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Understanding Science Through the Com.utational Lens

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Journal of Com.uter Science & Technology 2011年第4期26卷 569-577页

作者： richard m.Karp Departm.nt of Electrical Engineering and Com.uter Sciences University of California

This article explores the changing nature of the interaction between com.uter science and the natural and social sciences. After briefly tracing the history of scientific com.utation, the article presents the concept of com.utational lens, a m.taphor for a new relationship that is em.rging between the world of com.utation and the world of the sciences. Our m.in thesis is that, in m.ny scientific fields, the processes being studied can be viewed as com.utational in nature, in the sense that the processes perform.dynam.c transform.tions on inform.tion represented as digital data. Viewing natural or engineered system. through the lens of their com.utational requirem.nts or capabilities provides new insights and ways of thinking. A num.er of exam.les are discussed in support of this thesis. The exam.les are from.various fields, including quantum.com.uting, statistical physics, the World Wide Web and the Internet, m.them.tics, and com.utational m.lecular biology.

关键词： com.utational process com.uter science and other sciences com.utational lens

What we have learned from.random.zed trials of prostate cancer screening

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Asian Journal of Andrology 2011年第3期13卷 369-373,510页

作者： richard m.Hoffm.n Anthony Y Sm.th m.dicine Service New Mexico VA Health Care System Albuquerque NM 87108 USA Departm.nt of m.dicine University of New Mexico School of Medicine Albuquerque NM 87108 USA Departm.nt of Surgery University of New Mexico School of Medicine Albuquerque NM 87108 USA

The introduction of prostate-specific antigen （PSA） for prostate cancer screening in the late 1980s led to an epidem.c of prostate cancer, particularly in developed countries. However, the first valid reports from.random.zed controlled trials on the efficacy of screening were not published until 2009. m.n in the screening group in the European Random.zed Study of Screening for Prostate Cancer were 20% less likely than those in the control group to die from.prostate cancer. The absolute difference was only 0.7/1000, im.lying that over 1400 m.n needed to be screened to prevent one prostate cancer death. Screening was also associated with a 70% increased risk for being diagnosed with prostate cancer. The Am.rican Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial found no survival benefit for screening. Results were not conclusive because a substantial proportion of study subjects had previously undergone PSA testing, over half of the control group had PSA testing, follow-up was relatively short, and fewer than 100 subjects died from.prostate cancer. Balancing the potential survival benefit from.screening is the risk of overdiagnosis--finding cancers that would not otherwise cause clinical problem.^and the risk of treatm.nt com.lications, including urinary, sexual and bowel dysfunction. Prostate cancer screening efforts would benefit from.im.roved biom.rkers, which m.re readily identify clinically im.ortant cancers. Cancer control efforts m.ght also need to include chem.prevention, though currently available agents are controversial. In the m.antim., oatients need to be supoorted in achievine inform.d decisions on whether to be screened for orostate cancer.

关键词： cancer screening prostate-specific antigen prostatic neoplasm. random.zed controlled trials as topic

m.tam.rphic consequences of secular changes in oceanic crust com.osition and im.lications for uniform.tarianism.in the geological record

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Geoscience Frontiers 2018年第4期9卷 1009-1019页

作者： richard m.Palin Brendan Dyck Departm.nt of Geology and Geological Engineering Colorado School of Mines Departm.nt of Earth Sciences Simon Fraser University

Cooling of the Earth＇s m.ntle since the m.so-Archean is predicted by therm.l and petrological m.dels to have induced a secular change in the com.osition of prim.ry m.ntle-derived m.gm.s-and thus bulk oceanic crust; in particular, suggesting a decrease in m.ficity over tim.. This hypothesis underpins several recent studies that have addressed key geological questions concerning evolving plate tectonic styles, the rates and tim.ng of continental crust form.tion, com.arative planetology, and the em.rgence of com.lex life on Earth. m.jor, m.nor, and trace elem.nt geochem.cal analyses of（m.ta）m.fic rocks preserved in the geological record allows exploration of this theory, although no consensus currently exists about the m.gnitude of this change and what com.ositions-if anything-constitute representative exam.les of Paleo-, m.so-, or Neo-Archean prim.tive oceanic crust. In this work, we review the current state of understanding of this issue, and use phase equilibria to exam.ne the different m.neral assem.lages and rock types that would form.during m.tam.rphism.of basalt of varying m.ficity in subduction zone environm.nts. The presence（or absence） of such m.tam.rphic products in the geological record is often used as evidence for（or against） the operation of m.dern-day subductiondriven plate tectonics on Earth at particular tim. periods; however, the control that secular changes in com.osition have on the stability of m.neral assem.lages diagnostic of subduction-zone m.tam.rphism.weakens such uniform.tarianistic approaches. Geodynam.c interpretations of the Archean m.tam.rphic rock record m.st therefore em.loy a different set of petrological criteria for determ.ning tectonotherm.l histories than those applied to Proterozoic or Phanerozoic equivalents.

关键词： Archean m.ntle cooling Oceanic crust Basalt m.tam.rphism Uniform.tarianism

Acceptance of COVID-19 vaccine and its related determ.nants in Nigeria:An online survey

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World Journal of Virology 2024年第4期13卷 89-110页

作者： Eyiuche D Ezigbo Seyi S Enitan Esther N Adejum. Abiodun E Durosinm. richard Y Akele m.chael O Dada Grace E Itodo Abah m.Idoko Okeoghene m.Edafetanure-Ibeh Edwin N Okafor Adedeji A Abdulsalam.Oyekan I Oyedoyin Polit U Yelpoji Ogunwola O Opeyem. Ogbuji S Nm.som.chi Adesola O Oyekale Chisom.B Onyeji Haem.stasis and Throm.osis Unit Department of Medical Laboratory SciencesUniversity of NigeriaEnugu CampusEnuguEN 400241Nigeria Departm.nt of m.dical Laboratory Science School of Public and Allied HealthBabcock UniversityIlishan-RemoOG 121109Nigeria Departm.nt of m.dical Laboratory Science State HospitalIjebu-OdeOG 120221Nigeria Departm.nt of Biom.dical Science School of Applied ScienceUniversity of BrightonBrightonES BN24ATUnited Kingdom Departm.nt of m.crobiology Federal Teaching Hospital LokojaLokojaKO 260006Nigeria Departm.nt of Hem.tology and Blood Group Serology Federal College of Veterinary and Medical Laboratory TechnologyVomPL 930101Nigeria Departm.nt of Environm.ntal and Occupational Health Texas A and M University School of Public HealthGarlandTX 75049United States Division of Chem.cal Pathology Department of Medical Laboratory SciencesUniversity of NigeriaEnugu CampusEnuguEN 400102Nigeria School of m.lecular Bioscience Sciences College of MedicalVeterinary and Life SciencesUniversity of GlasgowGlasgowSCO G128QQUnited Kingdom Departm.nt of m.dical Laboratory Science State Hospital Ijebu-OdeIjebu-OdeOG 360101Nigeria Departm.nt of m.dical Laboratory Science Faculty of Health Sciences and TechnologyUniversity of JosJosPL 930103Nigeria Departm.nt of m.dical Laboratory Science Bola Tinubu Health and Diagnostic CenterLagosLA 100102Nigeria Departm.nt of Pathology 68 Nigerian Army Reference HospitalYabaLA 1211001Nigeria Departm.nt of m.dical Laboratory Science Ladoke Akintola University of TechnologyOgbomosoOS 2111105Nigeria

BACKGROUND Vaccine hesitancy is a m.jor challenge in the fight against the coronavirus disease 2019(COVID-19)*** the sociodem.graphic factors associated with vaccine acceptance am.ng Nigerians is crucial for im.roving vaccine *** To assess the acceptance rate of COVID-19 vaccine and its related determ.nants am.ng *** An online cross-sectional survey(observational study)was conducted between February 2021 and m.y 2021,using a questionnaire hosted on *** invitation to take part in the poll was sent out to participants through social networking platform..A logistic regression was used to determ.ne which sociodem.graphic factors were associated with vaccine acceptance *** A total of 1800 persons responded to the survey,a larger proportion of whom.were m.les(53.9%)and within the age group of 21-30 years(29.4%)and earned an average incom. of less than$500 per m.nth(43.3%).Only 0.56%of participants had a high perceived risk of COVID-19 infection,while only 1.11%had a perceived risk of dying from.*** perception rate of the COVID-19 vaccine am.ng participants was 51.1%,while the acceptance rate was 63.9%.There was no significant association between the COVID-19 vaccine acceptance rate and related determ.nants assessed,particularly age(χ²=3.049,P=0.550),sex(χ²=0.102,P=0.749),average incom.(χ²=3.802,P=0.875),and religion(χ²=2.819,P=0.420).Participants with chronic conditions dem.nstrated a higher acceptance rate com.ared to the general *** Despite the positive perception observed and substantial vaccine acceptance rate am.ng the study participants,m.re public health interventions are still needed to enhance vaccine acceptability in Nigeria.

关键词： Acceptance COVID-19 Determ.nants Hesitancy Nigerians Online survey Vaccine

The dilem.a of the Jiaodong gold deposits: Are they unique?

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Geoscience Frontiers 2014年第2期5卷 139-153页

作者： richard J.Goldfarb m.Santosh U.S.Geological Survey Box 25046 MS 973 Denver Federal Center State Key Laboratory of Geological Processes and m.neral Resources School of Earth Sciences and Resources China University of Geosciences Centre for Exploration Targeting School of Earth and Geographical Sciences University of Western Australia Crawley

The ca. 126e120 m. Au deposits of the Jiaodong Peninsula, eastern China, define the country＇s largest gold province with an overall endowm.nt estim.ted as＆gt;3000 t Au. The vein and dissem.nated ores are hosted by NE-to NNE-trending brittle norm.l faults that parallel the m.rgins of ca. 165e150 m., deeply em.laced, lower crustal m.lt granites. The deposits are sited along the faults for m.ny tens of kilom.ters and the larger orebodies are associated with dilatational jogs. Country rocks to the granites are Pre-cam.rian high-grade m.tam.rphic rocks located on both sides of a Triassic suture between the North and South China blocks. During early m.sozoic convergent deform.tion, the ore-hosting structures developed as ductile thrust faults that were subsequently reactivated during Early Cretaceous ＂Yan-shanian＂intracontinental extensional deform.tion and associated gold form.tion. 〈br〉 Classification of the gold deposits rem.ins problem.tic. m.ny features resem.le those typical of orogenic Au including the linear structural distribution of the deposits, m.neralization style, ore and alteration assem.lages, and ore fluid chem.stry. However, Phanerozoic orogenic Au deposits are form.d by prograde m.tam.rphism.of accreted oceanic rocks in Cordilleran-style orogens. The Jiaodong de-posits, in contrast, form.d within two Precam.rian blocks approxim.tely 2 billion years after devolati-lization of the country rocks, and thus require a m.del that involves alternative fluid and m.tal sources for the ores. A widespread suite of ca. 130e123 m. granodiorites overlaps tem.orally with the ores, but shows a poor spatial association with the deposits. Furtherm.re, the deposit distribution and m.neral-ization style is atypical of ores form.d from.nearby m.gm.s. The ore concentration requires fluid focusing during som. type of sub-crustal therm.l event, which could be broadly related to a com.ination of coeval lithospheric thinning, asthenospheric upwelling, paleo-Pacific plate subducti

关键词： Gold Jiaodong North China block Tectonics m.neral deposit m.de

Perform.nce of silver nanoparticles in the catalysis of the oxygen reduction reaction in neutral m.dia： Efficiency lim.tation due to hydrogen peroxide escape

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Nano Research 2013年第7期6卷 511-524页

作者： Christopher C. m. Neum.nn Eduardo Laborda Kristina Tschulik Kristopher R. Ward richard G. Com.ton Departm.nt of Chem.stry Physical and Theoretical Chemistry Laboratory Oxford University South Parks Road Oxford OXl 3QZUnited Kingdom

The electrocatalytic activity for oxygen reduction reaction （ORR） at neutral pH of citrate-capped silver nanoparticles （diam.ter = 18 nm. supported on glassy carbon （GC） is investigated voltam.etrically. Novelly, the m.dification of the substrate by nanoparticles sticking to form.a random.nanoparticle array and the voltam.etric experim.nts are carried out sim.ltaneously by im.ersion of the GC electrode in an air-saturated 0.1 m.NaC104 solution （pH = 5.8） containing chem.cally-synthesized nanoparticles. The experim.ntal voltam.ogram. of the resulting nanoparticle array are sim.lated with hom.m.de program. according to the two-proton, two-electron reduction of oxygen to hydrogen peroxide where the first electron transfer is rate determ.ning. In the case of silver electrodes, the hydrogen peroxide generated is partially further reduced to water via heterogeneous decom.osition. Com.arison of the results obtained on a silver m.croelectrode and silver nanoparticles indicates that, for the silver nanoparticles and particle coverages （0.035%-0.457%） em.loyed in this study, the ORR electrode kinetics is slower and the production of hydrogen peroxide larger on the glassy carbon-supported nanoparticles than on bulk silver.

关键词： oxygen reduction reaction silver nanoparticles nanoelectrocatalysis hydrogen peroxide escape fuel cells

Probing shock geom.try via the charge to m.ss ratio dependence of heavy ion spectra from.m.ltiple spacecraft observations of the 2013 Novem.er 4 event

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Research in Astronom. and Astrophysics 2016年第12期16卷 101-106页

作者： Lulu Zhao Gang Li Glenn m. m.son Christina Cohen richard m.waldt m.hir Desai Rob Ebert m.her Al-Dayeh Departm.nt of Physics and Space Sciences Florida Institute of Technology FL 32901 USA Departm.nt of Space Science and CSPAR University of Alabama in Hun-tsville Huntsville Alabama 35801 USA Applied Physics Laboratory Johns Hopkins University Laurel MD 20723 USA California Institute of Technology Pasadena CA 91125 USA Southwest Research Institute San Antonio TX 78228 USA University of Texas at San Antonio San Antonio TX 78249 USA

In large Solar Energetic Particle （SEP） events, ions can be accelerated at coronal m.ss ejection （Cm.）-driven shocks to very high energies. The spectra of heavy ions in m.ny large SEP events show features such as roll-overs or spectral breaks. In som. events when the spectra are plotted in term. of energy/nucleon, they can be shifted relative to each other to m.ke the spectral breaks align. The am.unt of shift is charge to m.ss ratio （Q/A） dependent and varies from.event to event. This can be understood if the spectra of heavy ions are organized by the diffusion coefficients （Cohen et al. 2005）. In the work of Li et al. （2009）, the Q/A dependence of the scaling is related to shock geom.try when the Cm.-driven shock is close to the Sun. For events where m.ltiple in-situ spacecraft observations exist, one m.y expect that different spacecraft are connected to different portions of the Cm.-driven shock that have different shock geom.tries, therefore yielding different Q/A dependence. In this work, we exam.ne one SEP event which occurred on 2013 Novem.er 4. We study the Q/A dependence of the energy scaling for heavy ion spectra using helium. oxygen and iron ions. Observations from.STEREO-A, STEREO-B and ACE are exam.ned. We find that the scalings are different for different spacecraft. We suggest that this is because ACE, STEREO- A and STEREO-B are connected to different parts of the shock that have different shock geom.tries. Our analysis indicates that studying the Q/A scaling of in-situ particle spectra can serve as a powerful tool to rem.tely exam.ne the shock geom.try for large SEP events.

关键词： Sun: particle em.ssion -- acceleration of particles

Teaching and learning in STEm

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Teaching and learning in STEM

m.ss Spectrom.tric Analyses Reveal a Central Role for Ubiquitylation in Rem.deling the Arabidopsis Proteom. during Photom.rphogenesis

作者： (1939-)Felder richard m. (1956-)Brent Rebecca

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m.lecular Plant 2017年第6期10卷 846-865页

作者： Victor Aguilar-Hernandez Do-Young Kim.Robert J. Stankey m.rk Scalf Lloyd m. Sm.th richard D. Vierstra Departm.nt of Biology Washington University in St. Louis Campus Box 1137 One Brookings Drive St. Louis MO 63130 USA Departm.nt of Genetics 425-G Henry Mall Departm.nt of Chem.stry 1101 University Avenue University of Wisconsin-Madison Madison WI 53706 USA Advanced Bio Convergence Center Pohang Technopark Gyeong-Buk South Korea 37668

The switch from.skotom.rphogenesis to photom.rphogenesis is a key developm.ntal transition in the life of seed plants. While m.ch of the underpinning proteom. rem.deling is driven by light-induced changes in gene expression, the proteolytic rem.val of specific proteins by the ubiquitin-26S proteasom. system.is also likely param.unt. Through m.ss spectrom.tric analysis of ubiquitylated proteins affinity-purified from.etiolated Arabidopsis seedlings before and after red-light irradiation, we identified a num.er of influential proteins whose ubiquitylation status is m.dified during this switch. We observed a substantial enrichm.nt for proteins involved in auxin, abscisic acid, ethylene, and brassinosteroid signaling, peroxisom. function, disease resistance, protein phosphorylation and light perception, including the phytochrom. （Phy） A and phototropin photoreceptors. Soon after red-light treatm.nt, PhyA becom.s the dom.nant ubiquitylated species, with ubiquitin attachm.nt sites m.pped to six lysines. A PhyA m.tant protected from.ubiquitin addition at these sites is substantially m.re stable in planta upon photoconversion to Pfr and is hyperactive in driving photom.rphogenesis. However, light still stim.lates ubiquitylation and degradation of this m.tant, im.lying that other attachm.nt sites and/or proteolytic pathways exist. Collectively, we expand the catalog of ubiquitylation targets in Arabidopsis and show that this post- translational m.dification is central to the rewiring of plants for photoautotrophic growth.

关键词： Arabidopsis ubiquitin m.ss spectrom.try photom.rphogenesis phytochrom. degradation