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Early detection and classification of live bacteria using time-lapse coherent imaging and deep learning

Light(Science & Applications) 2020年第1期9卷 890-906页

作者： Hongda Wang Hatice Ceylan Koydemir Yunzhe Qiu Bijie Bai Yibo Zhang Yiyin Jin Sabiha Tok Enis Cagatay Yilmaz Esin Gumustekin yair Rivenson Aydogan Ozcan Electrical and Computer Engineering Department University of CaliforniaLos AngelesCA 90095USA Bioengineering Department University of CaliforniaLos AngelesCA 90095USA California NanoSystems Institute University of CaliforniaLos AngelesCA 90095USA Department of Biophysics Istanbul Medical FacultyIstanbul UniversityIstanbul 22000Turkey Department of Microbiology Immunologyand Molecular GeneticsUniversity of CaliforniaLos AngelesCA 90095USA Department of Surgery David Geffen School of MedicineUniversity of CaliforniaLos AngelesCA 90095USA

Early identification of pathogenic bacteria in food,water,and bodily fluids is very important and yet challenging,owing to sample complexities and large sample volumes that need to be rapidly *** screening methods based on plate counting or molecular analysis present various tradeoffs with regard to the detection time,accuracy/sensitivity,cost,and sample preparation ***,we present a computational live bacteria detection system that periodically captures coherent microscopy images of bacterial growth inside a 60-mm-diameter agar plate and analyses these time-lapsed holograms using deep neural networks for the rapid detection of bacterial growth and the classification of the corresponding *** performance of our system was demonstrated by the rapid detection of Escherichia coli and total coliform bacteria(i.e.,Klebsiella aerogenes and Klebsiella pneumoniae ***)in water samples,shortening the detection time by >12 h compared to the Environmental Protection Agency(EPA)-approved *** the preincubation of samples in growth media,our system achieved a limit of detection(LOD)of ~1 colony forming unit(CFU)/L in≤9 h of total test *** platform is highly cost-effective(~$0.6/test)and has high-throughput with a scanning speed of 24 cm2/min over the entire plate surface,making it highly suitable for integration with the existing methods currently used for bacteria detection on agar *** by deep learning,this automated and cost-effective live bacteria detection platform can be transformative for a wide range of applications in microbiology by significantly reducing the detection time and automating the identification of colonies without labelling or the need for an expert.

关键词： coherent Early lapse

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Computational imaging without a computer:seeing through random diffusers at the speed of light

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eLight 2022年第1期2卷 42-57页

作者： Yi Luo Yifan Zhao Jingxi Li Ege Çetintaş yair Rivenson Mona Jarrahi Aydogan Ozcan Electrical and Computer Engineering Department University of CaliforniaLos AngelesLos AngelesCA 90095USA Bioengineering Department University of CaliforniaLos AngelesLos AngelesCA 90095USA California NanoSystems Institute University of CaliforniaLos AngelesLos AngelesCA 90095USA.

Imaging through diffusers presents a challenging problem with various digital image reconstruction solutions demonstrated to date using ***,we present a computer-free,all-optical image reconstruction method to see through random diffusers at the speed of *** deep learning,a set of transmissive diffractive surfaces are trained to all-optically reconstruct images of arbitrary objects that are completely covered by unknown,random phase *** the training stage,which is a one-time effort,the resulting diffractive surfaces are fabricated and form a passive optical network that is physically positioned between the unknown object and the image plane to all-optically reconstruct the object pattern through an unknown,new phase *** experimentally demonstrated this concept using coherent THz illumination and all-optically reconstructed objects distorted by unknown,random diffusers,never used during *** digital methods,all-optical diffractive reconstructions do not require power except for the illumination *** diffractive solution to see through diffusers can be extended to other wavelengths,and might fuel various applications in biomedical imaging,astronomy,atmospheric sciences,oceanography,security,robotics,autonomous vehicles,among many others.

关键词： Imaging through diffusers Computational imaging Diffractive neural network Deep learning

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伊斯卡为医疗器械小零件加工提供大方案

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工具技术 2017年第7期51卷 I0002-I0004页

作者： yair Selek 伊斯卡端面切槽及小零件工业经理

为应对来自医疗器械工业的特殊需求，伊斯卡开发出与医疗器械工业应用范围相关的切削刀具。除技术创新的全新刀具外，伊斯卡研发部门的工作人员还对已有的受市场欢迎的一系列刀具进行修调，使其能高效而经济地加工小零件。

关键词：医疗器械工业零件加工切削刀具工业应用技术创新工作人员小零件

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Retrospective study of the associations between hepatitis C virus infection and metabolic factors

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World Journal of Hepatology 2016年第30期8卷 1269-1278页

作者： Shira yair-Sabag Elchanan Nussinson Ofir Ben-Assuli Fahmi Shibli Azmi Shahbari Shira Zelber-Sagi Gastroenterology Institute Emek Medical Center School of Public Health University of Haifa Ono Academic College

AIMTo evaluate the bidirectional association between metabolic syndrome (MS) components and antiviral treatment response for chronic hepatitis C virus (HCV) infection. METHODSThis retrospective cohort study included 119 HCV + patients treated with pegylated-interferon-α and ribavirin. Metabolic characteristics and laboratory data were collected from medical records. Differences in baseline clinical and demographic risk factors between responders and non-responders were assessed using independent samples t-tests or χ2 tests. The effects of sustained viral response (SVR) to antiviral treatment on de novo impairments in MS components, including impaired fasting glucose (IFG) and type 2 diabetes mellitus (T2DM), were assessed using univariable and multivariable logistic regression analysis, while the effect of MS components on SVR was assessed using univariable logistic regression analysis. RESULTSOf the 119 patients, 80 (67%) developed SVR over the average 54 ± 13 mo follow-up. The cumulative risks for de novo T2DM and IFG were 5.07- (95%CI: 1.261-20.4, P = 0.022) and 3.87-fold higher (95%CI: 1.484-10.15, P = 0.006), respectively for non-responders than responders, when adjusted for the baseline risk factors age, sex, HCV genotype, high viral load, and steatosis. Post-treatment triglyceride levels were significantly lower in non-responders than in responders (OR = 0.27; 95%CI: 0.069-0.962, P = 0.044). Age and HCV genotype 3 were significantly different between responders and non-responders, and MS components were not significantly associated with SVR. Steatosis tended to attenuate SVR (OR = 0.596; 95%CI: 0.331-1.073, P = 0.08). CONCLUSIONSVR was associated with lower de novo T2DM and IFG incidence and higher triglyceride levels. Patients infected with HCV should undergo T2DM screening and antidiabetic treatment.

关键词： Hepatitis C virus Type 2 diabetes mellitus Antiviral therapy Sustained viral response Metabolic syndrome Hepatic steatosis Peg interferon alpha Ribavirin Direct acting antiviral agents

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Effects of fibroblast transplantation into the internal pallidum on levodopa-induced dyskinesias in parkinsonian non-human primates

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Neuroscience Bulletin 2015年第6期31卷 705-713页

作者： Arun Singh Claire A.Gutekunst Subramaniam Uthayathas John P.M.Finberg Klaus Mewes Robert E. Gross Stella M.Papa yair Feld Neuropharmacology and Neurologic Diseases Yerkes National Primate Research Center Department of Neurosurgery Emory University School of Medicine Molecular Pharmacology Department Rappaport Faculty of Medicine Department of Neurology Emory University School of Medicine Gene Grafts Ltd

Recent studies have shown that fibroblast transplantation can modify the activity of basal ganglia networks in models of Parkinson＇s disease. To determine its effects on parkinsonian motor symptoms, we performed autologous dermal fibroblast transplantation into the internal pallidum （GPi） in two parkinsonian rhesus monkeys with stable levodopa- induced dyskinesias （LIDs）. Levodopa responses were assessed every week after transplantation for three months. A reduction of between 58% and 64% in total LIDs on the contralateral side was observed in both animals. No clear LID changes were observed on the ipsilateral side. These effects lasted the entire 3-month period in one monkey, but declined after 6-8 weeks in the other. The antiparkinsonian effects of levodopa did not diminish, The results of this pilot study indicate that fibroblast transplantation into the GPi may have beneficial effects on LIDs and warrant further investigation for potential therapeutic use.

关键词： globus pallidum autologous levodopa antiparkinsonian monkeys

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Class-specific differential detection in diffractive optical neural networks improves inference accuracy

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Advanced Photonics 2019年第4期1卷 2-14页

作者： Jingxi Li Deniz Mengu Yi Luo yair Rivenson Aydogan Ozcan University of California at Los Angeles Department of Electrical and Computer EngineeringLos AngelesCaliforniaUnited States University of California at Los Angeles Department of BioengineeringLos AngelesCaliforniaUnited States University of California at Los Angeles California NanoSystems InstituteLos AngelesCaliforniaUnited States

Optical computing provides unique opportunities in terms of parallelization,scalability,power efficiency,and computational speed and has attracted major interest for machine *** deep neural networks have been introduced earlier as an optical machine learning framework that uses task-specific diffractive surfaces designed by deep learning to all-optically perform inference,achieving promising performance for object classification and *** demonstrate systematic improvements in diffractive optical neural networks,based on a differential measurement technique that mitigates the strict nonnegativity constraint of light *** this differential detection scheme,each class is assigned to a separate pair of detectors,behind a diffractive optical network,and the class inference is made by maximizing the normalized signal difference between the photodetector *** this differential detection scheme,involving 10 photodetector pairs behind 5 diffractive layers with a total of 0.2 million neurons,we numerically achieved blind testing accuracies of 98.54%,90.54%,and 48.51%for MNIST,Fashion-MNIST,and grayscale CIFAR-10 datasets,***,by utilizing the inherent parallelization capability of optical systems,we reduced the cross-talk and optical signal coupling between the positive and negative detectors of each class by dividing the optical path into two jointly trained diffractive neural networks that work in *** further made use of this parallelization approach and divided individual classes in a target dataset among multiple jointly trained diffractive neural *** this class-specific differential detection in jointly optimized diffractive neural networks that operate in parallel,our simulations achieved blind testing accuracies of 98.52%,91.48%,and 50.82%for MNIST,Fashion-MNIST,and grayscale CIFAR-10 datasets,respectively,coming close to the performance of some of the earlier generations of all-electronic deep n

关键词： optical computation optical neural networks deep learning optical machine learning diffractive deep neural networks

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Success of acupuncture treatment in patients with initially low sperm output is associated with a decrease in scrotal skin temperature

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Asian Journal of Andrology 2009年第2期11卷 200-208页

作者： Shimon Siterman Fina Eltes Liora Schechter yair Maimon Hanny Lederman Benjamin Bartoov Maccabi Fund Complementary Medicine Kaufman StreetTel Aviv 68012Israel Refuot-Integrative Medical Centre Ramat Aviv GimelTel Aviv 69123Israel Male Fertility Laboratory Mina&Everard Goodman Faculty of Life SciencesBar Ilan UniversityRamat Gan 52900Israel

Poor spermatogenesis in patients with inflammation of the genital tract is associated with scrotal *** patients can benefit from acupuncture *** conducted a study to verify whether the influence of acupuncture treatment on sperm output in patients with low sperm density is associated with a decrease in scrotal *** experimental group included 39 men who were referred for acupuncture owing to low sperm *** control group,which comprised 18 normal fertile men,was used to define a threshold(30.5℃)above which scrotal skin temperature was considered to be ***,34 of the 39 participants in the experimental group initially had high scrotal skin temperature;the other five had normal *** skin temperature and sperm concentration were measured before and after acupuncture *** five patients with initially normal scrotal temperatures were not affected by the acupuncture *** treatment,17 of the 34 patients with hyperthermia,all of whom had genital tract inflammation,had normal scrotal skin temperature;in 15 of these 17 patients,sperm count was *** the remaining 17 men with scrotal hyperthermia,neither scrotal skin temperature nor sperm concentration was affected by the *** 90%of the latter patients suffered from high gonadotropins or mixed etiological *** sperm count in patients with inflammation of the genital tract seems to be associated with scrotal hyperthermia,and,consequently,acupuncture treatment is recommended for these men.

关键词： acupuncture poor spermatogenesis scrotal skin hyperthermia

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PhaseStain:the digital staining of label-free quantitative phase microscopy images using deep learning

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Light(Science & Applications) 2019年第1期8卷 983-993页

作者： yair Rivenson Tairan Liu Zhensong Wei Yibo Zhang Kevin de Haan Aydogan Ozcan Electrical and Computer Engineering Department University of CaliforniaLos AngelesCA 90095USA Bioengineering Department University of CaliforniaLos AngelesCA 90095USA California NanoSystems Institute(CNSI) University of CaliforniaLos AngelesCA 90095USA Department of Surgery David Geffen School of MedicineUniversity of CaliforniaLos AngelesCA 90095USA

Using a deep neural network,we demonstrate a digital staining technique,which we term PhaseStain,to transform the quantitative phase images(QPI)of label-free tissue sections into images that are equivalent to the brightfield microscopy images of the same samples that are histologically *** pairs of image data(QPI and the corresponding brightfield images,acquired after staining),we train a generative adversarial network and demonstrate the effectiveness of this virtual-staining approach using sections of human skin,kidney,and liver tissue,matching the brightfield microscopy images of the same samples stained with Hematoxylin and Eosin,Jones’stain,and Masson’s trichrome stain,*** digital-staining framework may further strengthen various uses of label-free QPI techniques in pathology applications and biomedical research in general,by eliminating the need for histological staining,reducing sample preparation related costs and saving *** results provide a powerful example of some of the unique opportunities created by data-driven image transformations enabled by deep learning.

关键词： network image Phase

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Adenocarcinoma of the small bowel in a patient with occlusive Crohn's disease

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World Journal of Gastrointestinal Oncology 2012年第7期4卷 184-186页

作者： Lior Drukker yair Edden Petachia Reissman Department of General Surgery Shaare Zedek Medical Center Hebrew University Hadassah School of Medicine PO Box 3235 Jerusalem 91031 Israel

A 40-year-old male, diagnosed with mild Crohn's disease (CD) 11 years ago but with no prior abdominal surgeries, was diagnosed with a small bowel stricture, due to ongoing abdominal pain and intolerance of enteral diet, and referred for surgical treatment. Exploratory laparoscopy revealed a white solid mass causing a near total jejunal obstruction with significant proximal dilatation. An adjacent small node was sampled for frozen biopsy, revealing a lymph node infiltrated with adenocarcinoma. Laparoscopic assisted small bowel resection and appendectomy were carried out. Final pathological results supported the initial report of diffuse small bowel adenocarcinoma. In conclusion, once a small bowel stricture associated with CD is suspected, rapid action should be considered to avoid late diagnosis of a neoplasia.

关键词： Inflammatory bowel disease Crohn’s disease Small bowel obstruction Small bowel stricture Small bowel adenocarcinoma

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北京地区闪电活动与气溶胶浓度的关系研究

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地球物理学报 2020年第5期63卷 1766-1774页

作者：孙萌宇郄秀书刘冬霞 Yoav yair 夏祥鳌袁善锋王东方卢晶雨 Abhay Srivastava Didier Ntwali 中国科学院大气物理研究所中层大气与全球环境探测重点实验室北京100029 School of Sustainability Interdisciplinary Center(IDC)Herzliya 中国科学院大学地球与行星科学学院北京100049

基于2015—2017年北京闪电定位网(BLNET)总闪资料与35个自动空气质量监测站PM 2.5数据,分析了北京地区(39.5°N—41.0°N,115.0°E—117.5°E)夏季(6—8月)闪电活动与PM 2.5的时空分布特征,同时针对117次雷暴天气,探讨了气溶胶浓度变化... 详细信息

基于2015—2017年北京闪电定位网(BLNET)总闪资料与35个自动空气质量监测站PM 2.5数据,分析了北京地区(39.5°N—41.0°N,115.0°E—117.5°E)夏季(6—8月)闪电活动与PM 2.5的时空分布特征,同时针对117次雷暴天气,探讨了气溶胶浓度变化对闪电活动的可能影响.结果表明:PM 2.5浓度及总闪密度均呈现自西北向东南升高的空间分布特征.闪电峰值在污染背景下出现的时间(19∶00LT)晚于清洁背景下(15∶00LT)约4 h,且总闪百分比(~20%)可达清洁背景下(~9%)的两倍.对雷暴前1~4 h的PM 2.5浓度与时间窗(12∶00—22∶00LT)内总闪数目的中位数进行相关分析,发现PM 2.5浓度低于130μg·m-3时,PM 2.5与总闪数存在明显正相关,此时气溶胶可能通过影响云微物理过程进而影响雷暴的对流发展,增强闪电活动;PM 2.5大于150μg·m-3时,总闪数随PM 2.5浓度的增加呈减少趋势,可能的原因是高气溶胶浓度下地面太阳辐射显著下降,对流活动受到抑制,导致闪电活动减少.当PM 2.5浓度在130~150μg·m-3时,两者关系不明显.

关键词：闪电活动气溶胶微物理作用辐射效应

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