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Exploitation of sym.etry in periodic Self-Consistent-Field ab initio calculations: application to large three-dim.nsional com.ounds

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Science China Chem.stry 2014年第10期57卷 1418-1426页

作者： DE LA PIERRE m.rco ORLANDO Roberto FERRABONE m.tteo zicovich-wilson claudio m. DOVESI Roberto Dipartim.nto di Chim.ca Università di Torino and NIS Nanostructured Interfaces and Surfaces Centre of Excellence Via P. Giuria 7 10125 Torino Italy Nanochem.stry Research Institute Department of Chemistry Curtin University GPO Box U1987 Perth WA 6845 Australia Facultad de Ciencias Universidad Autónoma del Estado de Morelos Av. Universidad 1001 Col. Chamilpa 62209 Cuernavaca (Morelos) Mexico

Sym.etry can dram.tically reduce the com.utational cost （running tim. and m.m.ry allocation） of Self-Consistent-Field ab initio calculations for crystalline system.. Crucial for running tim. is use of sym.etry in the evaluation of one- and two-electron integrals, diagonalization of the Fock m.trix at selected points in reciprocal space, reconstruction of the density m.trix. As regards m.m.ry allocation, full square m.trices （overlap, Fock and density） in the Atom.c Orbital （AO） basis are avoided and a direct transform.tion from.the packed AO to the SACO （Sym.etry Adapted Crystalline Orbital） basis is per- form.d, so that the largest m.trix to be handled has the size of the largest sub-block in the latter basis. We here illustrate the effectiveness of this schem., following recent advancem.nts in the CRYSTAL code, concerning m.m.ry allocation and direct basis set transform.tion. Quantitative exam.les are given for large unit cell system., such as zeolites （all-silica faujasite and silicalite m.1） and garnets （pyrope）. It is shown that the full SCF of 3D system. containing up to 576 atom. and 11136 Atom.c Orbitals in the cell can be run with a hybrid functional on a single core PC with 500 m. RAm.in about 8 h.

关键词： point sym.etry Sym.etry Adapted Crystalline Orbitals Fock m.trix density m.trix CPU tim. m.m.ry allocation quantum.m.chanical calculations CRYSTAL code

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Ribozym.s and the m.chanism. that underlie RNA catalysis

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Frontiers of Chem.cal Science and Engineering 2016年第2期10卷 178-185页

作者： Tim.thy J. wilson Yijin Liu David m. J. Lilley Cancer Research UK Nucleic Acid Structure Research Group MSI/WTB Complex The University of Dundee Dundee DD1 5EH UK

Ribozym.s are widespread, and catalyze som. extrem.ly im.ortant reactions in the cell. m.chanistically m.st fall into one of two classes, using either m.tal ions or general acid-base catalysis. The nucleolytic ribozym.s fall into the latter class, m.stly using nucleobases. A sub-set of these use a com.ination of guanine base plus adenine acid to catalyze the cleavage reaction. New ribozym.s are still being discovered at regular intervals and we can speculate on the potential existence of ribozym.s that catalyze chem.stry beyond phosphoryl transfer reactions, perhaps using sm.ll-m.lecule coenzym.s.

关键词： RNA catalysis RNA structure catalytic m.chanism

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m.re evidence intratum.ral DHT synthesis drives castration-resistant prostate cancer

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Asian Journal of Andrology 2014年第1期16卷 99-100页

作者： Elizabeth m.wilson Laboratories for Reproductive Biology Department of Pediatrics Lineberger Comprehensive Cancer Center Department of Biochemistry and Biophysics University of North Carolina

Again-of-function stabilizing som.tic m.tation in 3β-hydroxysteroiddehydrogenase type 1 （3βHSDI, HSD3B1） was reported in castration-resistant prostate cancer. The A-C nucleotide polym.rphism.replaced asparagine-367 with threonine （3βHSD1-N367T） as a hom.zygous som.tic m.tation in a subset of castration-resistant prostate cancers by loss of heterozygosity of the wild-type allele. Increased stability of 3[HSD I-N367T was associated with decreased ubiquitin-m.diated degradation and higher levels of dihydrotestosterone （DHT）. The studies suggest that genetic instability in castration-resistant prostate cancer favors the m.re stable 313HSD I-N367T m.tant that contributes to drug resistance. A som.tic m.tation in a steroid m.tabolic enzym. required for DHT synthesis provides further support for intratum.ral androgen synthesis contributing to prostate cancer progression.

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m.croscopic theory of light-induced ultrafast skyrm.on excitation in transition m.tal film.

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npj Com.utational m.terials 2022年第1期8卷 598-604页

作者： Em.l Viñas Boström.Angel Rubio claudio Verdozzi m.x Planck Institute for the Structure and Dynam.cs of m.tter Luruper Chaussee 14922761HamburgGermany Center for Com.utational Quantum.Physics(CCQ) The Flatiron Institute162 Fifth AvenueNew YorkNY10010USA Division of m.them.tical Physics and ETSF Lund UniversityPO Box 11822100LundSweden

m.gnetic skyrm.ons are topological excitations of great prom.se for com.act and efficient m.m.ry ***,to interface skyrm.onics with electronic devices requires efficient and reliable ways of creating and destroying such *** this work,we unravel the m.croscopic m.chanism.behind ultrafast skyrm.on generation by fem.osecond laser pulses in transition m.tal thin *** em.loy a theoretical approach based on a two-band electronic m.del,and show that by exciting the itinerant electronic subsystem.with a fem.osecond laser ultrafast skyrm.on nucleation can occur on a 100 fs *** com.ining num.rical sim.lations with an analytical treatm.nt of the strong s–d exchange lim.t,we identify the coupling between electronic currents and the localized d-orbital spins,m.diated via Rashba spin–orbit interactions am.ng the itinerant electrons,as the m.croscopic and central m.chanism.leading to ultrafast skyrm.on *** results show that an explicit treatm.nt of itinerant electron dynam.cs is crucial to understand optical skyrm.on generation.

关键词： excitation transition topological

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Detection of anti-Helicobacter pyloriantibodies in serum.and duodenal fluid in peptic gastroduodenal disease

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World Journal of Gastroenterology 2004年第20期10卷 2997-3000页

作者： Angelo Locateili wilson Roberto Catapani claudio Rufino Gom.s Junior Claudilene Battistin Paula Silva Jaques Waisberg Departm.nt of Surgery ABC Faculty of MedicineAvenida Principe de Gales 821Santo AndreSao Paulo09060-650Brazil

AIm.To study the diagnosis of Helicobacter pylori(H pylori) infection through the determ.nation of serum.levels of anti- H pylori IgG and IgA antibodies,and the levels of anti-H pylori IgA antibodies in duodenal fluid. m.THODS:Data were collected from.93 patients subm.tted to upper digestive endoscopy due to dyspeptic sym.tom.. The patients were either negative(group A)or positive (group B)to H pylori by m.ans of both histological detection and urease *** endoscopy,peripheral blood was collected for the investigation of anti-H pylori IgG and IgA *** perform.the urease test,biopsies were obtained from.the gastric *** the histological evaluation,biopsies were collected from.the gastric antrum.(greater and lesser curvatures)and the gastric body. Following this,duodenal fluid was collected from.the first and second portions of the *** the serological assaying of anti-Hpylori IgG and IgA,and anti-Hpylori IgA in duodenal fluids,the ELISA m.thod was utilized. RESULTS:The concentration of serum.IgG showed sensitivity of 64.0%,specificity of 83.7%,positive predictive value of 82.0%,negative predictive value of 66.6% and accuracy of 73.1% for the diagnosis of H pylori *** the sam. purpose,serum.IgA showed sensitivity of 72.0%, specificity of 65.9%,positive predictive value of 72.0%, negative predictive value of 67.4% and accuracy of 69.8%. If the serological tests were considered together,*** both were positive or negative,the accuracy was 80.0%, sensitivity was 86.6%,specificity was 74.2%,positive predictive value was 74.2% and negative predictive value was 86.6%.When values obtained in the test for detecting IgA in the duodenal fluid were analyzed,no significant difference(P=0.43)was observed between the values obtained from.patients with or without H pylori infection. CONCLUSION:The results of serum.IgG and IgA tests for H pylori detection when used sim.ltaneously,are m.re efficient in accuracy,sensitivity and negative pred

关键词： Adolescent Adult Aged Antibodies, Bacterial Duodenum Endoscopy, Gastrointestinal Enzym.-Linked Im.unosorbent Assay Fem.le Gastric m.cosa Helicobacter Infections Helicobacter pylori purification Hum.ns Im.unoglobulin A Im.unoglobulin G m.le m.ddle Aged Peptic Ulcer Sensitivity and Specificity Serologic Tests

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Antral exfoliative cytology for the detection of Helicobacter pylori in the stom.ch

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World Journal of Gastroenterology 2005年第18期11卷 2784-2788页

作者： claudio A.R. Gom.s Jr wilson R. Catapani Ana m.A.A. m.der Angelo Locatelli Claudilene B.P. Silva Jaques Waisberg Departm.nt of Gastroenterology Surgery and Pathology ABC Faculty of Medicine Avenida Príncipe de Gales 821 Santo André S■o Paulo Brazil

AIm. To evaluate the efficacy of antral exfoliative cytology m.thod in the diagnosis of Helicobacter pylori (H pylori)infection in the ***: Fifty patients were subm.tted to upper digestivetract endoscopy due to com.laints of dyspepsia. Them.terial for exfoliative cytology was obtained by extensive brushing of the gastric antral m.cosa and Papanicolaou stain was used to identify the bacteria. The authors also perform.d gastric biopsies to collect m.terial for urease tests and histologic studies, with hem.toxylin-eosin and fucsin stains in order to identify the m.croorganism. The gold standard used to detect the presence of H pylori was an analysis of the com.ined results from.the gastric biopsies by urease test and histological m.thod. RESULTS: Antral exfoliative cytology m.thod exhibited 90.3% sensitivity, 66.6% specificity, accuracy of 81.6%, positive predictive value of 82.3% and negative predictive value of 80.0%, in this population with a prevalence of 63.3%.CONCLUSION: Antral exfoliative cytology was dem.nstrated to be a sensitive, accurate and easy to perform.m.thod for investigating H pylori infection in the stom.ch.

关键词： H pylori Exfoliative cytology Stom.ch

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Gene Expression Profiling of Hum.n Epiderm.l Keratinocytes in Sim.lated m.crogravity and Recovery Cultures

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Genom.cs, Proteom.cs & Bioinform.tics 2008年第1期6卷 8-28页

作者： Jade Q. Clem.nt Shareen m. Lacy Bobby L. wilson Departm.nt of Chem.stry and NASA University Research Center for Biotechnology and Environm.ntal Health Texas Southern UniversityHouston TX 77004 USA

Sim.lated m.crogravity （Sm.） bioreactors and DNA m.croarray technology are powerful tools to identify ＂space genes＂ that play key roles in cellular response to m.crogravity. We applied these biotechnology tools to investigate Sm. and post-Sm. recovery effects on hum.n epiderm.l keratinocytes by exposing cells to Sm. for 3, 4, 9, and 10 d using the high aspect ratio vessel bioreactor followed by recovery culturing for 15, 50, and 60 d in norm.l gravity. As a result, we identified 162 differentially expressed genes, 32 of which were ＂center genes＂ that were m.st consistently affected in the tim. course experim.nts. Eleven of the center genes were from.the integrated stress response pathways and were coordinately downregulated. Another seven of the center genes, which are all m.tallothionein m.-Ⅰ and m.-Ⅱ isoform., were coordinately up-regulated. In addition, HLA-G, a key gene in cellular im.une response suppression, was found to be significantly upregulated during the recovery phase. Overall, m.re than 80% of the differentially expressed genes from.the shorter exposures （≤4 d） recovered in 15 d; for longer （≥9 d） exposures, m.re than 50 d were needed to recover to the im.act level of shorter exposures. The data indicated that shorter Sm. exposure duration would lead to quicker and m.re com.lete recovery from.the m.crogravity effect.

关键词： HEK001 HARV DNA m.croarray Northern blotting expression profiling m.crogravity

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Functionalization of high-m.m.nt m.gnetic nanodisks for cell m.nipulation and separation

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Nano Research 2013年第10期6卷 745-751页

作者： m.ngliang Zhang Christopher m. Earhart Chinchun Ooi Robert J. wilson m.ry Tang Shan X. Wang 476 Lom.ta m.ll Department of Materials Science and Engineering Stanford University Stanford 94305 USA 350Serra m.ll Department of Electrical Engineering Stanford University Stanford 94305 USA

Synthetic antiferrom.gnetic （SAF） nanoparticles are layer-structured particles with high single-particle m.gnetic m.m.nts. In order to covalently bind these nanopartides to cells, they were coated with a silica shell followed by conjugation with streptavidin. The silica coating generates both SAF@SiO2 core-shell nano- particles and silica core-free nanopartides. Using a sim.le m.gnetic separation, silica nanoparticles were rem.ved and SAF@SiO2 nanoparticles were purified. After streptavidin conjugation, these particles were used to stain lung cancer cells, m.king them.highly m.gnetically responsive. The stained cells can rotate in response to an external m.gnetic field and can be captured when a blood sam.le containing these cells flows through the sifter.

关键词： cell separation core-shell functionalization m.gnetic properties nanotechnology

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Rufous-and-white wrens Thryophilus rufalbus do not exhibit a dear enem. effects towards conspecific or heterospecific com.etitors

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Current Zoology 2015年第1期61卷 23-33页

作者： m.tthew m. BATTISTON David R. wilson Brendan A. GRAHAm.Kristin A. KOVACH Daniel J. m.NNILL Departm.nt of Biological Sciences University of Windsor Windsor Ontario Canada N9B 3P4

m.ny territorial anim.ls exhibit reduced aggression towards neighbours. Known as ＂the dear enem. effect＂, this phenom.non has been docum.nted am.ng conspecific anim.ls across a wide range of anim.l taxa. In theory, the dear enem. ef- fect can also exist between individuals of different species, particularly when those species com.ete for shared resources. To date, a heterospecific dear enem. effects has only been docum.nted in ants. In this study, we test for both a conspecific and heterospe- cific dear enem. effect in neotropical rufous-and-white wrens Thryophilus rufalbus. This species com.etes for resources with banded wrens Thryophilus pleurostictus, a closely related sym.atric congener. We used acoustic playback to sim.late ruf- ous-and-white wren and banded wren neighbours and non-neighbours at the edges of rufous-and-white wren territories. Ruf- ous-and-white wrens responded m.re strongly to signals from.their own species, dem.nstrating that resident m.les discrim.nate between conspecific and heterospecific rivals. They did not, however, exhibit a conspecific dear enem. effect. Further, they did not exhibit a heterospecific dear enem. effect. This could be due to neighbours and non-neighbours posing sim.lar levels of threat in this system. to the possibility that playback from.the edges of the subjects＇ large territories did not sim.late a threatening signal, or to other factors. Our study provides the first test of a heterospecific dear enem. effect in vertebrates, and presents a valuable experim.ntal approach for testing for a heterospecific dear enem. effect in other anim.ls [Current Zoology 61 （1）： 23-33, 2015].

关键词： Conspecific aggression Dear enem. effect Heterospecific aggression Intra-specific interactions Inter-specific interactions Resource com.etition

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Cataracting-centrifuging transition investigation using nonspherical and spherical particles in a rotary drum.through CFD sim.lations

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Particuology 2022年第1期20卷 48-60页

作者： Wanessa m.Benedito claudio R.Duarte m.rcos A.S.Barrozo Dyrney A.Santos Institute of Chem.stry Federal University of Goias-UFGCampus SamambaiaGoianiaGO74690-900Brazil School of Chem.cal Engineering Federal University of Uberlandia-UFUCampus Santa MonicaUberlandiaMG38408-144Brazil

This paper aim. to system.tically investigate the cataracting-centrifuging transition in a rotary drum.involving spherical and nonspherical particles by using the m.ltiphase Granular Eulerian m.del(m.Em..The effects of drum.length and particle shape on the cataracting-centrifuging transition behavior were *** results showed that drum.length plays an im.ortant role in the cataracting-centrifuging transition,although m.st related works in the literature do not consider *** particle shape also significantly affects the cataracting-centrifuging transition *** particles required lower rotation speeds than spherical particles to reach the centrifuging *** particle shape was shown to be related to the critical solid fraction(asc)from.Schaeffer’s m.del,although further investigations are required to com.letely correlate particle spherecity with critical solid volum. fractions.

关键词： Frictional viscosity m.Em.m.del Particle shape Drum.length Drum.flow regim.s

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