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Journal of Systems Science & Complexity 2015年第2期28卷 504-516页

作者： LI Limin aoki-kinoshita kiyoko f CHING Wai-Ki JIANG Hao Institute of Information and System Science Xi'an Jiaotong University Department of Bioinformatics Faculty of EngineeringSoka University Advanced Modeling and Applied Computing Laboratory Department of MathematicsThe University of Hong Kong Department of Mathematics School of InformationRenmin University of China

String kernels are popular tools for analyzing protein sequence data and they have been successfully applied to many computational biology problems. The traditional string kernels assume that different substrings are independent. However, substrings can be highly correlated due to their substructure relationship or common physico-chemical properties. This paper proposes two kinds of weighted spectrum kernels： The correlation spectrum kernel and the AA spectrum kernel. We evMuate their performances by predicting glycan-binding proteins of 12 glycans. The results show that the correlation spectrum kernel and the AA spectrum kernel perform significantly better than the spectrum kernel for nearly all the 12 glycans. By comparing the predictive power of AA spectrum kernels constructed by different physico-chemical properties, the authors can also identify the physico- chemical properties which contributes the most to the glycan-protein binding. The results indicate that physico-chemical properties of amino acids in proteins play an important role in the mechanism of glycamprotein binding.

关键词： AAindex AA spectrum kernel correlation spectrum kernel physico-chemical properties string kernel weighted spectrum kernel.

MODELING GENETIC REGULATORY NETWORKS:A DELAY DISCRETE DYNAMICAL MODEL APPROACH

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Journal of Systems Science & Complexity 2012年第6期25卷 1052-1067页

作者： Hao JIANG Wai-Ki CHING kiyoko f.aoki-kinoshita Dianjing GUO Advanced Modeling and Applied Computing Laboratory Department of MathematicsThe University of Hong Kong Department of Bioinformatics Faculty of EngineeringSoka University Department of Biology The Chinese University of Hong Kong

Modeling genetic regulatory networks is an important research topic in genomic research and computationM systems biology. This paper considers the problem of constructing a genetic regula- tory network （GRN） using the discrete dynamic system （DDS） model approach. Although considerable research has been devoted to building GRNs, many of the works did not consider the time-delay effect. Here, the authors propose a time-delay DDS model composed of linear difference equations to represent temporal interactions among significantly expressed genes. The authors also introduce interpolation scheme and re-sampling method for equalizing the non-uniformity of sampling time points. Statistical significance plays an active role in obtaining the optimal interaction matrix of GRNs. The constructed genetic network using linear multiple regression matches with the original data very well. Simulation results are given to demonstrate the effectiveness of the proposed method and model.

关键词： Delay effect discrete dynamic system model genetic regulatory networks k-means clustering method linear multiple regression.

Numerical Simulations of Rarefied Gases in Curved Channels: Thermal Creep, Circulating flow, and Pumping Effect

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Communications in Computational Physics 2009年第10期6卷 919-954页

作者： Kazuo aoki Pierre Degond Luc Mieussens Department of Mechanical Engineering and Science Graduate School of EngineeringKyoto UniversityKyoto 606-8501Japan Universite de Toulouse UPSINSAUT1UTMInstitut de Mathematiques de ToulouseF-31062 ToulouseFrance CNRS Institut de Mathematiques de Toulouse UMR 5219F-31062 ToulouseFrance Universite de Bordeaux Institut de Mathematiques de Bordeaux351cours de la Liberation33405 Talence cedexFrance

We present numerical simulations of a new system of micro-pump based on the thermal creep effect described by the kinetic theory of *** device is made of a simple smooth and curved channel with a periodic temperature *** the Boltzmann-BGK model as the governing equation for the gas flow,we develop a numerical method based on a deterministic finite volume scheme,implicit in time,with an implicit treatment of the boundary *** method is comparatively less sensitive to the slow flow velocity than the usual Direct Simulation Monte Carlo method in case of long devices,and turns out to be accurate enough to compute macroscopic quantities like the pressure field in the *** simulations show the ability of the device to produce a one-way flow that has a pumping effect.

关键词： Knudsen compressor thermal creep flow transpiration flow BGK model implicit scheme

Quantum information entropies of the eigenstates for the Pschl-Teller-like potential

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Chinese Physics B 2013年第5期22卷 113-117页

作者： Guo-Hua Sun M. Avila aoki Shi-Hai Dong Centro Universitario Valle de Chalco Universidad Autónoma del Estado de México Departamento de física Escuela Superior de Física y MatemáticsInstituto Politécnico Nacional

Shannon entropy for lower position and momentum eigenstates of Ptschl-Teller-like potential is evaluated. Based on the entropy densities demonstrated graphically, we note that the wave through of the position information entropy density p （x） moves right when the potential parameter V1 increases and its amplitude decreases. However, its wave through moves left with the increase in the potential parameter 丨V2丨. Concerning the momentum information entropy density p（p）, we observe that its amplitude increases with increasing potential parameter V1, but its amplitude decreases with increasing丨V2丨. The Bialynicki-Birula-Mycielski （BBM） inequality has also been tested for a number of states. Moreover, there exist eigenstates that exhibit squeezing in the momentum information entropy. finally, we note that position information entropy increases with V1, but decreases with 丨V2丨, However, the variation of momentum information entropy is contrary to that of the position information entropy.

关键词： bound states quantum information entropy Poschl-Teller-like potential

Acute Stress Symptoms in families of Patients Admitted to the Intensive Care Unit during the first 24 Hours following Admission in Japan

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Open Journal of Nursing 2015年第4期5卷 325-335页

作者： Miyuki Komachi kiyoko Kamibeppu Department of Nurse Practitioner Training Division of Healthcare Graduate School of Medical Welfare International University of Health and Welfare Tokyo Japan Department of family Nursing Division of Health Sciences & Nursing Graduate School of Medicine University of Tokyo Tokyo Japan

families of patients in the intensive care unit often experience sever stress. Understanding their experience is important for providing family-centered care during this difficult period. Little is known about the experience of families of patients admitted to the intensive care unit (ICU). To evaluate the prevalence and factors associated with acute stress symptoms among families of patients admitted to the ICU, we carried out a cross-sectional study at a teaching and advanced treatment hospital. The mean total Impact of Event Scale-Revised (IES-R) score differed significantly between planned and unplanned ICU admissions (t = 4.03, p ffect of admission type (f = 18.5, p ficant main effect of relationship (f = 0.05, p = 0.82) or interaction effect of admission type and relationship (f = 0.54, p = 0.47). Multiple regression analysis indicated that admission type was significantly associated with acute stress symptoms (B = 18.09, β = 0.47, p f the variance in total IES-R score. Whether a patient had a planned or unplanned admission to the ICU influenced symptoms associated with acute stress symptoms of family members more than did getting support from nurses, being the patient’s spouse, or the severity of illness of the patient.

关键词： Intensive Care Unit families within 24 Hours Acute Stress Symptoms Post-Traumatic Stress Disorder

Merging bound states in the continuum in an open acoustic resonator

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Science China(Physics,Mechanics & Astronomy) 2025年第1期Mechanics & Astronomy) .卷 124-131页

作者： Lujun Huang Bin Jia Artem S.Pilipchuk Sibo Huang Chen Shen Almas f.Sadreev Yong Li Andrey E.Miroshnichenko School of Physics and Electronic Sciences East China Normal University Institute of Acoustics Tongji University L.V.Kirensky Institute of Physics Department of Mechanical Engineering Rowan University School of Engineering and Technology University of New South Wales at Canberra

Bound states in the continuum （BICs） are perfectly localized resonances despite embedding in the continuum ***,an isolated BIC is very sensitive to the structure ***,we report merging acoustic BICs in a single open resonator,robust against the structure *** find that both symmetry-protected BIC and friedrich-Wintgen BIC are sustained in a single coupled waveguide-resonator *** varying the height and length of the resonator,these two BICs move toward each other and merge into a single one at a critical *** to an individual BIC,the merged BIC is robust against fabrication error because its Q-factor is proportional to ΔL-4,whereΔL embodies the structure *** essence of this extraordinary phenomenon is perfectly explained by the two-and three-level approximations of the effective nonHermitian ***,we present direct experimental demonstrations of the moving and merging of BICs in a coupled 3D waveguide-resonator,which are evidenced by the vanishing of the linewidth of fano resonance in the transmission *** results may find exciting applications in designing high-quality acoustic sources,sensors and filters.

关键词： acoustic resonances bound state in the continuum high-Q resonances

Phase Composition of Sputtered film from a Mixture Target of Hydroxyapatite and Strontium-apatite

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Journal of Materials Science & Technology 2013年第1期29卷 1-6页

作者： K.Ozeki T.Hoshino H.aoki T.Masuzawa Department of Mechanical Engineering Ibaraki University International Apatite Co. Ltd.

To obtain an Sr-substituted hydroxyapatite thin film, sputter-coating was performed on a cellulose filter acting as a substrate from the mixture target of hydroxyapatite （HA） and strontium-apatite （SrAp） at an Ar pressure of 0.5-5.0 Pa. The ratio of the SrAp in the mixture target was varied from 25% to 100%. After coating, the films were heated at 700 ℃ to remove the cellulose filter substrate, and the crystalline phases were identified by X-ray diffraction （XRD）. The sputter-coated film was identified as the Sr-substituted /3-tri-calcium phosphate （TCP） and the Sr-substituted/3-calcium pyrophosphate （CPP） as well as the Sr-substituted HA. The weight ratio of the Sr-substituted HA decreased with increasing Ar pressure or with an increasing ratio of SrAp to HA in the target. The average Sr/（Ca ＋ Sr） molar ratio in the film was 1.9%-3.5% slightly lower than the initial SrAp ratio of the target, and the ratio was not influenced by the Ar pressure. In the （Sr ＋ Ca）/P ratio, the ratio decreased while increasing the SrAp ratio in the target.

关键词： Sputtering Hydroxyapatite Strontium Strontium-apatite Crystal phase

Discovery of a strongly r-process enhanced extremely metal-poor star LAMOST J110901.22+075441.8

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Research in Astronomy and Astrophysics 2015年第8期15卷 1264-1274页

作者： Hai-Ning Li Wako aoki Satoshi Honda Gang Zhao Norbert Christlieb Takuma Suda Key Laboratory of Optical Astronomy National Astronomical ObservatoriesChinese Academy of Sciences National Astronomical Observatory of Japan 2-21-1 OsawaMitakaTokyo181-8588Japan Department of Astronomical Science School of Physical SciencesThe Graduate University of Advanced Studies (SOKENDAI)2-21-1 OsawaMitakaTokyo 181-8588Japan University of Hyogo Center for AstronomyNishigaichiSayo-choSayoHyogo679-5313Japan Zentrum für Astronomie der Universitt Heidelberg LandessternwarteKnigstuhl 12D-69117 HeidelbergGermany Research Center for the Early Universe The University of TokyoHongo 7-3-1Bunkyo-kuTokyo 113-0033Japan

We report the discovery of an extremely metal-poor（EMP） giant,LAMOST J110901.22＋075441.8, which exhibits a large excess of r-process elements with [Eu/fe] ～＋1.16. The star is one of the newly discovered EMP stars identified from the LAMOST low-resolution spectroscopic survey and a highresolution follow-up observation with the Subaru Telescope. Stellar parameters and elemental abundances have been determined from the Subaru spectrum. Accurate abundances for a total of 23 elements including 11 neutron-capture elements from Sr through Dy have been derived for LAMOST J110901.22＋075441.8. The abundance pattern of LAMOST J110901.22＋075441.8 in the range of C through Zn is in line with the ＂normal＂ population of EMP halo stars, except that it shows a notable underabundance in carbon. The heavy element abundance pattern of LAMOST J110901.22＋075441.8 is in agreement with other well studied cool r-II metal-poor giants such as CS 22892-052 and CS 31082-001. The abundances of elements in the range from Ba through Dy match the scaled solar r-process pattern *** J110901.22＋075441.8 provides the first detailed measurements of neutroncapture elements among r-II stars at such low metallicity with [fe/H]-3.4, and exhibits similar behavior as other r-II stars in the abundance ratio of Zr/Eu as well as Sr/Eu and Ba/Eu.

关键词： star: abundances—stars: PopulationⅡ— nucleosynthesis

Gut virome:New key players in the pathogenesis of inflammatory bowel disease

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World Journal of Methodology 2025年第2期15卷 27-43页

作者： Helal f Hetta Rehab Ahmed Yasmin N Ramadan Hayam fathy Mohammed Khorshid Mohamed M Mabrouk Mai Hashem Department of Medical Microbiology and Immunology Faculty of MedicineAssiut UniversityAssiut 71515Egypt Division of Microbiology Immunology and BiotechnologyFaculty of pharmacyUniversity of TabukTabuk 71491Saudi Arabia Division of Microbiology Immunology and BiotechnologyDepartment of Natural Products and Alternative MedicineFaculty of PharmacyUniversity of TabukTabuk 71491Saudi Arabia Department of Internal Medicine Division HepatogastroenterologyAssiut UniversityAssiut 71515Egypt Department of Clinical Research Egyptian Developers of Gastroenterology and Endoscopy FoundationCairo 11936Egypt Department of Internal Medicine Faculty of Medicine.Tanta UniversityTanta 31527Egypt Department of Tropical Medicine Gastroenterology and HepatologyAssiut University HospitalAssiut 71515Egypt

Inflammatory bowel disease(IBD)is a chronic inflammatory illness of the *** the mechanism underlying the pathogenesis of IBD is not fully under-stood,it is believed that a complex combination of host immunological response,environmental exposure,particularly the gut microbiota,and genetic suscept-ibility represents the major *** gut virome is a group of viruses found in great frequency in the gastrointestinal tract of *** gut virome varies greatly among individuals and is influenced by factors including lifestyle,diet,health and disease conditions,geography,and *** majority of research has focused on the significance of gut bacteria in the progression of IBD,although viral populations represent an important component of the *** conducted this review to highlight the viral communities in the gut and their expected roles in the etiopathogenesis of IBD regarding published research to date.

关键词： Inflammatory bowel disease Pathogenesis Gut virome Bacteriophage Eukaryotic viruses

Genetic ancestry analysis in non-alcoholic fatty liver disease patients from Brazil and Portugal

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World Journal of Hepatology 2015年第10期7卷 1433-1438页

作者： Lourianne Nascimento Cavalcante Jose Tadeu Stefano Mariana V Machado Daniel f Mazo fabiola Rabelo kiyoko Abe Sandes flair Jose Carrilho Helena Cortez-Pinto Andre Castro Lyra Claudia P de Oliveira Gastro-Hepatology Department Hospital Sao Rafael Division of Gastroenterology and Hepatology Department of GastroenterologyUniversity of Sao Paulo School of Medicine Department of Gastroenterology Laboratory of NutritionUniversity Hospital of Santa Maria University Life Sciences Department University of Bahia State faculty of Medicine Federal University of Bahia

AIM:To study the association between genetic ancestry,non-alcoholic fatty liver disease(NAfLD) metabolic characteristics in two cohorts of patients,from Brazil and Portugal. METHODS:We included 131 subjects from Brazil [(n = 45 with simple steatosis(S. Steatosis) and n = 86 with nonalcoholic steatohepatitis(NASH)] and 90 patients from Portugal(n = 66,S. Steatosis; n = 24,NASH). All patients had biopsy-proven NAfLD. In histologic evaluation NAfLD activity score was used to assess histology and more than 5 points defined NASH in this study. Patients were divided into two groups according to histology diagnosis:simple steatosis or non-alcoholic statohepatitis. Genetic ancestry was assessed using real-time polymerase chain reaction. Seven ancestry informative markers(AT3-I/D,LPL,Sb19.3,APO,fYNull,PV92,and CKMM) with the greatest ethnicgeographical differential frequencies(≥ 48%) were used to define genetic ancestry. Data were analyzed using R PROJECTS software. Ancestry allele frequencies between groups were analyzed by GENEPOP onlineand the estimation of genetic ancestry contribution was evaluated by ADMIX-95 software. The 5% alpha-error was considered as significant(P ficantly more frequent among the elderly patients with diabetes(NASH 56 ± 1.1 years old vs S. Steatosis 51 ± 1.5 years old,P = 3.7 x 10-9),dyslipidemia(NASH 63% vs S. Steatosis 37%,P = 0.009),higher fasting glucose levels(NASH 124 ± 5.2 vs S. Steatosis 106 ± 5.3,P = 0.001) and Homeostatic Model of Assessment index > 2.5 [NASH 5.3(70.8%) vs S. Steatosis 4.6(29.2%) P = 0.04]. In the Portuguese study population,dyslipidemia was present in all patients with NASH(P = 0.03) and hypertension was present in a larger percentage of subjects in the S. Steatosis group(P = 0.003,respectively). The genetic ancestry contribution among Brazilian and Portuguese individuals with NASH was similar to those with S. Steatosis from each cohort(Brazilian cohort:P = 0.75; Po

关键词： Ancestry Nonalcoholic fatty liver disease Simple steatosis Nonalcoholic steatohepatitis Admixed population