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International Conference on Computational Methods in Systems Biology, CMSB 2004

作者： Hunt, C. Anthony Ropella, Glen E. P. Roberts, Michael S. Yan, Li Dept. of Biopharmaceutical Sciences Biosystems Group University of California San Francisco CA 94143-0446 United States Department of Medicine University of Queensland Princess Alexandra Hospital Woolloongabba Q 4102 Australia Joint UCSF UC Berkeley Bioengineering Graduate Program

ISBN: (纸本)3540253750

We introduce biomimetic in silico devices, and means for validation along with methods for testing and refining them. The devices are constructed from adaptable software components designed to map logically to biological components at multiple levels of resolution. In this report we focus on the liver;the goal is to validate components that mimic features of the lobule (the hepatic primary functional unit) and dynamic aspects of liver behavior, structure, and function. An assembly of lobule-mimetic devices represents an in silico liver. We validate against outflow profiles for sucrose administered as a bolus to isolated, perfused rat livers. Acceptable in silico profiles are experimentally indistinguishable from those of the in situ referent. This new technology is intended to provide powerful new tools for challenging our understanding of how biological functional units function in vivo. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Biomimetic materials

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Spectral DiffuserCam: lensless snapshot hyperspectral imaging with a spectral filter array

arXiv

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arXiv 2020年

作者： Monakhova, Kristina Yanny, Kyrollos Aggarwal, Neerja Waller, Laura Department of Electrical Engineering & Computer Sciences University of California BerkeleyCA94720 United States UCB/UCSF Joint Graduate Program in Bioengineering University of California BerkeleyCA94720 United States

Hyperspectral imaging is useful for applications ranging from medical diagnostics to crop monitoring;however, traditional scanning hyperspectral imagers are prohibitively slow and expensive for widespread adoption. Snapshot techniques exist but are often confined to bulky bench-top setups or have low spatio-spectral resolution. In this paper, we propose a novel, compact, and inexpensive computational camera for snapshot hyperspectral imaging. Our system consists of a repeated spectral filter array placed directly on the image sensor and a diffuser placed close to the sensor. Each point in the world maps to a unique pseudorandom pattern on the spectral filter array, which encodes multiplexed spatio-spectral information. A sparsity-constrained inverse problem solver then recovers the hyperspectral volume with good spatio-spectral resolution. By using a spectral filter array, our hyperspectral imaging framework is flexible and can be designed with contiguous or non-contiguous spectral filters that can be chosen for a given application. We provide theory for system design, demonstrate a prototype device, and present experimental results with high spatio-spectral resolution. © 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement Copyright © 2020, The Authors. All rights reserved.

关键词： Spectroscopy

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Research: Association of low-amplitude QRSs with false-positive asystole alarms

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Biomedical Instrumentation and Technology 2016年第5期50卷 329-335页

作者： Pelter, Michele M. Fidler, Richard Hu, Xiao Department of Physiological Nursing United States United States UCSF School of Nursing United States Healthcare Simulation Programs United States Institute for Computational Health Sciences UCB/UCSF Joint Bio-Engineering Graduate Program at UCSF United States

Background: Although electrocardiographic monitoring is valuable for continuous surveillance of intensive care unit (ICU) patients, false alarms are common and have been cited as a cause of alarm fatigue. ANSI/ AAMI EC12:2002 states that electrocardiograms (ECGs) should not detect a QRS if the waveform is less than 0.15 mV (1.5 mm) for adult patients, in order to avoid mislabeling P waves or baseline noise as QRSs during complete heart block or asystole. However, ECG software algorithms often use more conservative QRS thresholds, which may result in false-positive asystole alarms in patients with low-amplitude QRS complexes. Objectives: To 1) assess the frequency of low QRS amplitude in a group of ICU patients with one or more false-positive asystole alarms and 2) determine whether low-amplitude QRSs are associated with false-positive asystole alarms during continuous ECG monitoring. Methods: Hospital-acquired standard 12-lead ECGs were examined in a group of 82 ICU patients who had one or more falsepositive asystole alarms. Low QRS amplitude was deined as a unidirectional (only positive or negative) QRS of less than 5 mm in two of four leads (I, II, III, and V1). Results: Low-amplitude QRSs were present in 45 of 82 (55%) patients. The presence of low-amplitude QRSs did not difer according to age, sex, or race. Patients treated in the cardiac ICU had the highest proportion of low-amplitude QRSs. An equivalent proportion of patients had false-positive asystole alarms by group (no low-amplitude QRSs 95% vs. low-amplitude QRSs 87%;P = 0.229). Eight patients (10%) had both true- and false-positive asystole alarms (two [5%] with no low-amplitude QRSs and six [13%] with low-amplitude QRSs;P = 0.229). Conclusion: Low-amplitude QRS, as assessed from hospital 12-lead ECGs, occurs frequently and is more common in cardiac ICU patients. However, this ECG feature did not identify patients with false-positive asystole alarms during continuous ECG monitoring. © Copyright AAMI 2016

关键词： Electrocardiograms

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The Effect of Repetition Rate on the Formation of Microtears in Tendon in an In Vivo Cyclical Loading Animal Model

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Proceedings of the Human Factors and Ergonomics Society Annual Meeting 2006年第21期50卷 2331 - 2335页

作者： Leena Nakama Karen King Swen Abrahamsson David Rempel UCB-UCSF Joint Graduate Group in Bioengineering University of California San Francisco Department of Medicine and University of California Berkeley Department of Bioengineering Malmo University Hospital Malmo Sweden University of California San Francisco Department of Medicine and University of California Berkeley Department of Bioengineering.

Previously (17), we reported the formation of microtears in an in vivo loaded FDP rabbit tendon with a repetition rate of 60 repetitions per minute and a peak force of 15% of maximum (Po). Pathophysiological changes were observed. The tear area as a percent of tendon area, tear density (tears/mm2) and mean tear size (μm2) were higher in tendons from the loaded limb compared to the unloaded limb. The purpose of the present study was to compare those results to results obtained with a lower repetition rate of 10 (per minute) while maintaining the same peak force and work (equal force-time integral) (n=8). Due to regional properties of the tendon, a strain gradient between the inner and outer sides of the FDP tendon exists. Therefore, microtears were quantified in four regions, two regions each along the inner and outer sides of the tendon. The tear area as a percent of total tendon area and the mean tear size were significantly greater in the loaded limb compared to the unloaded limb (p < 0.03). However, the effects were less than those observed at 60 repetitions/min. The high repetition rate loading pattern resulted in an increase in tear measures in all four regions, while the lower rate produced changes only in the outer regions of the tendon. This finding may establish where the initial sites of damage occur in tendons that insert into bone in a similar arrangement as the FDP. The results also suggest that repetition rate is associated with tendon damage in a dose-response pattern.

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Robust Assessment of Photoplethysmogram Signal Quality in the Presence of Atrial Fibrillation

Robust Assessment of Photoplethysmogram Signal Quality in th...

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Computers in Cardiology (CinC)

作者： Tania Pereira Kais Gadhoumi Mitchell Ma Rene Colorado Kevin J Keenan Karl Meisel Xiao Hu Department of Physiological Nursing School of Nursing University of California San Francisco CA USA UCSF Center for Physiologic Research USA Department of Neurology School of Medicine USA Core Member of UCB/UCSF Joint Bio-Engineering Graduate Program UCSF USA

ISBN: (纸本)9781728109244

A great deal of algorithms currently available to assess the quality of photoplethysmogram (PPG) signals is based on the similarity between pulses to derive signal quality indices. This approach has limitations when pulse morphology become variable due to the presence of some arrhythmia as in the case of atrial fibrillation (AFib). AFib is a heart arrhythmia characterized in the electrocardiogram mainly by an irregular irregularity. This arrhythmicity is reflected on PPG pulses by the presence of non-uniform pulses and poses challenges in the evaluation of the signal quality. In this work, we first test the performance of few algorithms from the body of methods reported in literature using a dataset of PPG records with AFib, and demonstrate their limitation. Second, we present a novel SVM-based classifier for PPG quality assessment in 30s-long segments of PPG records extracted from pulse oximetry data of 13 stroke patients admitted to the ucsf medical center neuro ICU. 40 time-domain, frequency domain and non-linear features were extracted from all segments. Using an independent test set, the classifier reached a 0.94 accuracy, 0.95 sensitivity and 0.91 specificity. These results demonstrate the robustness of the proposed method in properly evaluating PPG signal quality in the presence of atrial fibrillation.

关键词： Stroke (medical condition) Feature extraction Electrocardiography Standards Quality assessment Sensitivity Support vector machines

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Metabolic engineering of Escherichia coli for the biosynthesis of 2-pyrrolidone

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Metabolic Engineering Communications 2016年 3卷 1-7页

作者： Zhang, Jingwei Kao, Emily Wang, George Baidoo, Edward E.K. Chen, Matthew Keasling, Jay. D. UCSF-UCB Joint Graduate Group in Bioengineering University of California Berkeley Berkeley CA United States Joint BioEnergy Institute Emeryville CA United States Synthetic Biology Engineering Research Center University of California Berkeley CA United States Department of Chemical and Biomolecular Engineering University of California Berkeley Berkeley 94720 CA United States California Institute for Quantitative Biosciences University of California Berkeley Berkeley CA United States Biological Systems and Engineering Division Lawrence Berkeley National Laboratory Berkeley CA United States

2-Pyrrolidone is a valuable bulk chemical with myriad applications as a solvent, polymer precursor and active pharmaceutical intermediate. A novel 2-pyrrolidone synthase, ORF27, from Streptomyces aizunensis was identified to catalyze the ring closing dehydration of γ-aminobutyrate. ORF27's tendency to aggregate was resolved by expression at low temperature and fusion to the maltose binding protein (MBP). Recombinant Escherichia coli was metabolically engineered for the production of 2-pyrrolidone from glutamate by expressing both the genes encoding GadB, a glutamate decarboxylase, and ORF27. Incorporation of a GadB mutant lacking H465 and T466, GadB_δHT, improved the efficiency of one-pot 2-pyrrolidone biosynthesis in vivo. When the recombinant E. coli strain expressing the E. coli GadB_δHT mutant and the ORF27-MBP fusion was cultured in ZYM-5052 medium containing 9. g/L of l-glutamate, 7.7. g/L of l-glutamate was converted to 1.1. g/L of 2-pyrrolidone within 31. h, achieving 25% molar yield from the consumed substrate. © 2015.

关键词： 2-Pyrrolidone Biosynthesis E. coli Glutamate Metabolic engineering

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Layered Diffusion Model for One-Shot High Resolution Text-to-Image Synthesis

arXiv

引用

arXiv 2024年

作者： Khwaja, Emaad Rashwan, Abdullah Chen, Ting Wang, Oliver Kothawade, Suraj Li, Yeqing UC Berkeley UCSF Joint Bioengineering Graduate Program United States Computer Science Division UC Berkeley United States Google United States Google Deepmind United Kingdom

We present a one-shot text-to-image diffusion model that can generate high-resolution images from natural language descriptions. Our model employs a layered U-Net architecture that simultaneously synthesizes images at multiple resolution scales. We show that this method outperforms the baseline of synthesizing images only at the target resolution, while reducing the computational cost per step. We demonstrate that higher resolution synthesis can be achieved by layering convolutions at additional resolution scales, in contrast to other methods which require additional models for super-resolution synthesis. © 2024, CC BY.

关键词： Diffusion

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Representing intestinal drug transport in silico: an agent-oriented approach

Representing intestinal drug transport in silico: an agent-o...

引用

Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Yu Liu C.A. Hunt UCSF/UCB Joint Graduate Group in Bioengineering University of California Berkeley CA USA Biosystems Group Department of Biopharmaceutical Sciences University of California San Francisco CA USA Biosystems Group Department of Biopharmaceutical Sciences University of California Berkeley CA USA

A prototype epithelio-mimetic device (EMD) was developed and tested. EMD components are designed to map logically to biological components at multiple levels of resolution. Those components are engineered to represent actual components within an in vitro cellular system used to study intestinal drug transport. Our goal is that the behaviors of the EMD closely match observed behaviors of the in vitro systems for a wide variety of drugs. Early stage system verification is achieved. The general patterns of experimental results from the EMD for a set of hypothetical drugs having a variety of physicochemical properties reasonably match observed patterns for a wide range of experimental conditions.

关键词： Intestines Drugs In vitro Biological system modeling Prototypes Absorption Predictive models Biomembranes Testing Design engineering

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Functional slip reflexes aid bimanual grasp

Functional slip reflexes aid bimanual grasp

引用

Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： C. Whyne G. Moy P. Lum S. Lehman UCSF/UCB슠Joint슠Graduate Group슠in슠BioEngineering Berkeley CA USA U.C. Berkeley Department EECS Berkeley CA USA Palo Alto VA Rehab R and D Ctr Berkeley CA USA

When an object is held between the outstretched hands, feedback mechanisms help to maintain the grasp. This paper reports a stereotyped bimanual response in which the hands grasp an object tighter after it begins to slip. The response has both uncrossed and crossed components, each hand responding to slip across its own fingertips, as well as to slip from the opposite hand. Electromyographic (EMG) responses to slip occur at latencies between those of a monosynaptic stretch reflex and a voluntary response. The latency to EMG on the perturbed side is about 50 ms, and 80 ms on the unperturbed side. The size of the crossed response depends on the recent experience and expectation of the subject. Smaller crossed responses occur after a series of unimanual stimuli, or when stimulus to only one hand is expected. By analogy to postural reflexes of fixed latency but adaptive amplitude, this response should be classified as a functional slip reflex.

关键词： Electromyography Delay Force measurement Wrist Research and development Humans Biomedical engineering Feedback Thumb Fingers

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A local mechanism generates saturation in an in silico model of in vitro multicellular tumor spheroid growth

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Journal of Critical Care 2007年第4期22卷 331-331页

作者： Engelberg, Jesse A. Hunt, C. Anthony University of California San Francisco The UCSF/UCB Joint Graduate Group in Bioengineering

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