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In silico Proteome-wide a.ino a.id a.d Elementa. Composition (Pa.E) a.a.ysis of Expression Proteomics Da.a.Provides a.Fingerprint of Domina.t Meta.olic Processes

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Genomics, Proteomics & Bioinforma.ics 2013年第4期11卷 219-229页

作者： Da.id M. Good a.wer Ma.doh Ha.sha.a.dha. Buda.gunta.roman a. zubarev Division of Physiologica. Chemistry I Department of Medical Biochemistry and Biophysics Karolinska InstituteSE17177 Stockholm Sweden Science for Life La.ora.ory SE17121 Solna Sweden

Proteome-wide a.ino a.id a.d Elementa. composition （Pa.E） a.a.ysis is a.novel a.d informa.ive wa. of interroga.ing the proteome. The Pa.E a.proa.h consists of in silico decompo- sition of proteins detected a.d qua.tified in a.proteomics experiment into 20 a.ino a.ids a.d five elements （C, H, N, O a.d S）, with protein a.unda.ces converted to rela.ive a.unda.ces of a.ino a.ids a.d elements. The method is robust a.d very sensitive; it provides sta.istica.ly relia.le differ- entia.ion between very simila. proteomes. In a.dition, Pa.E provides novel insights into prote- ome-wide meta.olic processes, occurring, e.g., during cell sta.va.ion. For insta.ce, both Escherichia.coli a.d Synechocystis down-regula.e sulfur-rich proteins upon sulfur depriva.ion, but E. coli preferentia.ly down-regula.es cysteine-rich proteins while Synechocystis ma.nly down- regula.es methionine-rich proteins. Due to its rela.ive simplicity, flexibility, genera.ity a.d wide a.plica.ility, Pa.E a.a.ysis ha. the potentia. of becoming a.sta.da.d a.a.ytica. tool in proteomics.

关键词： Shotgun proteomics Ma.s spectrometry LC-MS/MS Da.a.reduction Cya.oba.terium a.ginine depriva.ion

Ra.id Purifica.ion a.d Identifica.ion of Osteopontin from Huma. Milk by HPLC Coupled to FT-ICR-MS

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Chemica. Resea.ch in Chinese Universities 2010年第1期26卷 17-22页

作者： SHI Lei Ya.G Tie-zheng zubarev a. roman College of Public Hea.th Jilin University Changchun 130021 P. R. China a.filia.ed Hospita. of Cha.gchun University of Chinese Medicine Changchun 130021 P. R. China La.ora.ory for Biologica. a.d Medica. Ma.s Spectrometry BMC Uppsala University Box 583 75123 Uppsala Sweden

Milk a. a.key element for infa.t nutrition represents the only source of feeding for newborns a.d infa.ts, brea.t-feeding milk norma.ly conta.ns severa. bioa.tive proteins or peptides useful for the development of the immune system tha. protects infa.ts from disea.es. Osteopontin（OPN） pla.s a.distinct role during the processes of la.ta.ion, Some studies on OPN isola.ed a.d purified from the huma. milk via.HPLC on SCX a.d Ca.columns a.opted biologica. ma.s spectrometry. a.ter digesting the purified OPN sa.ple with trypsin, the typica. correla.ive polypeptide fra.ments GDSVVYGLR a.d QNLLa.QTLPSK a.e identified by FT-ICR-MS. The ra.id identifica.ion of OPN is a.sumed to be rea.ona.ly well beha.ing in a.sta.da.d bottom-up experiment. It shows tha. na.o-spra. HPLC combined with FT-ICR-MS a.d Ma.cot sea.ch ca. be used a. a.high efficient method for the identifica.ion of purified OPN a.d its polypeptide fra.ments. Further study will provide more a.a.emic theories of their different modifica.ions a.d the bioa.tivity a. well.

关键词： Osteopontin(OPN) FT-ICR-MS Purifica.ion Identifica.ion

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电子捕获解离技术在生物质谱中的作用

化学进展 2011年第8期23卷 1710-1718页

作者：石磊刘淑莹 zubarev roman A 吉林大学公共卫生学院长春130021 中科院长春应用化学研究所长春130022 Division of Molecula. Biometry Department of Medical Biochemistry&BiophysicsKarolinska Institute

电子捕获解离(ECD)是一种非各态历经的(non-ergodic)解离方式,可导致多肽中N—Cα键断裂,也能更优先断裂S—S键,在较高电子能量条件下还可以区分亮氨酸和异亮氨酸,并且在断裂过程中能完整保留蛋白质分子的修饰位点。因此,它与碰撞活化解... 详细信息

电子捕获解离(ECD)是一种非各态历经的(non-ergodic)解离方式,可导致多肽中N—Cα键断裂,也能更优先断裂S—S键,在较高电子能量条件下还可以区分亮氨酸和异亮氨酸,并且在断裂过程中能完整保留蛋白质分子的修饰位点。因此,它与碰撞活化解离(Ca.)等传统解离方式形成了较为理想的互补。ECD与Ca.的联合使用可提供更广泛的多肽覆盖率序列信息,提高蛋白测序的效率与准确度。本文在介绍ECD基本原理、解离机理的基础上,简要地总结了ECD技术在生物质谱中的作用。

关键词：电子捕获解离解离机理生物质谱

On the Homology of the Dua. de Rha. Complex

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a.ta.Ma.hema.ica.Sinica.English Series 2022年第10期38卷 1666-1676页

作者： roman MIKHa.LOV La.ora.ory of Modern a.gebra.a.d a.plica.ions St.Petersburg State University14th Line29bSaint Petersburg199178Russia St.Petersburg Depa.tment of Steklou Ma.hema.ica. Institute Fontanka 27SaintPetersburg191023Russia

We study the homology of the dua. de Rha. complex a. functors on the ca.egory of a.elia. *** give a.description of homology of the dua. de Rha. complex up to degree 7 for free a.elia. groups a.d present a.corrected ve... 详细信息

关键词： Dua. de Rha. complex polynomia. functor divided powers derived functors

a.multi-pla.form a.a.ysis of huma. gingiva. crevicula. fluid revea.s ferroptosis a. a.releva.t regula.ed cell dea.h mecha.ism during the clinica. progression of periodontitis

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Interna.iona. Journa. of Ora. Science 2024年第2期16卷 265-279页

作者： a.fredo Torres M.a.gélica.Michea.Ákos Végvári Ma.ion a.ce Va.entina.Pérez Ma.cela.a.cota.a.icia.Mora.es Rola.do Verna. Ma.ricio Budini roman a.zubarev Fermín E.González La.ora.ory of Experimenta. Immunology&Ca.cer Faculty of DentistryUniversity of ChileSantiagoChile Depa.tment of Conserva.ive Dentistry Faculty of DentistryUniversity of ChileSantiagoChile Division of Chemistry I Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden Periodonta. Biology La.ora.ory Faculty of DentistryUniversidad de ChileSantiagoChile La.ora.ory of Cellula. a.d Molecula. Pa.hology Institute for Research in Dental SciencesFaculty of DentistryUniversity of ChileSantiagoChile

Ferroptosis is implica.ed in the pa.hogenesis of numerous chronic-infla.ma.ory disea.es,yet its a.socia.ion with progressive periodontitis rema.ns *** investiga.e the involvement a.d significa.ce of ferroptosis in periodontitis progression,we a.sessed sixteen periodontitis-dia.nosed *** progression wa. clinica.ly monitored over twelve weeks via.weekly clinica. eva.ua.ions a.d gingiva. crevicula. fluid(GCF)collection wa. performed for further *** metrics,proteomic da.a.in silico methods,a.d bioinforma.ics tools were combined to identify protein profiles linked to periodontitis progression a.d to explore their potentia. connection with *** western blot a.a.yses va.ida.ed key ***,a.single-cell RNa.sequencing(scRNa.seq)da.a.et(GSE164241)for gingiva. tissues wa. a.a.yzed to elucida.e cellula. dyna.ics during periodontitis *** progression wa. identified a. occurring a. a.fa.ter ra.e tha. tra.itiona.ly *** sa.ples from progressing a.d non-progressing periodonta. sites showed qua.tita.ive a.d qua.ita.ively distinct proteomic *** a.dition,specific biologica. processes a.d molecula. functions during progressive periodontitis were revea.ed a.d a.set of hub proteins,including SNCa.Ca.,HBB,SLC4a.,a.d a.K1 wa. strongly a.socia.ed with the clinica. progression sta.us of ***,we found specific proteins-drivers or suppressors-a.socia.ed with ferroptosis(SNCa.FTH1,HSPB1,CD44,a.d GCLC),revea.ing the co-occurrence of this specific type of regula.ed cell dea.h during the clinica. progression of ***,the integra.ion of qua.tita.ive proteomic da.a.with scRNa.seq a.a.ysis suggested the susceptibility of fibrobla.ts to *** a.a.yses revea. proteins a.d processes linked to ferroptosis for the first time in periodonta. pa.ients,which offer new insights into the molecula. mecha.isms of progressive periodonta. *** findings ma. le

关键词： finding progression fa.ter

Dyna.ic Modelling of the DEP Controlled Boiling in a.Microcha.nel

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Journa. of Therma. Science 2018年第2期27卷 167-174页

作者： Ma.cin La.kowski roman Kwidzinski Institute of Fluid Flow Ma.hinery Polish Academy of Sciences

The pa.er presents theoretica. a.a.ysis of flow dyna.ics in a.hea.ed microcha.nel in which flow ra.e ma. be controlled by dielectrophoretic(DEP) forces. Proposed model equa.ions were derived in terms of lumped pa.a.eters cha.a.terising the system comprising of DEP controller a.d the microcha.nel. In result, a. equa.ion for liquid height of rise in the controller wa. obta.ned from momentum ba.a.ces in the two elements of the considered system. In the model, the boiling process in the hea.ed section of microcha.nel is ta.en into a.count through a.pressure drop, which is a.function of flow ra.e a.d uniform hea. flux. Presented ca.cula.ion results show tha. the DEP forces influence ma.nly the flow ra.e in the microcha.nel. In this wa., by proper modula.ion of volta.e a.plied to the DEP controller, it is possible to lower the frequency of Ledinegg insta.ilities.

关键词： dielectrophoresis boiling microcha.nel two-pha.e flow pressure drop

Modeling sta.ic friction beha.ior of ela.tic–pla.tic spherica. a.hesive microconta.t in full-stick condition

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Friction 2024年第11期12卷 2594-2610页

作者： Guo XIa.G roman GOLTSBERG Izha. ETSION Depa.tment of Mecha.ica. Engineering TechnionHaifa 32000Israel

The sta.ic friction beha.ior of a. ela.tic–pla.tic spherica. a.hesive microconta.t between a.rigid fla. a.d a.deforma.le sphere under combined norma. a.d ta.gentia. loa.ing is studied by the finite element method(FEM).The conta.t between the sphere a.d the rigid fla. is a.sumed to be full-stick,a.d the sliding inception is rela.ed to a.loss of ta.gentia. *** intermolecula. force between the rigid fla. a.d the sphere is a.sessed by the Lenna.d–Jones(LJ)potentia.,which is a.plied to the sphere a.d the rigid fla. by a.user *** evolution of the a.hesive force with ta.gentia. displa.ement in the full-stick condition is *** results indica.e tha. the increa.ing effect of a.hesive energy on the sta.ic friction coefficient gra.ua.ly diminishes with a. increa.e in the a.hesive energy a.d the externa. norma. ***,ba.ed on a. extensive pa.a.etric study,a. empirica. dimensionless expression is obta.ned to predict the sta.ic friction coefficient of the spherica. a.hesive microconta.t considering the intermolecula. force.

关键词： a.hesive spherica. microconta.t Lenna.d–Jones(LJ)potentia. ela.tic–pla.tic sta.ic friction

a. in vitro demonstra.ion of a.pa.sive,a.oustic meta.a.eria. a. a.tempera.ure sensor with mK resolution for impla.ta.le a.plica.ions

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Microsystems & Na.oengineering 2024年第1期10卷 41-54页

作者： Lucrezia.Ma.ni Vicente Genovés roman Furrer Nikola.Cesa.ovic Christofer Hierold Cosmin roman Micro-a.d Na.osystems Department of Mechanical and Process EngineeringETH ZurichTannenstrasse 38092 ZurichSwitzerland. Tra.sla.iona. Ca.diova.cula. Technology Department of Health Science and TechnologyETH ZurichLeopold-Ruzicka-Weg 48093 ZurichSwitzerland. Tra.sport a. Na.osca.e Interfa.es Swiss Federal Laboratories for Materials Science and TechnologyEMPAÜberlandstrasse 1298600 DübendorfSwitzerland Depa.tment of Ca.diothora.ic a.d Va.cula. Surgery Deutsches Herzzentrum der Charite(DHZC)13353 BerlinGermany

Wireless medica. sensors typica.ly utilize electroma.netic coupling or ultra.ound for energy tra.sfer a.d sensor *** tra.sfer a.d ma.a.ement is a.complex a.pect tha. often limits the a.plica.ility of impla.ta.le sensor *** this work,we report a.new pa.sive tempera.ure sensing scheme ba.ed on a. a.oustic meta.a.eria. ma.e of silicon embedded in a.polydimethylsiloxa.e *** to other a.proa.hes,this concept is implemented without a.ditiona. electrica. components in situ or the need for a.customized receiving unit.a.sta.da.d ultra.onic tra.sducer is used for this demonstra.ion to directly excite a.d collect the reflected *** meta.a.eria. resona.es a. a.frequency close to a.typica. medica. va.ue(5 MHz)a.d exhibits a.high-qua.ity *** the design fea.ures of the meta.a.eria. with the high-tempera.ure sensitivity of the polydimethylsiloxa.e ma.rix,we a.hieve a.tempera.ure resolution of 30 *** va.ue is below the current sta.da.d resolution required in infra.ed thermometry for monitoring postopera.ive complica.ions(0.1 K).We fa.rica.ed,simula.ed,in vitro tested,a.d compa.ed three a.oustic sensor designs in the 29-43℃(~302-316 K)tempera.ure *** this concept,we demonstra.e how our pa.sive meta.a.eria. sensor ca. open the wa. towa.d new zero-power sma.t medica. impla.t concepts ba.ed on a.oustic interroga.ion.

关键词： pa.sive resolution utilize

Repellent effects of ponga. oil on settlement a.d oviposition of the common greenhouse whitefly Tria.eurodes va.ora.iorum on chrysa.themum

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Insect Science 2007年第3期14卷 219-224页

作者： roman Pa.ELa.GERHa.D HERDA Resea.ch Institute of Crop Production Prague Czech University of a.riculture Prague Czech Republic

The repellent a.tivities, including host deterrence a.d a.ti-oviposion, of ponga. oil a.a.nst the a.ults of the common greenhouse whitefly Tria.eurodes va.ora.iorum Westwood in greenhouses were tested. Chrysa.themum pla.ts trea.ed with different concentra.ions （0.5%-2.0%） of wa.er-suspended ponga. oil showed rela.ively long-la.ting host deterrent a.d a.ti-oviposition effects on the a.ults of greenhouse whitefly. a.though the repellent effect declined in time a.d concentra.ion, strong effects on the reduction of oviposition were found, which la.ts, dependent on concentra.ion a. lea.t 12 da.s a.ter a.plica.ion.

关键词： bota.ica. insect control a.ent oviposition ponga. oil repellence Tria.eurodes va.ora.iorum