluctuation-dissipation theorem can be utilized to derive analytic expressions for magnetic Johnson noise in certain situations. But when used in conjunction with finite element analysis tools, the combined approach is particularly powerful as it provides a practical means to calculate the magnetic Johnson noise arising from conductors of arbitrary geometry and permeability. In this paper, we demonstrate this method to be one of the most comprehensive approaches presently available to calculate thermal magnetic noise. In particular, its applicability is shown to not be limited to cases where the noise is evaluated at a point in space but also can be expanded to include cases where the magnetic field detector has a more general shape, such as a finite size loop, a gradiometer, or a detector that consists of a polarized atomic species trapped in a volume. Furthermore, some physics insights gained through studies made using this method are discussed.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11275706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141790307","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}

{"title":"Adapting Machine Learning Diagnostic Models to New Populations Using a Small Amount of Data: Results from Clinical Neuroscience.","authors":"Rongguang Wang, Guray Erus, Pratik Chaudhari, Christos Davatzikos","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Machine learning (ML) is revolutionizing many areas of engineering and science, including healthcare. However, it is also facing a reproducibility crisis, especially in healthcare. ML models that are carefully constructed from and evaluated on data from one part of the population may not generalize well on data from a different population group, or acquisition instrument settings and acquisition protocols. We tackle this problem in the context of neuroimaging of Alzheimer's disease (AD), schizophrenia (SZ) and brain aging. We develop a weighted empirical risk minimization approach that optimally combines data from a source group, e.g., subjects are stratified by attributes such as sex, age group, race and clinical cohort to make predictions on a target group, e.g., other sex, age group, etc. using a small fraction (10%) of data from the target group. We apply this method to multi-source data of 15,363 individuals from 20 neuroimaging studies to build ML models for diagnosis of AD and SZ, and estimation of brain age. We found that this approach achieves substantially better accuracy than existing domain adaptation techniques: it obtains area under curve greater than 0.95 for AD classification, area under curve greater than 0.7 for SZ classification and mean absolute error less than 5 years for brain age prediction on all target groups, achieving robustness to variations of scanners, protocols, and demographic or clinical characteristics. In some cases, it is even better than training on all data from the target group, because it leverages the diversity and size of a larger training set. We also demonstrate the utility of our models for prognostic tasks such as predicting disease progression in individuals with mild cognitive impairment. Critically, our brain age prediction models lead to new clinical insights regarding correlations with neurophysiological tests. In summary, we present a relatively simple methodology, along with ample experimental evidence, supporting the good generalization of ML models to new datasets and patient cohorts.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309344","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}

{"title":"wgatools: an ultrafast toolkit for manipulating whole genome alignments.","authors":"Wenjie Wei, Songtao Gui, Jian Yang, Erik Garrison, Jianbing Yan, Hai-Jun Liu","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Summary: </strong>With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed <i>wgatools</i>, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment (WGA) formats, offering practical tools for conversion, processing, statistical evaluation, and visualization of alignments, thereby facilitating population-level genome analysis and advancing functional and evolutionary genomics.</p><p><strong>Availability and implementation: </strong><i>wgatools</i> supports diverse formats and can process, filter, and statistically evaluate alignments, perform alignment-based variant calling, and visualize alignments both locally and genome-wide. Built with Rust for efficiency and safe memory usage, it ensures fast performance and can handle large datasets consisting of hundreds of genomes. <i>wgatools</i> is published as free software under the MIT open-source license, and its source code is freely available at https://github.com/wjwei-handsome/wgatools.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419180/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309272","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}

{"title":"Dendrites endow artificial neural networks with accurate, robust and parameter-efficient learning.","authors":"Spyridon Chavlis, Panayiota Poirazi","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Artificial neural networks (ANNs) are at the core of most Deep learning (DL) algorithms that successfully tackle complex problems like image recognition, autonomous driving, and natural language processing. However, unlike biological brains who tackle similar problems in a very efficient manner, DL algorithms require a large number of trainable parameters, making them energy-intensive and prone to overfitting. Here, we show that a new ANN architecture that incorporates the structured connectivity and restricted sampling properties of biological dendrites counteracts these limitations. We find that dendritic ANNs are more robust to overfitting and outperform traditional ANNs on several image classification tasks while using significantly fewer trainable parameters. These advantages are likely the result of a different learning strategy, whereby most of the nodes in dendritic ANNs respond to multiple classes, unlike classical ANNs that strive for class-specificity. Our findings suggest that the incorporation of dendritic properties can make learning in ANNs more precise, resilient, and parameter-efficient and shed new light on how biological features can impact the learning strategies of ANNs.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309346","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}

{"title":"CTLESS: A scatter-window projection and deep learning-based transmission-less attenuation compensation method for myocardial perfusion SPECT.","authors":"Zitong Yu, Md Ashequr Rahman, Craig K Abbey, Richard Laforest, Nancy A Obuchowski, Barry A Siegel, Abhinav K Jha","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Attenuation compensation (AC), while being beneficial for visual-interpretation tasks in myocardial perfusion imaging (MPI) by SPECT, typically requires the availability of a separate X-ray CT component, leading to additional radiation dose, higher costs, and potentially inaccurate diagnosis due to SPECT/CT misalignment. To address these issues, we developed a method for cardiac SPECT AC using deep learning and emission scatter-window photons without a separate transmission scan (CTLESS). In this method, an estimated attenuation map reconstructed from scatter-energy window projections is segmented into different regions using a multi-channel input multi-decoder network trained on CT scans. Pre-defined attenuation coefficients are assigned to these regions, yielding the attenuation map used for AC. We objectively evaluated this method in a retrospective study with anonymized clinical SPECT/CT stress MPI images on the clinical task of detecting defects with an anthropomorphic model observer. CTLESS yielded statistically non-inferior performance compared to a CT-based AC (CTAC) method and significantly outperformed a non-AC (NAC) method on this clinical task. Similar results were observed in stratified analyses with different sexes, defect extents and severities. The method was observed to generalize across two SPECT scanners, each with a different camera. In addition, CTLESS yielded similar performance as CTAC and outperformed NAC method on the metrics of root mean squared error and structural similarity index measure. Moreover, as we reduced the training dataset size, CTLESS yielded relatively stable AUC values and generally outperformed another DL-based AC method that directly estimated the attenuation coefficient within each voxel. These results demonstrate the capability of the CTLESS method for transmission-less AC in SPECT and motivate further clinical evaluation.</p>","PeriodicalId":93888,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309345","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}