ArXiv最新文献

{"title":"Timed material self-assembly controlled by circadian clock proteins.","authors":"Gregor Leech, Lauren Melcher, Michelle Chiu, Maya Nugent, Lily Burton, Janet Kang, Soo Ji Kim, Sourav Roy, Leila Farhadi, Jennifer L Ross, Moumita Das, Michael J Rust, Rae M Robertson-Anderson","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Active biological molecules present a powerful, yet largely untapped, opportunity to impart autonomous regulation to materials. Because these systems can function robustly to regulate when and where chemical reactions occur, they have the ability to bring complex, life-like behavior to synthetic materials. Here, we achieve this design feat by using functionalized circadian clock proteins, KaiB and KaiC, to engineer time-dependent crosslinking of colloids. The resulting material self-assembles with programmable kinetics, producing macroscopic changes in material properties, via molecular assembly of KaiB-KaiC complexes. We show that colloid crosslinking depends strictly on the phosphorylation state of KaiC, with kinetics that are synced with KaiB-KaiC complexing. Our microscopic image analyses and computational models indicate that the stability of colloidal super-structures depends sensitively on the number of Kai complexes per colloid connection. Consistent with our model predictions, a high concentration stabilizes the material against dissolution after a robust self-assembly phase, while a low concentration allows circadian oscillation of material structure. This work introduces the concept of harnessing biological timers to control synthetic materials; and, more generally, opens the door to using protein-based reaction networks to endow synthetic systems with life-like functional properties.</p>","PeriodicalId":8425,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10002811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9178982","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":"Optimization and Validation of the DESIGNER dMRI preprocessing pipeline in white matter aging.","authors":"Jenny Chen, Benjamin Ades-Aron, Hong-Hsi Lee, Subah Mehrin, Michelle Pang, Dmitry S Novikov, Jelle Veraart, Els Fieremans","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Various diffusion MRI (dMRI) preprocessing pipelines are currently available to yield more accurate diffusion parameters. Here, we evaluated accuracy and robustness of the optimized Diffusion parameter EStImation with Gibbs and NoisE Removal (DESIGNER) pipeline in a large clinical dMRI dataset and using ground truth phantoms. DESIGNER has been modified to improve denoising and target Gibbs ringing for partial Fourier acquisitions. We compared the revisited DESIGNER (Dv2) (including denoising, Gibbs removal, correction for motion, EPI distortion, and eddy currents) against the original DESIGNER (Dv1) pipeline, minimal preprocessing (including correction for motion, EPI distortion, and eddy currents only), and no preprocessing on a large clinical dMRI dataset of 524 control subjects with ages between 25 and 75 years old. We evaluated the effect of specific processing steps on age correlations in white matter with DTI and DKI metrics. We also evaluated the added effect of minimal Gaussian smoothing to deal with noise and to reduce outliers in parameter maps compared to DESIGNER (Dv2)'s noise removal method. Moreover, DESIGNER (Dv2)'s updated noise and Gibbs removal methods were assessed using ground truth dMRI phantom to evaluate accuracy. Results show age correlation in white matter with DTI and DKI metrics were affected by the preprocessing pipeline, causing systematic differences in absolute parameter values and loss or gain of statistical significance. Both in clinical dMRI and ground truth phantoms, DESIGNER (Dv2) pipeline resulted in the smallest number of outlier voxels and improved accuracy in DTI and DKI metrics as noise was reduced and Gibbs removal was improved. Thus, DESIGNER (Dv2) provides more accurate and robust DTI and DKI parameter maps as compared to no preprocessing or minimal preprocessing.</p>","PeriodicalId":8425,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9608654","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":"Overcompensation of transient and permanent death rate increases in age-structured models with cannibalistic interactions.","authors":"Mingtao Xia, Xiangting Li, Tom Chou","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>There has been renewed interest in understanding the mathematical structure of ecological population models that lead to overcompensation, the process by which a population recovers to a higher level after suffering a permanent increase in predation or harvesting. Here, we apply a recently formulated kinetic population theory to formally construct an age-structured single-species population model that includes a cannibalistic interaction in which older individuals prey on younger ones. Depending on the age-dependent structure of this interaction, our model can exhibit transient or steady-state overcompensation of an increased death rate as well as oscillations of the total population, both phenomena that have been observed in ecological systems. Analytic and numerical analysis of our model reveals sufficient conditions for overcompensation and oscillations. We also show how our structured population partial integrodifferential equation (PIDE) model can be reduced to coupled ODE models representing piecewise constant parameter domains, providing additional mathematical insight into the emergence of overcompensation.</p>","PeriodicalId":8425,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/52/6b/nihpp-2303.00864v1.PMC10002760.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9497802","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":"SlicerTMS: Real-Time Visualization of Transcranial Magnetic Stimulation for Mental Health Treatment.","authors":"Loraine Franke, Tae Young Park, Jie Luo, Yogesh Rathi, Steve Pieper, Lipeng Ning, Daniel Haehn","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>We present a real-time visualization system for Transcranial Magnetic Stimulation (TMS), a non-invasive neuromodulation technique for treating various brain disorders and mental health diseases. Our solution targets the current challenges of slow and labor-intensive practices in treatment planning. Integrating Deep Learning (DL), our system rapidly predicts electric field (E-field) distributions in 0.2 seconds for precise and effective brain stimulation. The core advancement lies in our tool's real-time neuronavigation visualization capabilities, which support clinicians in making more informed decisions quickly and effectively. We assess our system's performance through three studies: First, a real-world use case scenario in a clinical setting, providing concrete feedback on applicability and usability in a practical environment. Second, a comparative analysis with another TMS tool focusing on computational efficiency across various hardware platforms. Lastly, we conducted an expert user study to measure usability and influence in optimizing TMS treatment planning. The system is openly available for community use and further development on GitHub: https://github.com/lorifranke/SlicerTMS.</p>","PeriodicalId":8425,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/69/bb/nihpp-2305.06459v3.PMC10246060.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9619778","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":"Limit theorems for the site frequency spectrum of neutral mutations in an exponentially growing population.","authors":"Einar Bjarki Gunnarsson, Kevin Leder, Xuanming Zhang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The site frequency spectrum (SFS) is a widely used summary statistic of genomic data. Motivated by recent evidence for the role of neutral evolution in cancer, we investigate the SFS of neutral mutations in an exponentially growing population. Using branching process techniques, we establish (first-order) almost sure convergence results for the SFS of a Galton-Watson process, evaluated either at a fixed time or at the stochastic time at which the population first reaches a certain size. We finally use our results to construct consistent estimators for the extinction probability and the effective mutation rate of a birth-death process.</p>","PeriodicalId":8425,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10350102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9882595","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 Prototype Scintillator Real-Time Beam Monitor for Ultra-high Dose Rate Radiotherapy.","authors":"Daniel S Levin, Peter S Friedman, Claudio Ferretti, Nicholas Ristow, Monica Tecchio, Dale W Litzenberg, Vladimir Bashkirov, Reinhard Schulte","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Background: </strong>FLASH Radiotherapy (RT) is an emergent cancer radiotherapy modality where an entire therapeutic dose is delivered at more than 1000 times higher dose rate than conventional RT. For clinical trials to be conducted safely, a precise and fast beam monitor that can generate out-of-tolerance beam interrupts is required. This paper describes the overall concept and provides results from a prototype ultra-fast, scintillator-based beam monitor for both proton and electron beam FLASH applications.</p><p><strong>Purpose: </strong>A FLASH Beam Scintillator Monitor (FBSM) is being developed that employs a novel proprietary scintillator material. The FBSM has capabilities that conventional RT detector technologies are unable to simultaneously provide: 1) large area coverage; 2) a low mass profile; 3) a linear response over a broad dynamic range; 4) radiation hardness; 5) real-time analysis to provide an IEC-compliant fast beam-interrupt signal based on true two-dimensional beam imaging, radiation do-simetry and excellent spatial resolution.</p><p><strong>Methods: </strong>The FBSM uses a proprietary low mass, less than 0.5 mm water equivalent, non-hygroscopic, radiation tolerant scintillator material (designated HM: hybrid material) that is viewed by high frame rate CMOS cameras. Folded optics using mirrors enable a thin monitor profile of ~10 cm. A field programmable gate array (FPGA) data acquisition system (DAQ) generates real-time analysis on a time scale appropriate to the FLASH RT beam modality: 100-1000 Hz for pulsed electrons and 10-20 kHz for quasi-continuous scanning proton pencil beams. An ion beam monitor served as the initial development platform for this work and was tested in low energy heavy-ion beams (⁸⁶Kr⁺²⁶ and protons). A prototype FBSM was fabricated and then tested in various radiation beams that included FLASH level dose per pulse electron beams, and a hospital radiotherapy clinic with electron beams.</p><p><strong>Results: </strong>Results presented in this report include image quality, response linearity, radiation hardness, spatial resolution, and real-time data processing. The HM scintillator was found to be highly radiation damage resistant. It exhibited a small 0.025%/kGy signal decrease from a 216 kGy cumulative dose resulting from continuous exposure for 15 minutes at a FLASH compatible dose rate of 237 Gy/s. Measurements of the signal amplitude vs beam fluence demonstrate linear response of the FBSM at FLASH compatible dose rates of > 40 Gy/s. Comparison with commercial Gafchromic film indicates that the FBSM produces a high resolution 2D beam image and can reproduce a nearly identical beam profile, including primary beam tails. The spatial resolution was measured at 35-40 μm. Tests of the firmware beta version show successful operation at 20,000 Hz frame rate or 50 μs/frame, where the real-time analysis of the beam parameters is achieved in less than 1 μs.</p><p><strong>Con","PeriodicalId":8425,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246063/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9622247","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":"Tomographic Image Reconstruction Using an Advanced Score Function (ADSF).","authors":"Wenxiang Cong, Wenjun Xia, Ge Wang","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Computed tomography (CT) reconstructs volumetric images using X-ray projection data acquired from multiple angles around an object. For low-dose or sparse-view CT scans, the classic image reconstruction algorithms often produce severe noise and artifacts. To address this issue, we develop a novel iterative image reconstruction method based on maximum a posteriori (MAP) estimation. In the MAP framework, the score function, i.e., the gradient of the logarithmic probability density distribution, plays a crucial role as an image prior in the iterative image reconstruction process. By leveraging the Gaussian mixture model, we derive a novel score matching formula to establish an advanced score function (ADSF) through deep learning. Integrating the new ADSF into the image reconstruction process, a new ADSF iterative reconstruction method is developed to improve image reconstruction quality. The convergence of the ADSF iterative reconstruction algorithm is proven through mathematical analysis. The performance of the ADSF reconstruction method is also evaluated on both public medical image datasets and clinical raw CT datasets. Our results show that the ADSF reconstruction method can achieve better denoising and deblurring effects than the state-of-the-art reconstruction methods, showing excellent generalizability and stability.</p>","PeriodicalId":8425,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10312904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10117027","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":"Generative Representational Instruction Tuning","authors":"Niklas Muennighoff, Hongjin Su, Liang Wang, Nan Yang, Furu Wei, Tao Yu, Amanpreet Singh, Douwe Kiela","doi":"10.48550/arXiv.2402.09906","DOIUrl":"https://doi.org/10.48550/arXiv.2402.09906","url":null,"abstract":"All text-based language problems can be reduced to either generation or embedding. Current models only perform well at one or the other. We introduce generative representational instruction tuning (GRIT) whereby a large language model is trained to handle both generative and embedding tasks by distinguishing between them through instructions. Compared to other open models, our resulting GritLM 7B sets a new state of the art on the Massive Text Embedding Benchmark (MTEB) and outperforms all models up to its size on a range of generative tasks. By scaling up further, GritLM 8x7B outperforms all open generative language models that we tried while still being among the best embedding models. Notably, we find that GRIT matches training on only generative or embedding data, thus we can unify both at no performance loss. Among other benefits, the unification via GRIT speeds up Retrieval-Augmented Generation (RAG) by>60% for long documents, by no longer requiring separate retrieval and generation models. Models, code, etc. are freely available at https://github.com/ContextualAI/gritlm.","PeriodicalId":8425,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139962170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-Stage Algorithm for Group Testing with Prior Statistics","authors":"Ayelet C. Portnoy, Alejandro Cohen","doi":"10.48550/arXiv.2402.10018","DOIUrl":"https://doi.org/10.48550/arXiv.2402.10018","url":null,"abstract":"In this paper, we propose an efficient multi-stage algorithm for non-adaptive Group Testing (GT) with general correlated prior statistics. The proposed solution can be applied to any correlated statistical prior represented in trellis, e.g., finite state machines and Markov processes. We introduce a variation of List Viterbi Algorithm (LVA) to enable accurate recovery using much fewer tests than objectives, which efficiently gains from the correlated prior statistics structure. Our numerical results demonstrate that the proposed Multi-Stage GT (MSGT) algorithm can obtain the optimal Maximum A Posteriori (MAP) performance with feasible complexity in practical regimes, such as with COVID-19 and sparse signal recovery applications, and reduce in the scenarios tested the number of pooled tests by at least $25%$ compared to existing classical low complexity GT algorithms. Moreover, we analytically characterize the complexity of the proposed MSGT algorithm that guarantees its efficiency.","PeriodicalId":8425,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139962409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Not Just Novelty: A Longitudinal Study on Utility and Customization of AI Workflows","authors":"Tao Long, Katy Ilonka Gero, Lydia B. Chilton","doi":"10.48550/arXiv.2402.09894","DOIUrl":"https://doi.org/10.48550/arXiv.2402.09894","url":null,"abstract":"Generative AI brings novel and impressive abilities to help people in everyday tasks. There are many AI workflows that solve real and complex problems by chaining AI outputs together with human interaction. Although there is an undeniable lure of AI, it's uncertain how useful generative AI workflows are after the novelty wears off. Additionally, tools built with generative AI have the potential to be personalized and adapted quickly and easily, but do users take advantage of the potential to customize? We conducted a three-week longitudinal study with 12 users to understand the familiarization and customization of generative AI tools for science communication. Our study revealed that the familiarization phase lasts for 4.3 sessions, where users explore the capabilities of the workflow and which aspects they find useful. After familiarization, the perceived utility of the system is rated higher than before, indicating that the perceived utility of AI is not just a novelty effect. The increase in benefits mainly comes from end-users' ability to customize prompts, and thus appropriate the system to their own needs. This points to a future where generative AI systems can allow us to design for appropriation.","PeriodicalId":8425,"journal":{"name":"ArXiv","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139962463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}