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scDPN for High-throughput Single-cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 346-357页

作者： Liang Wu Miaomiao Jiang Yuzhou Wang Biaofeng Zhou Yunfan Sun Kaiqian Zhou Jiarui Xie Yu Zhong Zhikun Zhao michael dean Yong Hou Shiping Liu BGI Education Center University of Chinese Academy of SciencesShenzhen 518083China BGI-Shenzhen Beishan Industrial ZoneShenzhen 518083China Shenzhen Key Laboratory of Single-Cell Omics BGI-ShenzhenShenzhen 518100China Department of Liver Surgery&Transplantation Liver Cancer InstituteZhongshan HospitalFudan UniversityMOE Key Laboratory of Carcinogenesis and Cancer InvasionShanghai 200032China School of Biology and Biological Engineering South China University of TechnologyGuangzhou 510640China Laboratory of Translational Genomics Division of Cancer Epidemiology&GeneticsNational Cancer InstituteGaithersburgMD 20877USA

Single-cell genomics provides substantial resources for dissecting cellular heterogeneity and cancer evolution.Unfortunately,classical DNA amplification-based methods have low throughput and introduce coverage bias during sample preamplification.We developed a single-cell DNA library preparation method without preamplification in nanolitre scale(scDPN)to address these issues.The method achieved a throughput of up to 1800 cells per run for copy number variation(CNV)detection.Also,our approach demonstrated a lower level of amplification bias and noise than the multiple displacement amplification(MDA)method and showed high sensitivity and accuracy for cell line and tumor tissue evaluation.We used this approach to profile the tumor clones in paired primary and relapsed tumor samples of hepatocellular carcinoma(HCC).We identified three clonal subpopulations with a multitude of aneuploid alterations across the genome.Furthermore,we observed that a minor clone of the primary tumor containing additional alterations in chromosomes 1q,10q,and 14q developed into the dominant clone in the recurrent tumor,indicating clonal selection during recurrence in HCC.Overall,this approach provides a comprehensive and scalable solution to understand genome heterogeneity and evolution.

关键词： Single-cell sequencing Hepatocellular carcinoma Heterogeneity Clonal evolution Relapse

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梦你所想

中学生英语（高中版） 2006年第8期 20-21页

作者：高素菊 michael dean 河北省邢台市职教中心中学部

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Love actually

Temporal variability of problem drinking on Twitter

2008年

作者： Richard Curtis retold by michael dean.

来源：畅想之星图书光盘版（南... 评论

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Open Journal of Preventive Medicine 2012年第1期2卷 43-48页

作者： Joshua Heber West Parley Cougar Hall Carl Lee Hanson Kyle Prier Christophe Giraud-Carrier E. Shannon Neeley michael dean Barnes Department of Health Science Brigham Young University Provo USA

Twitter is a micro-blogging application, which is commonly used as a way for individuals to maintain social connections. Social scientists have also begun using Twitter as a data source for understanding more about human interactions. There is very little research about Twitter’s utility for monitoring health related attitudes, beliefs and behaviors. The purpose of this study was to examine the extent to which individuals tweeted about problem drinking, and to identify if such tweets corresponded with time periods when problem drinking was likely to occur. Data from this study came from tweets originating in one of 9 randomly selected states, one from each of the nine census geographies in the US. Twitter’s API was used to collect tweets during the month of October 2010, and again during the time period surrounding New Year’s Eve 2010. Keywords were selected which indicated problem-drinking behaviors, and tweets were coded for the presence or absence of these keywords. Twitter users were most likely to tweet about problem drinking on Friday, Saturday and Sunday during the hours from 10 pm to 2 am. Tweets originating during the New Year’s Eve holiday (0.53%) were twice as common when compared to tweets during weekends in the month of October (0.34%). Twitter may be a valid data source for social scientists, given that tweets about problem drinking corresponded with expected time periods of actual problem drinking. Furthermore, tweets that mention problem drinking may be problematic for public health if they establish incorrect normative beliefs that such behaviors are acceptable and expected. Social norms interventions may be an effective tool in correcting misperceptions related to problem drinking by informing Twitter followers that problem drinking behaveiors are not normative.

关键词： Twitter Problem Drinking Temporal Variance

A survey of image-based computational learning techniques for frost detection in plants

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Information Processing in Agriculture 2023年第2期10卷 164-191页

作者： Sayma Shammi Ferdous Sohel dean Diepeveen Sebastian Zander michael G.K.Jones Discipline of Information Technology Murdoch UniversityMurdochWA 6150Australia Centre for Crop and Food Innovation Food Futures InstituteMurdoch UniversityMurdochWA 6150Australia Department of Primary Industries and Regional Development Western AustraliaSouth PerthWA 6151Australia

Frost damage is one of the major concerns for crop growers as it can impact the growth of the plants and hence,yields.Early detection of frost can help farmers mitigating its impact.In the past,frost detection was a manual or visual process.Image-based techniques are increasingly being used to understand frost development in plants and automatic assessment of damage resulting from frost.This research presents a comprehensive survey of the state-of the-art methods applied to detect and analyse frost stress in plants.We identify three broad computational learning approaches i.e.,statistical,traditional machine learning and deep learning,applied to images to detect and analyse frost in plants.We propose a novel taxonomy to classify the existing studies based on several attributes.This taxonomy has been developed to classify the major characteristics of a significant body of published research.In this survey,we profile 80 relevant papers based on the proposed taxonomy.We thoroughly analyse and discuss the techniques used in the various approaches,i.e.,data acquisition,data preparation,feature extraction,computational learning,and evaluation.We summarise the current challenges and discuss the opportunities for future research and development in this area including in-field advanced artificial intelligence systems for real-time frost monitoring.

关键词： Frost Cold stress Machine learning Image analysis Crop Plant

Non-invasive determination of murine placental and foetal functional parameters with multispectral optoacoustic tomography

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Light(Science & Applications) 2019年第1期8卷 553-562页

作者： Kausik Basak Xose Luis dean-Ben Sven Gottschalk michael Reiss Daniel Razansky Faculty of Medicine Technical University MunichMunichGermany Institute for Biological and Medical Imaging Helmholtz Center MunichNeuherbergGermany Faculty of Medicine and Institute of Pharmacology and Toxicology University of ZurichZurichSwitzerland Institute for Biomedical Engineering and Department of Information Technology and Electrical Engineering ETH ZurichZurichSwitzerland Institute of Advanced Studies and Research JIS UniversityKolkataWest BengalIndia

Despite the importance of placental function in embryonic development,it remains poorly understood and challenging to characterize,primarily due to the lack of non-invasive imaging tools capable of monitoring placental and foetal oxygenation and perfusion parameters during pregnancy.We developed an optoacoustic tomography approach for real-time imaging through entire ~4 cm cross-sections of pregnant mice.Functional changes in both maternal and embryo regions were studied at different gestation days when subjected to an oxygen breathing challenge and perfusion with indocyanine green.Structural phenotyping of the cross-sectional scans highlighted different internal organs,whereas multi-wavelength acquisitions enabled non-invasive label-free spectroscopic assessment of blood-oxygenation parameters in foeto-placental regions,rendering a strong correlation with the amount of oxygen administered.Likewise,the placental function in protecting the embryo from extrinsically administered agents was substantiated.The proposed methodology may potentially further serve as a probing mechanism to appraise embryo development during pregnancy in the clinical setting.

关键词： rendering placental sectional

Hurricane disturbances, tree diversity, and succession in North Carolina Piedmont forests, USA

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Journal of Forestry Research 2019年第1期30卷 219-231页

作者： Weimin Xi Robert K.Peet michael T.Lee dean L.Urban Department of Biology University of North Carolina at Chapel Hill Department of Biological and Health Sciences Texas A & M University-Kingsville The Nicholas School of the Environment Duke University

Windthrow plays a critical role in maintaining species diversity in temperate forests. Do large-scale strong wind events(i.e., tropical cyclones, including hurricanes,typhoons and severe cyclonic storms) increase tree diversity in severely damaged forest areas? Do hurricanes(tropical cyclones that occurs in the Atlantic Ocean and northeastern Pacific Ocean) lead to altered relative abundance of shade-tolerant and shade-intolerant species? Did historic hurricanes alter the succession trajectory of the damaged forests? We used nearly 70-year tree demographic data to assess the effects of two major hurricanes on woody species diversity in Piedmont forests, North Carolina, USA. Species richness(S) and Shannon–Wiener's diversity index(H') were used to evaluate the changes in tree diversity. The changes in composition were assessed with Nonmetric Multidimensional Scaling. The pre-hurricane successional phase can strongly influence both the damage severity and subsequent responses. Although there is often an immediate drop in diversity following a hurricane, understory tree diversity quickly increases to levels that exceed those prior to the disturbance. This leads to an increase in diversity in stands that were substantially damaged. Hurricanes significantly decrease the dominance of shade-intolerant canopy species while increasing preestablished, more shade-tolerant species. We conclude that large, and infrequent hurricanes help to maintain local tree diversity, but also accelerate the increase in dominance of understory species such as red maple and beech.

关键词： Wind disturbance Tree species diversity Plant succession Disturbance-diversity relationship Piedmont forests

Respiratory plasticity following spinal cord injury:perspectives from mouse to man

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Neural Regeneration Research 2022年第10期17卷 2141-2148页

作者： Katherine C.Locke Margo L.Randelman Daniel J.Hoh Lyandysha V.Zholudeva michael A.Lane Department of Neurobiology&Anatomy Drexel UniversityPhiladelphiaPAUSA Marion Murray Spinal Cord Research Center PhiladelphiaPAUSA Lillian S.Wells Department of Neurosurgery University of FloridaGainesvilleFLUSA Cardiovascular Disease Gladstone InstitutesSan FranciscoCAUSA

The study of respiratory plasticity in animal models spans decades.At the bench,researchers use an array of techniques aimed at harnessing the power of plasticity within the central nervous system to restore respiration following spinal cord injury.This field of research is highly clinically relevant.People living with cervical spinal cord injury at or above the level of the phrenic motoneuron pool at spinal levels C3-C5 typically have significant impairments in breathing which may require assisted ventilation.Those who are ventilator dependent are at an increased risk of ventilator-associated co-morbidities and have a drastically reduced life expectancy.Pre-clinical research examining respiratory plasticity in animal models has laid the groundwork for clinical trials.Despite how widely researched this injury is in animal models,relatively few treatments have broken through the preclinical barrier.The three goals of this present review are to define plasticity as it pertains to respiratory function post-spinal cord injury,discuss plasticity models of spinal cord injury used in research,and explore the shift from preclinical to clinical research.By investigating current targets of respiratory plasticity research,we hope to illuminate preclinical work that can influence future clinical investigations and the advancement of treatments for spinal cord injury.

关键词： breathing phrenic plasticity rehabilitation respiration spinal cord injury translation

Surface Characterization of As-Spun and Supercontracted <i>Nephila clavipes</i>Dragline Silk

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Journal of Surface Engineered Materials and Advanced Technology 2013年第3期3卷 18-26页

作者： Benoit Faugas michael S. Ellison Delphine dean Marian S. Kennedy Department of Bioengineering Clemson University Clemson USA. Department of Materials Science & Engineering Clemson University Clemson USA

Dragline spider silks have relatively high mass-based mechanical properties (tensile strength, elongation to break and rupture energy) and are environmentally responsive (supercontraction). In order to produce new synthetic fibers with these properties, many research groups have focused on identifying the chemical composition of these fibers and the structure of the fiber core. Since each fiber also has an outer skin, our study will provide a detailed understanding of the silk surface morphology, the response of the surface morphology to environmental conditions and processing variables, and also determine if the silk surface has a definitive patterning of charged amino acids. Specifically, by using force microscopy and functionalized nanoparticles, the present study examines 1) how the silk surface (topography, average roughness) is altered due to prior mechanical loading (viz. reeling speed), 2) alterations in morphology due to environmental conditions (supercontraction, storage time), and 3) the negatively and positively charged regions along with the surface using both force and nanoparticle mapping. Roughness data taken on dragline silk collected from Nephila clavipes spiders revealed that the surface comprised both smooth (5 nm RMS) and rough (65 nm RMS) regions. Supercontracted silk (from immersion in0.01 MPBS during AFM testing) showed higher surface roughness values compared to spider silk tested in the air, indicating that the surface might be reorganized during supercontraction. No correlation was found between surface roughness and neither collection speed nor aging time for the as-spun or supercontracted fiber, demonstrating the surface stability of the dragline silk over time in terms of roughness. Both the force microscopy and the nanoparticle methods suggested that the density of negatively charged amino acids (glutamic acid, aspartic acid) was higher than that of the positively charged amino acids (lysine, asparagine, and histidine).

关键词： Spider Dragline Silk Surface Roughness Supercontraction Amino Acids AFM Force Microscopy Na-noparticles