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Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics

Fungal Diversity 2020年第5期104卷 267-289页

作者： Natalie Vandepol Julian Liber Alessandro Desirò Hyunsoo Na Megan Kennedy Kerrie Barry Igor V.Grigoriev Andrew N.Miller Kerry O’Donnell jason e.stajich Gregory Bonito Department of Microbiology and Molecular Genetics Michigan State UniversityEast LansingMI 48824USA Department of Plant Biology Michigan State UniversityEast LansingMI 48824USA Department of Plant Soil and Microbial Sciences Michigan State UniversityEast LansingMI 48824USA Joint Genome Institute BerkeleyCA 94720USA Illinois Natural History Survey University of Illinois Urbana-ChampaignChampaignIL 61820USA United States Department of Agriculture Agricultural Research ServicePeoriaIL 61604USA Department of Microbiology and Plant Pathology&Institute for Integrative Genome Biology University of California-RiversideRiversideCA 92521USA

early efforts to classify Mortierellaceae were based on macro-and micromorphology,but sequencing and phylogenetic studies with ribosomal DNA(rDNA)markers have demonstrated conflicting taxonomic groupings and polyphyletic *** some taxonomic confusion in the family has been clarified,rDNA data alone is unable to resolve higher level phylogenetic relationships within *** this study,we applied two parallel approaches to resolve the Mortierel-laceae phylogeny:low coverage genome(LCG)sequencing and high-throughput,multiplexed targeted amplicon sequenc-ing to generate sequence data for multi-gene *** then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon *** the Mortierellaceae phylogeny into monophyletic genera resulted in 13 genera,7 of which are newly ***-coverage genome sequencing proved to be a relatively cost-effective means of generating a high-confidence *** multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach,but has limitations *** present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity and evolution.

关键词： Mortierellaceae Phylogenomics Molecular systematics Taxonomy Multi-locus sequence typing

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Prostate-specific antigen （PSA） screening： has the pendulum swung too far？

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Asian Journal of Andrology 2011年第5期13卷 655-656页

作者： jason M Phillips e David Crawford Department of Urology University of Colorado HealthSciences Center Aurora CO 80045 USA

Prostate-specific antigen （PSA） along with digital rectal exam has been the standard for prostate cancer screening in the United States for the past 20 years.1 During this time period, the improved detection of prostate cancer decreased related mortality more than 30%.2 In fact, metastases and their comorbidities have decreased more than 75% since the early 1990s, resulting in a higher incidence of early organ-confined disease. While it is clear that prostate cancer mortality statistics have improved, it is unclear whether men are overscreened.

关键词： overscreened Prostate-specific

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Crustacean parasites associated with hermit crabs from the western Mediterranean Sea,with first documentation of egg predation by the burrowing barnacle Trypetesa lampas(Cirripedia:Acrothoracica:Trypetesidae)

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Integrative Zoology 2011年第1期6卷 13-27页

作者： jason D.WILLIAMS Alejandra GALLARDO Angela e.MURPHY Department of Biology Hofstra UniversityHempsteadNYUSA

Parasitic isopods(family Bopyridae)and burrowing barnacles(family Trypetesidae)infesting hermit crabs were investigated from shallow subtidal collections made along the southeastern coast of Spain in 2009.A total of 713 specimens of Clibanarius erythropus(Latreille,1818)and 82 Calcinus tubularis(L.,1767)were *** shells and worm tubes inhabited by hermit crabs were collected by hand while snorkeling and were cracked to determine host species,size,sex and presence of *** species of bopyrid isopods were found on ***:the branchial parasite Bopyrissa fraiseii(Carayon,1943)and the abdominal parasite Parathelges cardonae Codreanu and Codreanu in Codreanu,*** all *** examined,Bopyrissa fraiseii was found on 0.6%of hermit crabs and *** was found on 0.3%.A redescription of *** is provided and the species is documented with light and scanning electron microscopy for the first *** Calcinus tubularis harbored parasitic isopods,but one specimen was parasitized by an unidentified rhizocephalan barnacle of the genus Septosaccus(1.2%).The burrowing barnacle Trypetesa lampas(Hancock,1849)was found associated with both hermit crab species and evidence of predation on host eggs by this barnacle is shown for the first *** lampas was found in 4.2%of the shells *** present study expands our knowledge of the parasite fauna of hermit crabs from the Mediterranean Sea and indicates that additional research is needed to determine the impact of trypetesid egg predators on hermit crab populations.

关键词： Bopyridae egg predator Isopoda parasitism Rhizocephala

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Utility of positron emission tomography-computed tomography scan in detecting residual hepatocellular carcinoma post treatment:Series of case reports

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World Journal of Gastrointestinal Oncology 2020年第3期12卷 358-364页

作者： jason T Cheng Nelly e Tan Michael L Volk Transplantation Institute Loma Linda University Medical CenterSan BernardinoCA 92408United States Department of Radiology Loma Linda University Medical CenterLoma LindaCA 92354United States

BACKGROUND Multi-phase computed tomography(CT)or magnetic resonance imaging(MRI)has been the standard of care for hepatocellular carcinoma(HCC)diagnosis for *** SUMMARY We report a case series of four patients in whom positron emission tomographycomputed tomography(PeT-CT)scan complemented the conventional CT/MRI scans in evaluating treatment *** these four cases the conventional multi-phase CT and MRI failed to identify residual HCC disease post-treatment,while PeT-CT complemented and aided in treatment response *** each case,the addition of PeT-CT identified and located residual HCC disease,allowed retreatment,and altered medical *** This case series suggests that PeT-CT should perhaps play a role in the HCC management algorithm,in addition to the conventional contrast-enhanced multiphase scans.

关键词： Hepatocellular carcinoma Positron emission tomography Contrast-enhanced multiphase scan Cirrhosis Residual cancer Treatment response evaluation Case series

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A Composite State Convergence Scheme for Bilateral Teleoperation Systems

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Ieee/CAA Journal of Automatica Sinica 2019年第5期6卷 1166-1178页

作者： Muhammad Usman Asad Umar Farooq jason Gu Ghulam Abbas Rong Liu Valentina e.Balas the Department of electrical &Computer engineering Dalhousie UniversityN.S.Canada the Department of electrical & Computer engineering Dalhousie UniversityN.S.Canada the Department of electrical engineering University of the Punjab LahorePakistan the Department of electrical engineering The University of LahorePakistan the Department of Biomedical engineering Dalian University of TechnologyChina the Department of Automatics &Applied Software “Aurel Vlaicu” University of AradRomania

State convergence is a novel control algorithm for bilateral teleoperation of robotic systems. First, it models the teleoperation system on state space and considers all the possible interactions between the master and slave systems. Second, it presents an elegant design procedure which requires a set of equations to be solved in order to compute the control gains of the bilateral loop. These design conditions are obtained by turning the master-slave error into an autonomous system and imposing the desired dynamic behavior of the teleoperation system. Resultantly, the convergence of master and slave states is achieved in a well-defined manner. The present study aims at achieving a similar convergence behavior offered by state convergence controller while reducing the number of variables sent across the communication channel. The proposal suggests transmitting composite master and slave variables instead of full master and slave states while keeping the operator's force channel intact. We show that,with these composite and force variables;it is indeed possible to achieve the convergence of states in a desired way by strictly following the method of state convergence. The proposal leads to a reduced complexity state convergence algorithm which is termed as composite state convergence controller. In order to validate the proposed scheme in the absence and presence of communication time delays, MATLAB simulations and semi-real time experiments are performed on a single degree-of-freedom teleoperation system.

关键词： Composite variables linear control systems state convergence teleoperation time delay

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Rapid, continuous projection multi-photon 3D printing enabled by spatiotemporal focusing of femtosecond pulses

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Light(Science & Applications) 2021年第10期10卷 1987-1997页

作者： Paul Somers Zihao Liang jason e.Johnson Bryan W.Boudouris Liang Pan Xianfan Xu School of Mechanical engineering and Birck Nanotechnology Center Purdue UniversityWest LafayetteINUSA Charles D.Davidson School of Chemical engineering Purdue UniversityWest LafayetteINUSA Department of Chemistry Purdue UniversityWest LafayetteINUSA

There is demand for scaling up 3D printing throughput,especially for the multi-photon 3D printing process that provides sub-micrometer structuring capabilities required in diverse *** this work,high-speed projection multiphoton printing is combined with spatiotemporal focusing for fabrication of 3D structures in a rapid,layer-by-layer,and continuous *** focusing confines printing to thin layers,thereby achieving print thicknesses on the micron and sub-micron *** projection of dynamically varying patterns with no pause between patterns,a continuous fabrication process is established.A numerical model for computing spatiotemporal focusing and imaging is also presented which is verified by optical imaging and printing *** 3D structures with smooth features are fabricated,with millimeter scale printing realized at a rate above 10−3 mm3 s−*** method is further scalable,indicating its potential to make fabrications of 3D structures with micro/nanoscale features in a practical time scale a reality.

关键词： projection continuous thereby

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Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway＇s involvement in juvenile myelomonocytic leukemia

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Frontiers of electrical and electronic engineering in China 2018年第1期6卷 85-97页

作者： Saad M Khan jason e Denney Michael X Wang Dong Xu Informatics Institute and C. S. Bond Life Sciences Center Universitv of Missouri. Columbia. MO 65211 USA Department of Pathology and Anatomical Sciences University of Missouri Columbia MO 65211 USA Department of computer Science University of Missouri Columbia MO 65211 USA

Background： Clinical studies and genetic analyses have revealed that juvenile myelomonocytic leukemia （JMML） is caused by somatic and/or germline mutations of genes involved in the RAS/MAPK signalling pathway. Given the vastly different clinical prognosis among individual patients that have had this disease, mutations in genes of other pathways may be involved. Methods： In this study, we conducted whole-exome and cancer-panel sequencing analyses on a bone marrow sample from a 2-year old juvenile myelomonocytic leukemia patient. We also measured the microRNA profile of the same patient＇s bone marrow sample and the results were compared with the normal mature monocytic cells from the pooled peripheral blood. Results： We identified additional novel mutations in the Pi3K/AKT pathway and verified with a cancer panel targeted sequencing. We have confirmed the previously tested PTPNII gene mutation （exon 3 181G〉T） in the same sample and identified new nonsynonymous mutations in NTRKI, HMGA2, MLH3, MYH9 and AKT1 genes. Many of the microRNAs found to be differentially expressed are known to act as oncogenic MicroRNAs （onco^MicroRNAs or oncomiRs）, whose target genes are enriched in the PI3K/AKT signalling pathway. Conclusions： Our study suggests an alternative mechanism for JMML pathogenesis in addition to RAS/MAPK pathway. This discovery may provide new genetic markers for diagnosis and new therapeutic targets for JMML patients in the future.

关键词： single-cell RNA-Seq differential expression

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ADVANCeS IN SUSTAINABLe SeCURITY SYSTeMS eNGINeeRING WITH DRAMA THeORY (DT) Ⅱ

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Journal of Systems Science and Systems engineering 2009年第4期18卷 403-422页

作者： jason K. LeVY Nigel HOWARD Wilder School of Government and Public Affairs Virginia Commonwealth University Sheffield Hallam University

We put forth Drama Theory II （DT II） as a formal multiple participant decision making framework that can be used to systematically model complex security challenges, and advance the field of Sustainable Security Systems engineering. DT II is defined as a theory of ＂large world＂ pre-game communication and equilibrium selection. While game theoretic tools have been widely applied to resolve environmental conflicts and promote global security, traditional game theory assumes that decision makers, options, and preferences are fixed. A mathematical treatment of key drama theoretic concepts （i.e. positions, intentions, doubts and dilemmas） is provided. The dynamics of the drama theoretic process are discussed and the expected equilibrium set is derived. The fundamental theorem of drama theory is proven and all theoretical results are applied to promote sustainable security solutions. It is emphasized that DT II represents a flexible systems engineering technique to address time-sensitive, multi-faceted, and complex multiple participant negotiations.

关键词： Drama Theory II sustainable security systems engineering game theory

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Microparticles with tunable,cell-like properties for quantitative acoustic mechanophenotyping

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Microsystems & Nanoengineering 2023年第4期9卷 129-141页

作者： Ryan Dubay eric MDarling jason Fiering Center for Biomedical engineering Brown UniversityProvidenceRI 02912USA Biological Microsystems DraperCambridgeMA 02139USA Department of Pathology and Laboratory Medicine Brown UniversityProvidenceRI 02912USA School of engineering Brown UniversityProvidenceRI 02912USA Department of Orthopaedics Brown UniversityProvidenceRI 02912USA

Mechanical properties of biological cells have been shown to correlate with their biomolecular state and function,and therefore methods to measure these properties at scale are of *** microfluidic technologies can measure the mechanical properties of cells at rates over 20,000 cells/s,which is more than four orders of magnitude faster than conventional ***,precise and repeatable means to calibrate and test these new tools remain lacking,since cells themselves are by nature ***,microfluidic tools use rigid polymer microspheres for calibration because they are widely available in cell-similar sizes,but conventional microspheres do not fully capture the physiological range of other mechanical properties that are equally important to device function(e.g.,elastic modulus and density).Here,we present for the first time development of monodisperse polyacrylamide microparticles with both tunable elasticity and tunable *** these size,elasticity,and density tunable particles,we characterized a custom acoustic microfluidic device that makes single-cell measurements of mechanical *** then applied the approach to measure the distribution of the acoustic properties within samples of human leukocytes and showed that the system successfully discriminates lymphocytes from other *** initial demonstration shows how the tunable microparticles with properties within the physiologically relevant range can be used in conjunction with microfluidic devices for efficient high-throughput measurements of mechanical properties at single-cell resolution.

关键词： tunable elasticity function

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Properties of alkylbenzimidazoles for CO_2 and SO_2 capture and comparisons to ionic liquids

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Science China Chemistry 2012年第8期55卷 1638-1647,1-2页

作者： SHANNON Matthew S. HINDMAN Michelle S. DANIeLSeN Scott. P. O. TeDSTONe jason M. GILMORe Ricky D. BARA jason e. Department of Chemical & Biological engineering University of Alabama Tuscaloosa USA NSF-ReU Site: engineering Solutions for Clean energy Generation Storage and Consumption Department of Chemical & Biological Engineering University of Alabama Tuscaloosa USA Department of Chemical & Biomolecular engineering University of Pennsylvania Philadelphia USA Department of Chemical & Biomolecular engineering Clemson University Clemson USA

To date, few reports have been concerned with the physical properties of the liquid phases of imidazoles and benzimidazoles- potential starting materials for a great number of ionic liquids. Prior research has indicated that alkylimidazole solvents exhibit different, and potentially advantageous physical properties, when compared to corresponding imidazolium-based ionic liquids. Given that even the most fundamental physical properties of alkylimidazole solvents have only recently been reported, there is still a lack of data for other relevant imidazole derivatives, including benzimidazoles. In this work, we have synthesized a se- ries of eight 1-n-alkylbenzimidazoles, with chain lengths ranging from ethyl to dodecyl, all of which exist as neat liquids at ambient temperature. Their densities and viscosities have been determined as functions of both temperature and molecular weight. Alkylbenzimidazoles have been found to exhibit viscosities that are more similar to imidazolium-based ILs than al- kylimidazoles, owed to a large contribution to viscosity from the presence of a fused ring system. Solubilities of CO2 and SO2, two species of concern in the emission of coal-fired power generation, were determined for selected alkylbenzimidazoles to understand what effects a fused ring system might have on gas solubility. For both gases, alkylbenzimidazoles were deter- mined to experience physical, non-chemically reactive, interactions. The solubility of CO2 in alkylbenzimidazoles is 10%-30% less than observed for corresponding ILs and alkylimidazoles. 1-butylbenzimidazole was found to readily absorb at least 0.333 gram SO2 per gram at low pressure and ambient temperature, which could be readily desorbed under an N： flush, a behavior more similar to imidazolium-based ILs than alkylimidazoles. Thus, we find that as solvents for gas separations, benzimidazoles share characteristics with both ILs and alkylimidazoles.

关键词： benzimidazole imidazole ionic liquids carbon dioxide (CO2) capture sulfur dioxide (S02)

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