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第五届全国生物信息学与系统生物学学术大会暨国际生物信息...

作者： Brenda B.Su Marco Capecchi Cedric Manlhiot Yuqing Yan Edgar T Jaeggi earl d.silverman Robert M.Hamilton. 生命科学与生物技术学院哈尔滨师范大学哈尔滨医科大学生物信息科学与技术学院多伦多大学病童医院

Rational:Cardiac conduction disease is multifactorial complex *** factors play critical roles in formation of cardiac conductive tissue during fetal heart *** has been recognized that environmental factors also alter during fetal development increase the risk of cardiac conduction *** are few genes shown can be altered and effect on heart structure formation during the ***,the gene expression in conductive tissue in human fetal heart and the underlying molecular mechanisms remain poorly *** this study,we identify genes expressed preferentially within the atrial ventricular conductive junctional tissue(AVJ) in human fetal hearts as compared to the apical myocardium(Apx). Methods:Total RNA from six fetal hearts was extracted using Qiagen RNA kit and applied onto Affymetrix human Genome U133 plus 2(micro)*** results were analyzed by Affymetrix console and Partek? Genomics SuiteTM. Results:We found that 1532 genes significantly(pd in atrial ventricular conductive junctional tissue than that in apex at 20-23 weeks of gestation,including 496 genes greater than 2-fold differential expression between fetal cardiac atrial ventricular junction and ***1d,CACNA1G and HTR4 expressed preferentially in human atrial ventricular conductive tissue.A subset of the data was confirmed by Real-Time PCR and immunostaining.245 genes highly expressed in human atrial ventricular conductive junctional tissue were matched to the gene expression in mouse atrial ventricular nodal cells and 103 genes were matched to E10.5 mouse the atrial ventricular node(pde specific markers for the human fetal atrial ventricular conduction system,which might be important targets in the pathophysiology of cardiac conduction diseases in heart development.

关键词： cardiac conduction diseases gene expression microarray atrial ventricular tissue

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Preclinical-to-clinical Anti-cancer drug Response Prediction and Biomarker Identification Using TINdL

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Genomics, Proteomics & Bioinformatics 2023年第3期21卷 535-550页

作者： david earl Hostallero Lixuan Wei Liewei Wang Junmei Cairns Amin Emad department of Electrical and Computer Engineering McGill UniversityMontrealQC H3A 0E9Canada Mila–Quebec Artificial Intelligence Institute MontrealQC H2S 3H1Canada department of Molecular Pharmacology and Experimental Therapeutics Mayo ClinicRochesterMN 55905USA The Rosalind and Morris Goodman Cancer Institute McGill UniversityMontrealQC H3A 1A3Canada

Prediction of the response of cancer patients to different treatments and identification of biomarkers of drug response are two major goals of individualized ***,we developed a deep learning framework called TINdL,completely trained on preclinical cancer cell lines(CCLs),to predict the response of cancer patients to different *** utilizes a tissue-informed normalization to account for the tissue type and cancer type of the tumors and to reduce the statistical discrepancies between CCLs and patient ***,by making the deep learning black box interpretable,this model identifies a small set of genes whose expression levels are predictive of drug response in the trained model,enabling identification of biomarkers of drug *** data from two large databases of CCLs and cancer tumors,we showed that this model can distinguish between sensitive and resistant tumors for 10(out of 14)drugs,outperforming various other machine learning *** addition,our small interfering RNA(siRNA)knockdown experiments on 10 genes identified by this model for one of the drugs(tamoxifen)confirmed that tamoxifen sensitivity is substantially influenced by all of these genes in MCF7 cells,and seven of these genes in T47d ***,genes implicated for multiple drugs pointed to shared mechanism of action among drugs and suggested several important signaling *** summary,this study provides a powerful deep learning framework for prediction of drug response and identification of biomarkers of drug response in *** code can be accessed at https://***/ddhostallero/tindl.

关键词： drug response deep learning Explainable AI Cancer Gene knockdown experiment

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THE EFFECT OF TISSUE dISAGGREGATION METHOdS ON THE CLONOGENICITY OF SOLId HUMAN TUMOR CELLS

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中华医学杂志(英文版) 1992年第2期105卷 126-131页

作者：李同光 Lisa d Blackburn Ronnie d Horner Jan F silverman Albert L Wiley Jr. departments of Radiation Oncology Family Medicine Clinical Pathology and Diagnostic Medicine East Carolina University School of Medicine Greenville NC 27858 USA

The effect of mechanical,enzymatic and com-bined disaggregations on the same tumor tissue(n=154)to define variables related to clonogenic effi-ciency (CE) of human tumor clonogenic assay(HTCA)was ***,CE was highly asso-ciated with the percentage of malignant cells in theinoculative suspensions(Pd the total cellconcentration plated(P=0.03).However,there was nosignificant correlation between CE and thedisaggregation method,type of tumor,cell viability,proportion of macrophages in the inoculum,or lengthof incubation(10 or 20 days).In addition,a higher CEwas found in some nonadherent fractions when com-paring the CE of the original plating suspensions tothat of their nonadherent *** is concluded thatmechanical disaggregation is the simplest technique forobtaining the highest yield of malignant cells,which isa decisive factor for colony growth,and that anincubation time of 10 days and 1×10～6cells per plate is the best condition for the human tu-mor clonogenic assay.

关键词： SOFT-AGAR GROWTH ASSAY

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Active sorting of orbital angular momentum states of light with a cascaded tunable resonator

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Light(Science & Applications) 2020年第1期9卷 1904-1913页

作者： Shibiao Wei Stuart K.earl Jiao Lin Shan Shan Kou Xiao-Cong Yuan Nanophotonics Research Center Shenzhen Key Laboratory of Micro-Scale Optical Information TechnologyShenzhen UniversityShenzhen 518060China department of Chemistry and Physics La Trobe Institute for Molecular Science(LIMS)La Trobe UniversityVictoria 3086Australia School of Engineering RMIT UniversityMelbourneVictoria 3001Australia School of Physics The University of MelbourneTin AlleyMelbourneVictoria 3010Australia

The orbital angular momentum(OAM)of light has been shown to be useful in diverse fields ranging from astronomy and optical trapping to optical communications and data ***,one of the primary impediments preventing such applications from widespread adoption is the lack of a straightforward and dynamic method to sort incident OAM states without altering the ***,we report a technique that can dynamically filter individual OAM states and preserve the incident OAM states for subsequent *** the working principle of this technique is based on resonance,the device operation is not limited to a particular *** states with different wavelengths can resonate in the resonator without any additional modulation other than changing the length of the ***,we are able to demonstrate a reconfigurable OAM sorter that is constructed by cascading such optical *** approach does not require specially designed components and is readily amenable to integration into potential applications.

关键词： resonator tunable momentum

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Interpretatio Romana: an Influence on Old English Vocabulary

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外语教学 1997年第4期18卷 11-27页

作者： earl R. Anderson(department of EnglishCleveland State University)

: Latin influences on early English vocabulary usually are considered atomistically: the idea is that individual Latin words are berrowed, although sometimes these words belong to a semantic field that reflects the type of cultural or political contact that led to the borrowing. Thus, words borrowed from Latin into dritinental Germanic before the fifth century A. d. mostIy belong to the semantic fields of commerce and military activity; words borrowed during the seventh century, when the AngloSaxons gradually adopted Christianity, mostly belong to the semantic fields of religion, literacy and edu-cation; and words bormwed from ca. 950 - 1020- the time of the Bencdictine Reform, mootly are words of a bookish, learned, or technical character and are the by-product of translation of Latin scholarly treatises into Old English.

关键词： Be an Influence on Old English Vocabulary Interpretatio Romana

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Protective effect of hydroxychloroquine on rheumatoid arthritis-associated atherosclerosis

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Animal Models and Experimental Medicine 2019年第2期2卷 98-106页

作者： Na Shi Shuangyue Zhang Gregg silverman Mengtao Li Jun Cai Haitao Niu NHC Key Laboratory of Human disease Comparative Medicine (The Institute of Laboratory Animal Sciences CAMS&PUMC) Key Laboratory of Human Diseases Animal Model State Administration of Traditional Chinese Medicine Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases Beijing China department of Rheumatology Langone Medical Center New York University New York City New York Peking Union Medical College Hospital Beijing China Fuwai Hospital Chinese Academy of Medical Sciences Beijing China

Background: Patients with rheumatoid arthritis (RA) have an increased risk for cardiovascular disease. We examined the effect of gut microbiota in a mouse model of RA that develops atherosclerosis. Methods: We created three groups of K/BxN female mice that were positive for the anti‐glucose‐6‐phosphate isomerase (GPI) antibody: control diet (Cd), high fat diet (HFd), and HFd with hydroxychloroquine (HFd + HCQ). Serological tests were used to detect the serum levels of total cholesterol (TCHO), low‐density lipoprotein cholesterol (LdL‐C), triglyceride (TG), high‐density lipoprotein cholesterol (HdL‐C), anti‐ GPI antibody titers, and serum cytokines. Atherosclerotic plaque was determined by histological analysis, and gut microbiota were determined by 16sV4 sequencing. Results: Relative to mice given the Cd, those receiving the HFd had increased serum levels of LdL‐C, TCHO, and TG, decreased serum levels of HdL‐C, increased atherosclerotic lesions in the aortic root, and altered gut microbiota. Addition of HCQ to HFd decreased the serum levels of LdL‐C, TCHO, and TG, increased serum levels of HdL‐C, and decreased the atherosclerotic lesions in the aortic root. Mice receiving HFd + HCQ also had the greatest bacterial diversity among the three experimental groups. Moreover, HCQ treatment significantly increased the abundance of Akkermansia and Parabacteroides, and decreased the abundance of Clostridium sensu stricto cluster 1, and therefore may be responsible for the reduced RA‐associated atherosclerosis and dyslipidemia. Conclusion: Our mouse model of RA indicated that HFd increased ankle width and aggravated a therosclerosis a nd d yslipidemia, a nd t hat H CQ a lleviated t he d yslipidemia and atherosclerosis, but had no effect on ankle width.

关键词： atherosclerosis autoimmunity hydroxychloroquine intestinal microbiota rheumatoid arthritis

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dynamic Characteristics of double-Helical Planetary Gear Sets Under Time-Varying Mesh Stiffness

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Journal of Harbin Institute of Technology(New Series) 2016年第4期23卷 44-51页

作者： He Lin Sanmin Wang earl Hdowell Jincheng dong Cong Ma School of Mechanical Engineering Northwestern Polytechnical UniversityX i'an 710072China department of Materials Science and Mechanical Engineering Duke UniversityDurham 27705USA

Internal and external meshes are two of primary excitation sources which induce vibration while double-helical planetary gear sets are in transmission. Based on the analysis of tooth movement principle,three cases of mesh stiffness are derived via investigating the length of action lines,and catalogued in terms of β d β > β_0. The simulation demonstrates mesh stiffness between gear pairs performs as a trapezoid waveform( TW) and changes along with the line of action simultaneously,total mesh stiffness comes from the superposition of each engaged gear. While governing equations of motion contained 16 dOFs( degree of freedom) are constructed and effectively solved through the combination of numerical approaches. Comparing with sinusoidal waveform mesh stiffness( SW),the results show that dynamical factors and perturbation under the excitation of TW( β d remarkable than that from SW,with respect to the mean dynamic factors about 1. 51 and 1. 28,respectively. The fluctuation response between ring- planet( R- P) is stronger than sun-planet( S-P) which is also validated by both approach studies,frequency spectra analyses identifies larger distinct rotational resonance and more frequencies under TW excitation.

关键词： time-varying mesh stiffness trapezoid waveform mean dynamical factors frequency spectra

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Research methods for criminal justice and criminology (4E)/ 4th ed.

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2005年

作者： Michael G. Maxfield earl Babbie.

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Analysis of Residence Time in the Measurement of Radon Activity by Passive diffusion in an Open Volume: A Micro-Statistical Approach

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World Journal of Nuclear Science and Technology 2017年第4期7卷 252-273页

作者： M. P. silverman department of Physics Trinity College Hartford CT USA

Residence time in a flow measurement of radioactivity is the time spent by a pre-determined quantity of radioactive sample in the flow cell. In a recent report of the measurement of indoor radon by passive diffusion in an open volume (i.e. no flow cell or control volume), the concept of residence time was generalized to apply to measurement conditions with random, rather than directed, flow. The generalization, leading to a quantity δtr, involved use of a) a phenomenological alpha-particle range function to calculate the effective detection volume, and b) a phenomenological description of diffusion by Fick’s law to determine the effective flow velocity. This paper examines the residence time in passive diffusion from the micro-statistical perspective of single-particle continuous Brownian motion. The statistical quantity “mean residence time” Tr is derived from the Green’s function for unbiased single-particle diffusion and is shown to be consistent with δtr. The finite statistical lifetime of the randomly moving radioactive atom plays an essential part. For stable particles, Tr is of infinite duration, whereas for an unstable particle (such as 222Rn), with diffusivity d and decay rate λ, Tr is approximately the effective size of the detection region divided by the characteristic diffusion velocity . Comparison of the mean residence time with the time of first passage (or exit time) in the theory of stochastic processes shows the conditions under which the two measures of time are equivalent and helps elucidate the connection between the phenomenological and statistical descriptions of radon diffusion.

关键词： Radon diffusion Brownian Motion Random Walk Residence Time First-Passage Time Exit Time

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Optical force-induced nonlinearity and self-guiding of light in human red blood cell suspensions

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Light(Science & Applications) 2019年第1期8卷 927-935页

作者： Rekha Gautam Yinxiao Xiang Josh Lamstein Yi Liang Anna Bezryadina Guo Liang Tobias Hansson Benjamin Wetzel daryl Preece Adam White Matthew silverman Susan Kazarian Jingjun Xu Roberto Morandotti Zhigang Chen department of Physics and Astronomy San Francisco State UniversitySan FranciscoCA 94132USA department of Biomedical Engineering Vanderbilt UniversityNashvilleTN 37240USA MOE Key Lab of Weak-Light Nonlinear Photonics TEDA Applied Physics Institute and School of PhysicsNankai UniversityTianjin 300457China Guangxi Key Lab for Relativistic Astrophysics Guangxi Colleges and Universities Key Lab of Novel Energy Materials and Related TechnologySchool of Physical Science and TechnologyGuangxi UniversityNanningGuangxi 530004China department of Physics and Astronomy California State University NorthridgeNorthridgeCA 91330USA Institut National de la Recherche Scientifique Universite du QuebecVarennesQC J3X 1S2Canada department of Physics Chemistry and BiologyLinkoping UniversityLinkoping SE-58183Sweden School of Mathematical and Physical Sciences University of SussexSussex HouseFalmerBrighton BN19RHUK department of Biomedical Engineering University of California IrvineIrvineCAUSA Clinical Laboratory Science Program San Francisco State UniversitySan FranciscoCA 94132USA Institute of Fundamental and Frontier Sciences University of Electronic Science and Tech.of ChinaChengdu 610054China ITMO University Saint Petersburg 197101Russia

Osmotic conditions play an important role in the cell properties of human red blood cells(RBCs),which are crucial for the pathological analysis of some blood diseases such as *** the past decades,numerous efforts have mainly focused on the study of the RBC biomechanical properties that arise from the unique deformability of ***,we demonstrate nonlinear optical effects from human RBCs suspended in different osmotic ***,we observe self-trapping and scattering-resistant nonlinear propagation of a laser beam through RBC suspensions under all three osmotic conditions,where the strength of the optical nonlinearity increases with osmotic pressure on the *** tunable nonlinearity is attributed to optical forces,particularly the forward-scattering and gradient ***,in aged blood samples(with lysed cells),a notably different nonlinear behavior is observed due to the presence of free *** use a theoretical model with an optical force-mediated nonlocal nonlinearity to explain the experimental *** work on light self-guiding through scattering biosoft-matter may introduce new photonic tools for noninvasive biomedical imaging and medical diagnosis.

关键词： nonlinearity suspensions nonlinear

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